Citrus Sinensis ID: 033648

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110----
Protein Sequence
MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS
Secondary Structure (PSIPRED)
cccccHHHHHcccccccccccccccEEEEccccccccHHHHHHHHHHccccccccccEEEEEEcccccccEEEEEEcccHHHHHHHHHHHcccEEccEEEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHcccccccccccccccEEEEEcccccccHHHHHHHHHHHHHHccccccccEEEEEEcccccccEEEEEccHHHHHHHHHHHcccEEccEEcEEEEcccccccccc
Coil and Loop (DISEMBL)
mgklppeeilslpmfknytagnpaSVLYIKNLakdvvpddffFVFGSLFGSIDAAKSGLIVKLMQEgrmrgqafvtfpsVELAHRALNLvngyvfkgkpmiiqfgrnpaaakps
Flexible Loop (DISEMBL)
MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQfgrnpaaakps
Low Complexity Region (SEG)
MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKdvvpddfffvfGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS
Disordered region (IsUnstruct)
*********LSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG*********
Disordered Region (DISOPRED)
************************SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII************
Disordered Region (DISEMBL)
MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR********
Disordered Region (DISPRO)
***LPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS
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	114	2.2.26 [Sep-21-2011]
Q96IZ5	413	RNA-binding protein 41 OS	yes	no	0.885	0.244	0.476	2e-20
Q3MHP0	516	RNA-binding protein 40 OS	no	no	0.929	0.205	0.420	2e-17
Q8JZV4	413	RNA-binding protein 41 OS	yes	no	0.885	0.244	0.428	4e-17
Q5R6C7	517	RNA-binding protein 40 OS	yes	no	0.929	0.205	0.420	4e-17
Q4G055	515	RNA-binding protein 40 OS	no	no	0.929	0.205	0.420	4e-17
Q3UZ01	514	RNA-binding protein 40 OS	no	no	0.956	0.212	0.415	4e-17
Q96LT9	517	RNA-binding protein 40 OS	no	no	0.929	0.205	0.411	5e-17
O74968	249	U1 small nuclear ribonucl	yes	no	0.807	0.369	0.357	2e-09
Q06AA4	282	U1 small nuclear ribonucl	no	no	0.692	0.280	0.340	2e-05
Q2KIR1	282	U1 small nuclear ribonucl	no	no	0.692	0.280	0.340	2e-05

>sp|Q96IZ5|RBM41_HUMAN RNA-binding protein 41 OS=Homo sapiens GN=RBM41 PE=1 SV=2

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/105 (47%), Positives = 64/105 (60%), Gaps = 4/105 (3%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           +L  EEI  +PMF +Y  G P  VLY+KNL+  V   D      SLF      K   I  
Sbjct: 287 RLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQF 342

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
            M  GRMRGQAF+TFP+ E+A +AL+LVNGY   GK ++I+FG+N
Sbjct: 343 RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKN 387

May bind RNA.
Homo sapiens (taxid: 9606)

>sp|Q3MHP0|RBM40_BOVIN RNA-binding protein 40 OS=Bos taurus GN=RNPC3 PE=2 SV=1

 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/107 (42%), Positives = 68/107 (63%), Gaps = 1/107 (0%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLAK V   D  F+FG     S +  +    
Sbjct: 396 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKFIFGRYVDFSSETQRIMFD 455

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           ++LM+EGRM+GQAF+  P+ + A +AL   NGYV  GKPM++QF R+
Sbjct: 456 IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 502

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Bos taurus (taxid: 9913)

>sp|Q8JZV4|RBM41_MOUSE RNA-binding protein 41 OS=Mus musculus GN=Rbm41 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 45/105 (42%), Positives = 63/105 (60%), Gaps = 4/105 (3%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           +L  EEI ++PMF +Y  G P  VLY+KNL+  V   D      SLF      K   I  
Sbjct: 287 RLSEEEIRNIPMFSSYNPGEPNKVLYLKNLSPRVKERDLI----SLFARFQEKKGPPIQF 342

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
            M  GRMRGQAF+TFP+ ++A +AL+ +NGY   GK ++I+F ++
Sbjct: 343 RMMTGRMRGQAFLTFPNKDIAWQALHQINGYKLYGKILVIEFAKS 387

May bind RNA.

Mus musculus (taxid: 10090)

>sp|Q5R6C7|RBM40_PONAB RNA-binding protein 40 OS=Pongo abelii GN=RNPC3 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 45/107 (42%), Positives = 68/107 (63%), Gaps = 1/107 (0%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLAK V   D  ++FG     S +  +    
Sbjct: 397 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVEEKDLKYIFGRYVDFSSETRRIMFD 456

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           ++LM+EGRM+GQAFV  P+ + A +AL   NGYV  GKPM++QF R+
Sbjct: 457 IRLMKEGRMKGQAFVGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 503

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Pongo abelii (taxid: 9601)

>sp|Q4G055|RBM40_RAT RNA-binding protein 40 OS=Rattus norvegicus GN=Rnpc3 PE=2 SV=2

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 45/107 (42%), Positives = 68/107 (63%), Gaps = 1/107 (0%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLA+ V   D  F+FG     S +  +    
Sbjct: 396 GRISREEMETLSVFRSYEPGEPNCRIYVKNLARHVQEKDLKFIFGRYVDFSSETQRIMFD 455

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           ++LM+EGRM+GQAFV  P+ + A +AL   NGYV  GKPM++QF R+
Sbjct: 456 IRLMKEGRMKGQAFVGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 502

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Rattus norvegicus (taxid: 10116)

>sp|Q3UZ01|RBM40_MOUSE RNA-binding protein 40 OS=Mus musculus GN=Rnpc3 PE=2 SV=2

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 71/113 (62%), Gaps = 4/113 (3%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLA+ V   D  F+FG     S +  +    
Sbjct: 395 GRISREEMETLSVFRSYEPGEPNCRIYVKNLARHVQEKDLKFIFGRYVDFSSETQRIMFD 454

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           ++LM+EGRM+GQAFV  P+ + A +AL   NGYV  GKPM++QF R   +A+P
Sbjct: 455 IRLMKEGRMKGQAFVGLPNEKAAAKALKEANGYVLFGKPMVVQFAR---SARP 504

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Mus musculus (taxid: 10090)

>sp|Q96LT9|RBM40_HUMAN RNA-binding protein 40 OS=Homo sapiens GN=RNPC3 PE=1 SV=1

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/107 (41%), Positives = 68/107 (63%), Gaps = 1/107 (0%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLAK V   D  ++FG     S +  +    
Sbjct: 397 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 456

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           ++LM+EGRM+GQAF+  P+ + A +AL   NGYV  GKPM++QF R+
Sbjct: 457 IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 503

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m(7)G-capped U12 snRNA.

Homo sapiens (taxid: 9606)

>sp|O74968|RU1A_SCHPO U1 small nuclear ribonucleoprotein usp102 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=usp102 PE=1 SV=1

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 51/95 (53%), Gaps = 3/95 (3%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
           P  K   +  P+  LYI+N+ + +       +   LFGS       + V+  +  RMRGQ
Sbjct: 14  PSPKETDSQTPSETLYIRNIEEKIRLTMLKRILEHLFGSYGKV---IDVQARKTLRMRGQ 70

Query: 73  AFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           AFV F ++E A RAL  + GY   GKPM+IQ+ ++
Sbjct: 71  AFVVFDNLENASRALKDLQGYPLYGKPMMIQYSKS 105

Involved in nuclear mRNA splicing.

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

>sp|Q06AA4|SNRPA_PIG U1 small nuclear ribonucleoprotein A OS=Sus scrofa GN=SNRPA PE=2 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 43/88 (48%), Gaps = 9/88 (10%)

Query: 23  PASVLYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           P   +YI NL + +  D+     +   S FG I      L + + +  +MRGQAFV F  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQI------LDILVSRSLKMRGQAFVIFKE 61

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRN 107
           V  A  AL  + G+ F  KPM IQ+ + 
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQYAKT 89

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Sus scrofa (taxid: 9823)

>sp|Q2KIR1|SNRPA_BOVIN U1 small nuclear ribonucleoprotein A OS=Bos taurus GN=SNRPA PE=2 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 43/88 (48%), Gaps = 9/88 (10%)

Query: 23  PASVLYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           P   +YI NL + +  D+     +   S FG I      L + + +  +MRGQAFV F  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQI------LDILVSRSLKMRGQAFVIFKE 61

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRN 107
           V  A  AL  + G+ F  KPM IQ+ + 
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQYAKT 89

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Bos taurus (taxid: 9913)

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	114
359477912	463	PREDICTED: RNA-binding protein 40-like [	0.903	0.222	0.936	5e-54
359478163	463	PREDICTED: LOW QUALITY PROTEIN: RNA-bind	0.903	0.222	0.918	3e-53
297743789	263	unnamed protein product [Vitis vinifera]	0.973	0.422	0.918	5e-53
356560981	456	PREDICTED: uncharacterized protein LOC10	0.973	0.243	0.900	1e-52
255568988	450	RNA binding protein, putative [Ricinus c	0.973	0.246	0.864	2e-50
224123704	346	predicted protein [Populus trichocarpa]	0.982	0.323	0.866	2e-49
357128643	455	PREDICTED: RNA-binding protein 40-like [	0.982	0.246	0.857	3e-49
297849226	438	RNA recognition motif-containing protein	0.991	0.257	0.823	8e-49
212721632	450	uncharacterized protein LOC100193767 [Ze	0.982	0.248	0.839	1e-48
115452785	467	Os03g0326600 [Oryza sativa Japonica Grou	0.982	0.239	0.830	2e-48

>gi|359477912|ref|XP_002270244.2| PREDICTED: RNA-binding protein 40-like [Vitis vinifera] gi|298205172|emb|CBI17231.3| unnamed protein product [Vitis vinifera]

 Score =  214 bits (545), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 104/111 (93%), Positives = 107/111 (96%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
           GKLPPEEILSLPMFKNYTAGNPA VLYIKNLAKDVV DDF+F+FGSLFGS+DAAKSGL V
Sbjct: 351 GKLPPEEILSLPMFKNYTAGNPAPVLYIKNLAKDVVVDDFYFIFGSLFGSVDAAKSGLSV 410

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           KLMQEGRMRGQAFVTFPSVELAH ALNLVNGYVFKGKPMIIQFGRNPAAAK
Sbjct: 411 KLMQEGRMRGQAFVTFPSVELAHHALNLVNGYVFKGKPMIIQFGRNPAAAK 461

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478163|ref|XP_003632078.1| PREDICTED: LOW QUALITY PROTEIN: RNA-binding protein 40-like [Vitis vinifera]

 Score =  211 bits (538), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 102/111 (91%), Positives = 106/111 (95%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
           GKLPPEEILSLPMFKNY AGNPA VLYIKNLAKDVV DDF+F+FGSLFGS+DAAKSGL V
Sbjct: 351 GKLPPEEILSLPMFKNYAAGNPAPVLYIKNLAKDVVVDDFYFIFGSLFGSVDAAKSGLSV 410

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           KLMQEGRMRGQAFVTFPSVELAH ALN+VNGYVFKGKPMIIQFGRNPAAAK
Sbjct: 411 KLMQEGRMRGQAFVTFPSVELAHHALNVVNGYVFKGKPMIIQFGRNPAAAK 461

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743789|emb|CBI36672.3| unnamed protein product [Vitis vinifera]

 Score =  211 bits (536), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 102/111 (91%), Positives = 106/111 (95%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
           GKLPPEEILSLPMFKNY AGNPA VLYIKNLAKDVV DDF+F+FGSLFGS+DAAKSGL V
Sbjct: 151 GKLPPEEILSLPMFKNYAAGNPAPVLYIKNLAKDVVVDDFYFIFGSLFGSVDAAKSGLSV 210

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           KLMQEGRMRGQAFVTFPSVELAH ALN+VNGYVFKGKPMIIQFGRNPAAAK
Sbjct: 211 KLMQEGRMRGQAFVTFPSVELAHHALNVVNGYVFKGKPMIIQFGRNPAAAK 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560981|ref|XP_003548764.1| PREDICTED: uncharacterized protein LOC100818499 [Glycine max]

 Score =  210 bits (534), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 100/111 (90%), Positives = 106/111 (95%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
           GKLPPEEILSLPMFKNYTAGNPA VLYIKNLAKDV+ DDF+F+FGSLFGSI+AAKSGL V
Sbjct: 344 GKLPPEEILSLPMFKNYTAGNPAPVLYIKNLAKDVIADDFYFIFGSLFGSIEAAKSGLQV 403

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           KLMQEGRMRGQAF+TFPS+ELAH ALNLVNGYV KGKPMIIQFGRNPAAAK
Sbjct: 404 KLMQEGRMRGQAFITFPSIELAHHALNLVNGYVLKGKPMIIQFGRNPAAAK 454

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568988|ref|XP_002525464.1| RNA binding protein, putative [Ricinus communis] gi|223535277|gb|EEF36954.1| RNA binding protein, putative [Ricinus communis]

 Score =  202 bits (514), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 96/111 (86%), Positives = 104/111 (93%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
            KL PEEILSLP FKNYT GNPASVLYIKNL+KD+V DDFF++FGSLFGS+DAAK GL V
Sbjct: 338 NKLAPEEILSLPQFKNYTVGNPASVLYIKNLSKDMVADDFFYIFGSLFGSLDAAKVGLSV 397

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           KLMQEGRMRGQAFVTFPSVELAH+ALNLVNGYVFKGKPMIIQFGRNP+A+K
Sbjct: 398 KLMQEGRMRGQAFVTFPSVELAHQALNLVNGYVFKGKPMIIQFGRNPSASK 448

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123704|ref|XP_002319145.1| predicted protein [Populus trichocarpa] gi|222857521|gb|EEE95068.1| predicted protein [Populus trichocarpa]

 Score =  199 bits (505), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 97/112 (86%), Positives = 104/112 (92%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           +L PEEILSLP FKNYT GNPASVLYIKNL K+VV DDFF++FGSLFGSIDAAKSGL VK
Sbjct: 235 RLVPEEILSLPKFKNYTVGNPASVLYIKNLDKEVVADDFFYIFGSLFGSIDAAKSGLSVK 294

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           LMQEGRMRGQAFVTF SVELAH+ALNLVNGYVFK KPMIIQFGRNP+AAKP+
Sbjct: 295 LMQEGRMRGQAFVTFSSVELAHQALNLVNGYVFKDKPMIIQFGRNPSAAKPN 346

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357128643|ref|XP_003565980.1| PREDICTED: RNA-binding protein 40-like [Brachypodium distachyon]

 Score =  198 bits (504), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 96/112 (85%), Positives = 104/112 (92%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           KLP EEILSLPMFKNYT GNPASVLYIKNLAKDVV DDF++VFGS+F S+DAAKSGL +K
Sbjct: 344 KLPTEEILSLPMFKNYTPGNPASVLYIKNLAKDVVHDDFYYVFGSVFESMDAAKSGLSIK 403

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           LMQEGRMRGQAFVTFPSVELA RALNL +GYVFKGKPMIIQFGR+PAA+K S
Sbjct: 404 LMQEGRMRGQAFVTFPSVELAQRALNLTHGYVFKGKPMIIQFGRSPAASKAS 455

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849226|ref|XP_002892494.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297338336|gb|EFH68753.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  197 bits (500), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 93/113 (82%), Positives = 106/113 (93%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
           G+LPP+EILSLPMFKNYTAGNP+ VLYIKNLAKDVV DDF+++FGS F SI+AAK+ L V
Sbjct: 325 GRLPPQEILSLPMFKNYTAGNPSLVLYIKNLAKDVVIDDFYYIFGSQFESIEAAKTSLGV 384

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +LMQEGRMRGQAF+TFPSVE+AHRALNLVNG+VFKGKPMIIQFGRNP AAKP+
Sbjct: 385 RLMQEGRMRGQAFLTFPSVEVAHRALNLVNGFVFKGKPMIIQFGRNPGAAKPN 437

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|212721632|ref|NP_001132325.1| uncharacterized protein LOC100193767 [Zea mays] gi|194694084|gb|ACF81126.1| unknown [Zea mays] gi|414866589|tpg|DAA45146.1| TPA: hypothetical protein ZEAMMB73_529929 [Zea mays] gi|414866590|tpg|DAA45147.1| TPA: hypothetical protein ZEAMMB73_529929 [Zea mays]

 Score =  196 bits (499), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 94/112 (83%), Positives = 102/112 (91%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           KLPPEEILSLPMFKNYT GNPASVLYIKNLAKDV  DDF++VFGS+F S+D+A+ GL VK
Sbjct: 339 KLPPEEILSLPMFKNYTPGNPASVLYIKNLAKDVTHDDFYYVFGSVFESMDSARLGLSVK 398

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           LMQEGRMRGQAFVTFP+VELA RALNL +GYVFKGKPMIIQFGRNPAA K S
Sbjct: 399 LMQEGRMRGQAFVTFPTVELAQRALNLAHGYVFKGKPMIIQFGRNPAANKAS 450

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115452785|ref|NP_001049993.1| Os03g0326600 [Oryza sativa Japonica Group] gi|108707928|gb|ABF95723.1| RNA recognition motif family protein, expressed [Oryza sativa Japonica Group] gi|113548464|dbj|BAF11907.1| Os03g0326600 [Oryza sativa Japonica Group] gi|218192743|gb|EEC75170.1| hypothetical protein OsI_11395 [Oryza sativa Indica Group]

 Score =  196 bits (497), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 93/112 (83%), Positives = 103/112 (91%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           KLPPEEILSLPMFKNYT GNPASVLYIKNLAKDV+ DDF++VFGS+F ++D A+S L +K
Sbjct: 356 KLPPEEILSLPMFKNYTPGNPASVLYIKNLAKDVIQDDFYYVFGSVFENMDIARSSLSIK 415

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           LMQEGRMRGQAFVTFPSVELA RALNLV+G+VFKGKPMIIQFGRNPAA K S
Sbjct: 416 LMQEGRMRGQAFVTFPSVELAQRALNLVHGFVFKGKPMIIQFGRNPAANKSS 467

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	114
TAIR|locus:2195311	442	AT1G09230 [Arabidopsis thalian	0.991	0.255	0.734	2.3e-39
UNIPROTKB|G3X691	413	RBM41 "Uncharacterized protein	0.885	0.244	0.457	4.4e-18
UNIPROTKB|F1RXK8	412	RBM41 "Uncharacterized protein	0.885	0.245	0.457	7.3e-18
UNIPROTKB|Q96IZ5	413	RBM41 "RNA-binding protein 41"	0.885	0.244	0.457	1.2e-17
UNIPROTKB|F1NFC5	412	RBM41 "Uncharacterized protein	0.903	0.25	0.418	1.5e-17
UNIPROTKB|F1PU87	413	RBM41 "Uncharacterized protein	0.885	0.244	0.447	1.6e-17
UNIPROTKB|D4A6K1	425	Rbm41 "Protein Rbm41" [Rattus	0.885	0.237	0.419	6.1e-16
ZFIN|ZDB-GENE-060312-35	505	rnpc3 "RNA-binding region (RNP	0.956	0.215	0.407	9.5e-16
UNIPROTKB|H0YEY9	128	RNPC3 "RNA-binding protein 40"	0.929	0.828	0.383	9.8e-16
MGI|MGI:2444923	413	Rbm41 "RNA binding motif prote	0.885	0.244	0.409	5.5e-15

TAIR|locus:2195311 AT1G09230 [Arabidopsis thaliana (taxid:3702)]

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 83/113 (73%), Positives = 93/113 (82%)

Query:     2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIV 61
             G+LPP++ILSLPMFKNYTAGNP+ VLYIKNLAK           GS F S + AKS L V
Sbjct:   329 GRLPPQDILSLPMFKNYTAGNPSVVLYIKNLAKDVVIDDFYYIFGSQFESSEVAKSSLGV 388

Query:    62 KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
             +LMQEGRMRGQAF+TFPSVE+AHRALNLVNG+VFKGKPMIIQFGR P AAKP+
Sbjct:   389 RLMQEGRMRGQAFLTFPSVEVAHRALNLVNGFVFKGKPMIIQFGRTPGAAKPN 441

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|G3X691 RBM41 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 224 (83.9 bits), Expect = 4.4e-18, P = 4.4e-18
 Identities = 48/105 (45%), Positives = 62/105 (59%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI  +PMF +Y  G P  VLY+KNL+             SLF      K   I  
Sbjct:   287 RLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQF 342

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              M  GRMRGQAF+TFP+ E+A +AL LVNGY  +GK ++I+FG+N
Sbjct:   343 RMMTGRMRGQAFITFPNTEIAWQALRLVNGYKLRGKILVIEFGKN 387

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1RXK8 RBM41 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 222 (83.2 bits), Expect = 7.3e-18, P = 7.3e-18
 Identities = 48/105 (45%), Positives = 62/105 (59%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI  +PMF +Y  G P  VLY+KNL+             SLF      K   I  
Sbjct:   287 RLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTEKDLV----SLFARFQEKKGPPIQF 342

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              M  GRMRGQAF+TFP+ E+A +AL LVNGY  +GK ++I+FG+N
Sbjct:   343 RMMTGRMRGQAFITFPNKEIAWQALRLVNGYKLRGKILVIEFGKN 387

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q96IZ5 RBM41 "RNA-binding protein 41" [Homo sapiens (taxid:9606)]

 Score = 220 (82.5 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 48/105 (45%), Positives = 62/105 (59%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI  +PMF +Y  G P  VLY+KNL+             SLF      K   I  
Sbjct:   287 RLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQF 342

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              M  GRMRGQAF+TFP+ E+A +AL+LVNGY   GK ++I+FG+N
Sbjct:   343 RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKN 387

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NFC5 RBM41 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 208 (78.3 bits), Expect = 1.5e-17, Sum P(2) = 1.5e-17
 Identities = 46/110 (41%), Positives = 65/110 (59%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EE+ S+P F +Y  G P  VLY+KNL              SLF       + +  +
Sbjct:   290 RLSEEELRSIPRFSSYHPGEPNKVLYVKNLGPRVTMKDMV----SLFARFQQDSTPIQFR 345

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN--PAA 110
             L+  GRMRGQAF+TFP ++ A  A+ LVNGY  +GKPM+I+FG++  P+A
Sbjct:   346 LLS-GRMRGQAFITFPDIQSAQDAMLLVNGYRLQGKPMVIEFGKSKGPSA 394

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1PU87 RBM41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 219 (82.2 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 47/105 (44%), Positives = 63/105 (60%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI  +PMF +Y  G P  VLY+KNL+             SLF      K   I  
Sbjct:   287 RLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQF 342

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              +  GRMRGQAF+TFP+ E+A +AL+LVNGY  +GK ++I+FG+N
Sbjct:   343 RIMTGRMRGQAFITFPNKEIAWQALHLVNGYKLRGKILVIEFGKN 387

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|D4A6K1 Rbm41 "Protein Rbm41" [Rattus norvegicus (taxid:10116)]

 Score = 205 (77.2 bits), Expect = 6.1e-16, P = 6.1e-16
 Identities = 44/105 (41%), Positives = 62/105 (59%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI ++PMF +Y  G P  VLY+KNL+             SLF      K  LI  
Sbjct:   299 RLSEEEIRNIPMFSSYNPGEPNKVLYLKNLSPRVKERDLI----SLFARFQEKKGPLIQF 354

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              M  GRMRGQAF+TFP+ ++A +AL+ +NGY   GK ++I+F ++
Sbjct:   355 QMMTGRMRGQAFITFPNKDIAWQALHQINGYKLYGKILVIEFAKS 399

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-060312-35 rnpc3 "RNA-binding region (RNP1, RRM) containing 3" [Danio rerio (taxid:7955)]

 Score = 205 (77.2 bits), Expect = 9.5e-16, P = 9.5e-16
 Identities = 46/113 (40%), Positives = 63/113 (55%)

Query:     2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFG-SIDAAKSGLI 60
             G+L  +EI  L +FK Y  G P   LY+KN+AK           G     S +  ++   
Sbjct:   382 GRLSRDEIKKLSVFKKYEPGEPTCRLYVKNVAKHVEEKDLKFIYGRYIDISSEEERNMFD 441

Query:    61 VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
             + LM+EGRM+GQAF+  PS   A +AL   NGYV K KP+++QF R+   AKP
Sbjct:   442 IVLMKEGRMKGQAFIGLPSERSAQKALKETNGYVLKDKPLVVQFARS---AKP 491

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|H0YEY9 RNPC3 "RNA-binding protein 40" [Homo sapiens (taxid:9606)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 41/107 (38%), Positives = 63/107 (58%)

Query:     2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFG-SIDAAKSGLI 60
             G++  EE+ +L +F++Y  G P   +Y+KNLAK           G     S +  +    
Sbjct:     8 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 67

Query:    61 VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
             ++LM+EGRM+GQAF+  P+ + A +AL   NGYV  GKPM++QF R+
Sbjct:    68 IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 114

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:2444923 Rbm41 "RNA binding motif protein 41" [Mus musculus (taxid:10090)]

 Score = 196 (74.1 bits), Expect = 5.5e-15, P = 5.5e-15
 Identities = 43/105 (40%), Positives = 61/105 (58%)

Query:     3 KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVK 62
             +L  EEI ++PMF +Y  G P  VLY+KNL+             SLF      K   I  
Sbjct:   287 RLSEEEIRNIPMFSSYNPGEPNKVLYLKNLSPRVKERDLI----SLFARFQEKKGPPIQF 342

Query:    63 LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              M  GRMRGQAF+TFP+ ++A +AL+ +NGY   GK ++I+F ++
Sbjct:   343 RMMTGRMRGQAFLTFPNKDIAWQALHQINGYKLYGKILVIEFAKS 387

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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	114
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-41
smart00360	73	smart00360, RRM, RNA recognition motif	6e-13
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-08
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	7e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-07
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	3e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-07
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	8e-07
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	8e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-05
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	5e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.001
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.001
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.002
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.002
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.002
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.002
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	0.002
cd12505	75	cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.002
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.002
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.002
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.002
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.003
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.003
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.003
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.003
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.003

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score =  130 bits (330), Expect = 3e-41
 Identities = 47/81 (58%), Positives = 59/81 (72%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
             LY+KNL+K V  +D  ++FG    S    K+   ++LM EGRM+GQAFVTFPS E+A 
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 85  RALNLVNGYVFKGKPMIIQFG 105
           +ALNLVNGYV KGKPM+IQFG
Sbjct: 62  KALNLVNGYVLKGKPMVIQFG 82

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 58.8 bits (143), Expect = 6e-13
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
            L++ NL  D   ++   +F   FG +++ +   +V+  + G+ +G AFV F S E A +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSK-FGKVESVR---LVRDKETGKSKGFAFVEFESEEDAEK 56

Query: 86  ALNLVNGYVFKGKPMII 102
           AL  +NG    G+P+ +
Sbjct: 57  ALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 57.5 bits (140), Expect = 2e-12
 Identities = 30/84 (35%), Positives = 43/84 (51%), Gaps = 11/84 (13%)

Query: 27  LYIKNLAKDVVPDD----FFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           LYI NL + +  D+     + +F   FG +      L +   +  +MRGQAFV F  VE 
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQ-FGPV------LDIVASKTLKMRGQAFVVFKDVES 54

Query: 83  AHRALNLVNGYVFKGKPMIIQFGR 106
           A  AL  + G+ F  KPM IQ+ +
Sbjct: 55  ATNALRALQGFPFYDKPMRIQYAK 78

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

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

 Score = 55.0 bits (133), Expect = 2e-11
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ NL  D   +D   +F   FG I++ +    +   ++G+ +G AFV F S E A +A
Sbjct: 1   LFVGNLPPDTTEEDLRELFSK-FGEIESVR----IVRDKDGKSKGFAFVEFESPEDAEKA 55

Query: 87  LNLVNGYVFKGKPMIIQ 103
           L  +NG    G+ + + 
Sbjct: 56  LEALNGKELDGRKLKVS 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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 57.6 bits (138), Expect = 5e-11
 Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 4/92 (4%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
               +    + L++ NL  DV  +D   +F   FG +   +   +V+  + G+ RG AFV
Sbjct: 107 SRQKSKEENNTLFVGNLPYDVTEEDLRELF-KKFGPVKRVR---LVRDRETGKSRGFAFV 162

Query: 76  TFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
            F S E A +A+  +NG   +G+P+ +Q  + 
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQP 194

Length = 306

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

 Score = 50.7 bits (122), Expect = 8e-10
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ NL  D   +D   +F   FG I++ +    +   + GR +G AFV F   E A +A
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSK-FGPIESIR----IVRDETGRSKGFAFVEFEDEEDAEKA 55

Query: 87  LNLVNGYVFKGKPM 100
           L  +NG    G+ +
Sbjct: 56  LEALNGKELGGREL 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 46.0 bits (110), Expect = 7e-08
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSVELAH 84
           +Y+KNL +D+  +    +FG  +G I         K+M   EG+ +G  FV F + E A 
Sbjct: 4   VYVKNLGEDMDDEKLKELFGK-YGKI------TSAKVMKDDEGKSKGFGFVNFENHEAAQ 56

Query: 85  RALNLVNGYVFKGKPM 100
           +A+  +NG    GK +
Sbjct: 57  KAVEELNGKEVNGKKL 72

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

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

 Score = 45.4 bits (108), Expect = 7e-08
 Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LYI NL+ DV   D       LF       S ++VK        G AFV  P    A +A
Sbjct: 1   LYIGNLSSDVNESDL----RQLFEEHKIPVSSVLVK------KGGYAFVDCPDQSWADKA 50

Query: 87  LNLVNGYVFKGKPMII 102
           +  +NG + +GK + +
Sbjct: 51  IEKLNGKILQGKVIEV 66

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 9/76 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAH 84
           LY+KNL   +  +     F S FG+I +AK      +M +  GR +G  FV F S E A 
Sbjct: 4   LYVKNLDDSIDDERLREEF-SPFGTITSAK------VMTDEKGRSKGFGFVCFSSPEEAT 56

Query: 85  RALNLVNGYVFKGKPM 100
           +A+  +NG +  GKP+
Sbjct: 57  KAVTEMNGRIIGGKPL 72

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

 Score = 44.7 bits (105), Expect = 3e-07
 Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 9/87 (10%)

Query: 23  PASVLYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           P   +YI NL + +  D+         S FG I      L + + +  +MRGQAFV F  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQI------LDILVSRSLKMRGQAFVIFKE 55

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGR 106
           V  A  AL  + G+ F  KPM IQ+ +
Sbjct: 56  VSSATNALRSMQGFPFYDKPMRIQYAK 82

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

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

 Score = 44.1 bits (105), Expect = 3e-07
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL  +V  +D       LFG      S  ++   + GR RG  FV   + E A+ A
Sbjct: 2   LYVGNLPYNVTEEDL----KDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG  F G+ + +   R
Sbjct: 58  IEKLNGTDFGGRTLTVNEAR 77

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

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

 Score = 44.1 bits (105), Expect = 4e-07
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+++NL  D   +         F  +   K   +VK     + RG  +VTF   E A RA
Sbjct: 2   LFVRNLPYDTTDEQL----EEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRA 57

Query: 87  LNLVNGYVFKGKPMIIQF 104
           L       F G+ + ++F
Sbjct: 58  LEEKKKTKFGGRKIHVEF 75

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

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

 Score = 43.8 bits (104), Expect = 4e-07
 Identities = 16/40 (40%), Positives = 23/40 (57%)

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM 100
           VK   +GR +G   V F S E A RA+ + NGY  +G+ +
Sbjct: 30  VKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGREL 69

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

 Score = 43.9 bits (104), Expect = 5e-07
 Identities = 26/82 (31%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           + LY++N+A    PDD       LFG         I       R RG A+V F  V  A 
Sbjct: 1   TSLYVRNVADATRPDDL----RRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAE 56

Query: 85  RALNLVNGYVFKGKPMIIQFGR 106
            AL  ++   F G+ + IQF +
Sbjct: 57  DALYYLDRTRFLGREIEIQFAQ 78

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

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

 Score = 43.5 bits (102), Expect = 8e-07
 Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +YI NL   +  ++      +LF         + +K M   +MRGQAFV F  +  A  A
Sbjct: 4   IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTM---KMRGQAFVIFKELSSATNA 60

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           L  + G+ F GKPM IQ+ +
Sbjct: 61  LRQLQGFPFYGKPMRIQYAK 80

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

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

 Score = 43.0 bits (101), Expect = 8e-07
 Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 27  LYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           +YI NL + V  ++     +   S FG I      L +  ++  +MRGQAFV F  +  A
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQI------LDIVALKTLKMRGQAFVVFKDISSA 55

Query: 84  HRALNLVNGYVFKGKPMIIQFGR 106
             AL  + G+ F  KPM I + +
Sbjct: 56  TNALRSMQGFPFYDKPMRIAYSK 78

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

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

 Score = 42.5 bits (101), Expect = 1e-06
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEG-RMRGQAFVTFPSVELAHR 85
          LY++NL   V  +D    F   +G ++       V+L++   R RG AFV F S E A  
Sbjct: 1  LYVRNLPPSVTEEDLREFFSP-YGKVEG------VRLVRNKDRPRGFAFVEFASPEDAEA 53

Query: 86 ALNLVNGYVFKGKP 99
          AL  +NG V  G+ 
Sbjct: 54 ALKKLNGLVLDGRT 67

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           +LY++NL   +  ++ + +FG  +G+I   + G           RG AFV +  +  A  
Sbjct: 4   ILYVRNLPFKISSEELYDLFGK-YGAIRQIRIG------NTKETRGTAFVVYEDIYDAKN 56

Query: 86  ALNLVNGYVFKGKPMIIQF 104
           A + ++G+    + +++ +
Sbjct: 57  ACDHLSGFNVANRYLVVLY 75

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 13/87 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM------QEGRMRGQAFVTFPSV 80
           LY+ NL   V  +     FG  FG + +      VK+M      +  R R   FV F + 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGR-FGPLAS------VKIMWPRTEEERRRNRNCGFVAFMNR 56

Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRN 107
             A RAL+ ++G    G  + + +G+ 
Sbjct: 57  ADAERALDELDGKDVMGYELKLGWGKA 83

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

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

 Score = 42.2 bits (100), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL  ++  DD   +F   FG I+  +   + +  + GR +G  F+ F   E A +A
Sbjct: 1   LYVGNLHFNITEDDLRGIFEP-FGEIEFVQ---LQRDPETGRSKGYGFIQFADAEDAKKA 56

Query: 87  LNLVNGYVFKGKPM 100
           L  +NG+   G+P+
Sbjct: 57  LEQLNGFELAGRPI 70

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

 Score = 41.4 bits (98), Expect = 3e-06
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           + L + NL  DV  +D       LFG +   K  + +   + GR  G A V F   E A 
Sbjct: 1   TRLRVSNLHYDVTEEDL----EELFGRVGEVKK-VKINYDRSGRSEGTADVVFEKREDAE 55

Query: 85  RALNLVNGYVFKGKPMIIQF 104
           RA+   NG +  G+PM ++ 
Sbjct: 56  RAIKQFNGVLLDGQPMQVEL 75

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

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

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+KNL   V  +    +F S  G I +AK    V L ++G  RG  FV F + E A+RA
Sbjct: 288 LYVKNLDDTVTDEKLRELF-SECGEITSAK----VMLDEKGVSRGFGFVCFSNPEEANRA 342

Query: 87  LNLVNGYVFKGKPMII 102
           +  ++G +  GKP+ +
Sbjct: 343 VTEMHGRMLGGKPLYV 358

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

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

 Score = 41.0 bits (96), Expect = 5e-06
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          L+++NLA  V  +D        F  +   K  ++V   + G  RG  FVTF  +E A  A
Sbjct: 2  LFVRNLAFSVTQEDL----TDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEA 57

Query: 87 LNLVNGYVFKGK 98
          L  +      G+
Sbjct: 58 LAKLKNKKLHGR 69

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

 Score = 40.6 bits (96), Expect = 7e-06
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ +L  DV     + +F S  G + + +   + + +   R  G A+V F +   A RA
Sbjct: 2   LYVGDLHPDVTEAMLYEIF-SPAGPVLSIR---VCRDLITRRSLGYAYVNFQNPADAERA 57

Query: 87  LNLVNGYVFKGKPM-IIQFGRNP 108
           L+ +N  V KGKP+ I+   R+P
Sbjct: 58  LDTLNFDVIKGKPIRIMWSQRDP 80

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

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          +++  L      D     F S FG I+ A   +++   Q G+ RG  FVTF   E A RA
Sbjct: 3  IFVGGLPYHTTDDSLRKYF-SQFGEIEEA---VVITDRQTGKSRGYGFVTFKDKESAERA 58

Query: 87 L 87
           
Sbjct: 59 C 59

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

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

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 29 IKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALN 88
          + NL++D   DD   +F   FG I       + K  + G+ RG AFVTF + E A RA+ 
Sbjct: 4  VTNLSEDADEDDLRELFRP-FGPISRV---YLAKDKETGQSRGFAFVTFHTREDAERAIE 59

Query: 89 LVNGYVFK 96
           +NG+ + 
Sbjct: 60 KLNGFGYD 67

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|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 = 39.9 bits (94), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++  L+      +   +F   FG +   +  L++K  + G  RG  FVTF SVE A  A
Sbjct: 4   LFVSGLSTRTTEKELEALFSK-FGRV---EEVLLMKDPETGESRGFGFVTFESVEDADAA 59

Query: 87  LNLVNGYVFKGKPMIIQ 103
           +  +NG   +G+ + ++
Sbjct: 60  IRDLNGKELEGRVIKVE 76

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-05
 Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 3/40 (7%)

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM 100
           +KL++       AFVTF S E   +AL +++G+ +KG+ +
Sbjct: 36  IKLLKRQ---DFAFVTFRSEEERQKALEILDGFKWKGRVL 72

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

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

 Score = 39.1 bits (91), Expect = 3e-05
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL + +  D+   +F + +G+I       +++    G  RG AFV +   E A  A
Sbjct: 3   LYVTNLPRQLTEDELRKIFEA-YGNIVQCN---LLRDKSTGLPRGVAFVRYDKREEAQAA 58

Query: 87  LNLVNGYVFKGKPMIIQ 103
           ++ +NG +  G  M + 
Sbjct: 59  ISSLNGTIPPGSTMPLS 75

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 28/82 (34%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+KNL   V  D    +F   FG I +A     V     GR RG AFV F   E A +A
Sbjct: 181 LYVKNLDPSVNEDKLRELFAK-FGEITSAA----VMKDGSGRSRGFAFVNFEKHEDAAKA 235

Query: 87  LNLVNGYVFKG--KPMIIQFGR 106
           +  +NG       +   +  GR
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGR 257

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

 Score = 38.1 bits (89), Expect = 7e-05
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ NL  D      + +F   FG++   K   +++ +   + +G  FVT  + E A+ A
Sbjct: 4   IFVYNLPPDADESLLWQLFSP-FGAVTNVK---VIRDLTTNKCKGYGFVTMTNYEEAYSA 59

Query: 87  LNLVNGYVFKGKPMIIQF 104
           +  +NGY   G+ + + F
Sbjct: 60  IASLNGYRLGGRVLQVSF 77

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

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

 Score = 37.6 bits (88), Expect = 8e-05
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y++NL   +  DD   +F S FG +++ +        Q     G AFVTF     A  A
Sbjct: 3   IYVRNLDFKLDEDDLRGIF-SKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 87  LNLVNGYVFKGKPMIIQ 103
           L L NG    G+ + + 
Sbjct: 62  LQL-NGTELGGRKISVS 77

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

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 26 VLYIKNLAKDVVPDD---FFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
          V+ ++ L      +D   FF         +D    G+ +    +GR  G+A+V F S E 
Sbjct: 1  VVRLRGLPFSATEEDIRDFF-------SGLDIPPDGIHIVYDDDGRPTGEAYVEFASPED 53

Query: 83 AHRAL 87
          A RAL
Sbjct: 54 ARRAL 58

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++KNL K V     F  F S FG+I + K    V   + G+ RG  FV F   E A  A
Sbjct: 91  IFVKNLDKSVDNKALFDTF-SKFGNILSCK----VATDENGKSRGYGFVHFEKEESAKAA 145

Query: 87  LNLVNG 92
           +  VNG
Sbjct: 146 IQKVNG 151

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

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          ++IKNL K +     +  F S FG+I + K    V   + G  +G  FV F + E A RA
Sbjct: 5  IFIKNLDKSIDNKALYDTF-SAFGNILSCK----VATDENGGSKGYGFVHFETEEAAVRA 59

Query: 87 LNLVNGYVFKGK 98
          +  VNG +   K
Sbjct: 60 IEKVNGMLLNDK 71

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

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

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 18/88 (20%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           VLY++NL      +    +F S +G ++  K           +++  AFV F   + A +
Sbjct: 3   VLYVRNLPLSTTEEQLRELF-SEYGEVERVK-----------KIKDYAFVHFEERDDAVK 50

Query: 86  ALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           A+  +NG   +G P+ +        AKP
Sbjct: 51  AMEEMNGKELEGSPIEVSL------AKP 72

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

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

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          L +  L +D+  ++      SLF +I   +S  IV+    G+  G  FV +     A +A
Sbjct: 3  LIVNYLPQDMTQEELR----SLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58

Query: 87 LNLVNGYVFKGK 98
          +N +NG+  + K
Sbjct: 59 INTLNGFEIRNK 70

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

 Score = 36.6 bits (85), Expect = 3e-04
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L I  L + +  ++F     SLF ++   K+  IV+  + G   G  FV + S E A RA
Sbjct: 3   LIINYLPQTLTDEEFR----SLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA 58

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG   + K + + + R
Sbjct: 59  IRTLNGLQLQNKRIKVAYAR 78

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

 Score = 36.5 bits (85), Expect = 3e-04
 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ +LA DV        F + + S+  AK   +V     GR +G  FV F   +   RA
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAK---VVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 87  LNLVNGYVFKGKPM 100
           L  +NG     +PM
Sbjct: 61  LTEMNGVYCSSRPM 74

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

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

 Score = 36.3 bits (84), Expect = 4e-04
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ +L+ +V   D   +F S F S  +AK   I+     G  RG  FV F       RA
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAK---IMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 87  LNLVNGYVFKGKPMII 102
           L  + G    G+PM I
Sbjct: 61  LIEMQGVYCGGRPMRI 76

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

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

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDA-----AKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           L+I NL   +       +F S +G I        KSG       +G+ RG  FVTF + E
Sbjct: 2   LWIGNLDSRLTEFHLLKLF-SKYGKIKKFDFLFHKSG-----PLKGQPRGYCFVTFETKE 55

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGR 106
            A +AL  +NG    GK +++++  
Sbjct: 56  EAEKALKSLNGKTALGKKLVVRWAH 80

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 35.7 bits (82), Expect = 5e-04
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 64  MQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           M+ G+ +G   V F S E+A RA  ++NGY   G+ + ++  RN
Sbjct: 33  MENGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRIDRN 76

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ-AFVTFPSVELAHR 85
           +++  L+ DV  ++    F S  G I      L V L++        AF+ F   + A R
Sbjct: 6   IFVGQLSPDVTKEELNERF-SRHGKI------LEVNLIKRANHTNAFAFIKFEREQAAAR 58

Query: 86  ALNLVNGYVFKGKPMIIQF 104
           A+   N  + K K M +Q+
Sbjct: 59  AVESENHSMLKNKTMHVQY 77

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

>gnl|CDD|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 = 35.4 bits (82), Expect = 6e-04
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          L+++NL      ++   +F + FG I       +    +  R +G AFV+F   E A +A
Sbjct: 2  LFVRNLPFTTTEEELRELFEA-FGEISEVH---LPLDKETKRSKGFAFVSFMFPEHAVKA 57

Query: 87 LNLVNGYVFKGK 98
           + ++G +F+G+
Sbjct: 58 YSELDGSIFQGR 69

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

 Score = 35.5 bits (81), Expect = 6e-04
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  L +++  ++F     SLFGSI   +S  +V+    G+  G  FV +     A +A
Sbjct: 6   LIVNYLPQNMTQEEF----KSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +N +NG   + K + + + R
Sbjct: 62  INTLNGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 35.1 bits (80), Expect = 0.001
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 45  FGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
           F SLFGSI   +S  +V+    G+  G  FV +   + A +A+N +NG   + K + + +
Sbjct: 19  FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78

Query: 105 GR 106
            R
Sbjct: 79  AR 80

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

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

 Score = 34.9 bits (81), Expect = 0.001
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 34/97 (35%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE---------------GRMR 70
            +++ N+ + V  DDF                  I KL+++               G+++
Sbjct: 2   TVFVGNIPEGV-SDDF------------------IRKLLEKCGKVLSWKRVKDPSTGKLK 42

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
              F  F   E A RAL L+NG    GK ++++    
Sbjct: 43  AFGFCEFEDPEGALRALRLLNGLELGGKKLLVKVDAK 79

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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 26  VLYIKNL-AKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           VL + NL  + V PD  F +FG ++G +      + VK++     +  A +     + A 
Sbjct: 1   VLLVSNLNEEMVTPDALFTLFG-VYGDV------VRVKILF--NKKDTALIQMADPQQAQ 51

Query: 85  RALNLVNGYVFKGKPM 100
            AL  +NG    GK +
Sbjct: 52  TALTHLNGIRLHGKKL 67

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          L ++NL       D   +F S FG +        +    +G+ +G AFV F S   A +A
Sbjct: 2  LIVRNLPFKCTEADLKKLF-SPFGFVWEVT----IPRKPDGKKKGFAFVQFTSKADAEKA 56

Query: 87 LNLVNGYVFKGKP 99
          +  VNG   KG+P
Sbjct: 57 IKGVNGKKIKGRP 69

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

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

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ +L+ +V     F  F S F S   A+   ++  M+ GR RG  FV+F S + A  A
Sbjct: 2   IFVGDLSPEVTDATLFAAF-SAFPSCSDAR---VMWDMKSGRSRGYGFVSFRSQQDAENA 57

Query: 87  LNLVNGYVFKGKPM 100
           +N +NG     +P+
Sbjct: 58  INEMNGKWLGSRPI 71

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

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 10/77 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE---GRMRGQAFVTFPSVELA 83
           LY+ NL  ++   +   +F   FG I        V+L ++   GR +G  F+ F   E A
Sbjct: 189 LYVGNLHFNITEQELRQIFEP-FGDI------EDVQLHRDPETGRSKGFGFIQFHDAEEA 241

Query: 84  HRALNLVNGYVFKGKPM 100
             AL ++NG+   G+P+
Sbjct: 242 KEALEVMNGFELAGRPI 258

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

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 13/71 (18%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI--VKLMQE--GRMRGQAFVTFPSVEL 82
          +++  + +D+  D+   +F          K+G I  ++LM +  G  RG AFVT+ + E 
Sbjct: 4  VFVGKIPRDLFEDELVPLF---------EKAGPIYELRLMMDFSGLNRGYAFVTYTNKEA 54

Query: 83 AHRALNLVNGY 93
          A RA+  ++ Y
Sbjct: 55 AQRAVKQLHNY 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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 67  GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ 103
           GR RG AF+TF + E A RAL L +G    G+ + ++
Sbjct: 37  GRFRGIAFITFKTEEAAKRALAL-DGEDMGGRFLKVE 72

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

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

 Score = 33.6 bits (78), Expect = 0.002
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 8/63 (12%)

Query: 42  FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI 101
            +   S FG+++       +KL+++    G AFV F + E A +A+  +NG +F G+P+ 
Sbjct: 1   LYKLFSPFGNVEK------IKLLKKKP--GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLR 52

Query: 102 IQF 104
           + +
Sbjct: 53  VDY 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           L +  L+      D   VF S +G I+  +   +V   + GR RG  FV F SVE A  
Sbjct: 1  CLGVFGLSLYTTERDLREVF-SRYGPIEKVQ---VVYDQKTGRSRGFGFVYFESVEDAKE 56

Query: 86 ALNLVNGYVFKGKP 99
          A   +NG    G+ 
Sbjct: 57 AKERLNGMEIDGRR 70

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

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

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++  L K            S  G     +    + +   G+ RG AFV + + E A  A
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQ----LAIAPNGQPRGFAFVEYATAEDAEEA 60

Query: 87  LNLVNGYVFKGKPMIIQFG 105
              +NG+  +G P+ + FG
Sbjct: 61  QQALNGHSLQGSPIRVSFG 79

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|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 14/39 (35%), Positives = 25/39 (64%)

Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL 87
          F  +D    G+++ L + GR  G+A+V F + E+A++AL
Sbjct: 22 FRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKAL 60

This subfamily corresponds to the RRM2 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL + V  D    +   LF  I   KS    KL++E      AFV +     A  A
Sbjct: 1   LYVGNLDRTVTED----LLAELFSQIGPIKS---CKLIREHGNDPYAFVEYYDHRSAAAA 53

Query: 87  LNLVNGYVFKGKPM 100
           L  +NG +  G+ +
Sbjct: 54  LQTMNGRLILGQEI 67

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

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 47  SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
           SLF SI   +S  +++    G   G  FV + + + A RA+N +NG   + K + + + R
Sbjct: 20  SLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYAR 79

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

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

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 26/78 (33%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L + NL   V  DD   +F   FG++  A     V   + GR  G A V F     A +A
Sbjct: 3   LLVSNLDFGVSDDDIKELFAE-FGALKKAA----VHYDRSGRSLGTADVVFERRADALKA 57

Query: 87  LNLVNGYVFKGKPMIIQF 104
           +   NG    G+PM IQ 
Sbjct: 58  MKQYNGVPLDGRPMKIQL 75

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

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

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 49  FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM 100
           FG I  A+   +VK MQ G+ +G  FV+F   E A  A+  +NG    G+ +
Sbjct: 23  FGEISDAR---VVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 47  SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
           SLFGSI   +S  +V+    G+  G  FV +   + A +A+N +NG   + K + + + R
Sbjct: 23  SLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 82

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

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ NL+    PD    V   LFG   A ++  I++ +   + +G  FV+  + + A  A
Sbjct: 272 IFVYNLS----PDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA 327

Query: 87  LNLVNGYVFKGKPMIIQFGRNPA 109
           +  +NGY    + + + F  N A
Sbjct: 328 ILSLNGYTLGNRVLQVSFKTNKA 350

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

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

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          L++ NL+ D   D  +  FG  +G I + +   +      GR +G  +V F S E A  A
Sbjct: 1  LFVGNLSFDADEDSIYEAFGE-YGEISSVR---LPTDPDSGRPKGFGYVEFSSQEAAQAA 56

Query: 87 LNLVNGYVFKGKP 99
          L+ + G    G+P
Sbjct: 57 LDALGGTDLLGRP 69

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|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 33.5 bits (76), Expect = 0.003
 Identities = 13/38 (34%), Positives = 23/38 (60%)

Query: 66  EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ 103
           EG+ RG A V F   E   +A+ ++N +V  G+P+ ++
Sbjct: 37  EGKSRGCAVVEFKMEESMKKAVEVLNKHVLNGRPLKVK 74

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|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 = 33.4 bits (77), Expect = 0.003
 Identities = 11/38 (28%), Positives = 18/38 (47%)

Query: 67  GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
           G+ +G A+V F S   A      + G  F GK  ++ +
Sbjct: 39  GKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 33.4 bits (77), Expect = 0.003
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQ--EGRMRGQAFVTFPSVELA 83
           +YI  L  DV  D    +FG +     D      ++K+    E   +G+A VT+     A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 84  HRALNLVNGYVFKGKPMIIQF 104
             A+   NGY F+G  + +  
Sbjct: 61  QAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	114
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.83
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.79
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.77
KOG0122	270	consensus Translation initiation factor 3, subunit	99.76
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.73
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.7
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.69
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.69
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.67
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.67
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.67
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.67
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.67
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.64
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.64
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.64
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.63
PLN03213	759	repressor of silencing 3; Provisional	99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.63
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.63
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.63
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.62
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.61
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.61
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.61
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.61
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.6
smart00362	72	RRM_2 RNA recognition motif.	99.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.6
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.59
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.59
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.58
smart00360	71	RRM RNA recognition motif.	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.58
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.57
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.57
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.55
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.53
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.52
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.49
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.49
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.48
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.48
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.45
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.45
smart00361	70	RRM_1 RNA recognition motif.	99.44
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.44
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.41
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.4
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.39
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.37
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.35
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.32
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.32
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.32
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.3
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.28
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.23
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.21
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.19
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.16
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.13
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.12
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.12
KOG0151	877	consensus Predicted splicing regulator, contains R	99.11
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.09
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.08
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.05
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.95
KOG0226	290	consensus RNA-binding proteins [General function p	98.95
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.95
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.92
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.9
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.85
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.79
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.76
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.72
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.65
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.61
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.57
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.54
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.46
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.28
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.26
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.18
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.16
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.08
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.07
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.06
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.06
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.02
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.99
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.98
KOG4210	285	consensus Nuclear localization sequence binding pr	97.93
KOG3152	278	consensus TBP-binding protein, activator of basal	97.87
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.84
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.84
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.44
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.43
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.42
KOG2314	698	consensus Translation initiation factor 3, subunit	97.41
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.36
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.34
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.32
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.28
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.25
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.15
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.1
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.09
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.07
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.85
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.64
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.44
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.31
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.31
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	96.25
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.23
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.22
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.13
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.06
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.86
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.78
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.44
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.11
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.07
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.96
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	94.89
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.87
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.29
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.06
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.79
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.74
KOG2135	526	consensus Proteins containing the RNA recognition	90.96
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	90.68
KOG4210	285	consensus Nuclear localization sequence binding pr	88.74
KOG4483	528	consensus Uncharacterized conserved protein [Funct	81.05
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	80.11

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

Probab=99.87  E-value=6.5e-21  Score=117.87  Aligned_cols=86  Identities=22%  Similarity=0.332  Sum_probs=78.8

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ...+++|||+|||+++++++|+++|.+ ||.|..++   .+.+..++++++||||+|.+.++|+.|+..||+..++|+.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~-~G~I~~v~---i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAH-FGDVVDAK---VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCeEEEE---EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            355788999999999999999999999 99999887   46678899999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      +|+++..+..
T Consensus       107 ~V~~a~~~~~  116 (144)
T PLN03134        107 RVNPANDRPS  116 (144)
T ss_pred             EEEeCCcCCC
Confidence            9999986654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.83  E-value=9.6e-20  Score=126.59  Aligned_cols=83  Identities=24%  Similarity=0.487  Sum_probs=76.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +.+|||+|||+.+++++|+++|++ ||.|.+++   .+.+..+|.++|||||+|.+.++|.+|+..|||..++||.|+|.
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~-fG~v~~v~---i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~  344 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGP-FGAVQNVK---IIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVS  344 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHh-CCCeEEEE---EeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            447999999999999999999999 99999987   46677799999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 033648          104 FGRNPAA  110 (114)
Q Consensus       104 ~a~~~~~  110 (114)
                      |+.++..
T Consensus       345 ~~~~~~~  351 (352)
T TIGR01661       345 FKTNKAY  351 (352)
T ss_pred             EccCCCC
Confidence            9987653

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=5.5e-19  Score=122.77  Aligned_cols=84  Identities=24%  Similarity=0.432  Sum_probs=77.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +.++|||+|||..+++++|+++|++ ||.|.+++   .+.++.+|+++|||||+|.+.++|.+|+..|||..+.|+.|.|
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   77 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTS-IGEIESCK---LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKV   77 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHc-cCCEEEEE---EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEE
Confidence            4689999999999999999999999 99999987   4667778999999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      +++++...
T Consensus        78 ~~a~~~~~   85 (352)
T TIGR01661        78 SYARPSSD   85 (352)
T ss_pred             Eeeccccc
Confidence            99986653

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.79  E-value=1.2e-18  Score=121.04  Aligned_cols=85  Identities=25%  Similarity=0.473  Sum_probs=77.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ....++|||+|||+++++++|+++|.. ||.|..++   .+.+..++++++||||+|.+.++|++|++.|||..+.+++|
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~-~G~V~~v~---i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i  179 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRT-IGPINTCR---IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL  179 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCcee
Confidence            356789999999999999999999999 99999887   45677899999999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      +|.++++..
T Consensus       180 ~V~~a~p~~  188 (346)
T TIGR01659       180 KVSYARPGG  188 (346)
T ss_pred             eeecccccc
Confidence            999998653

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=99.77  E-value=6.6e-18  Score=91.98  Aligned_cols=70  Identities=37%  Similarity=0.581  Sum_probs=63.6

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      |||+|||+++++++|+.+|.+ ||.+..++    +....++..+++|||+|.+.++|+.|+..|||..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQ-FGKIESIK----VMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHT-TSTEEEEE----EEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHH-hhhccccc----ccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999 99998775    22337788999999999999999999999999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.76  E-value=4e-18  Score=110.86  Aligned_cols=82  Identities=28%  Similarity=0.462  Sum_probs=77.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++|.|+||+.++++++|+++|.+ ||.+.++.   ..+++.||.++|||||.|.+.++|.+|+..|||+-++.-.|.|
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~-fg~i~rvy---lardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRP-FGPITRVY---LARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhc-cCccceeE---EEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            4578999999999999999999999 99999886   5789999999999999999999999999999999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      +|++++
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            999986

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.73  E-value=5.4e-17  Score=112.79  Aligned_cols=84  Identities=27%  Similarity=0.516  Sum_probs=75.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--ceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--KPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~~l  100 (114)
                      ..++|||+|||..+++++|+++|++ ||.|..++   .+.+..+++.++||||+|.+.++|++|++.||+..+.+  ++|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~-fG~V~~v~---i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l  267 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGK-YGQIVQKN---ILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPL  267 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHh-cCCEEEEE---EeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeE
Confidence            4578999999999999999999999 99998886   45677799999999999999999999999999998865  689


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|.+|+....
T Consensus       268 ~V~~a~~~~~  277 (346)
T TIGR01659       268 TVRLAEEHGK  277 (346)
T ss_pred             EEEECCcccc
Confidence            9999986543

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).

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

Probab=99.70  E-value=8.9e-17  Score=117.68  Aligned_cols=81  Identities=22%  Similarity=0.350  Sum_probs=74.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...++|||+|||+.+++++|+.+|.+ ||.|.+++   .+.+..+|+++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~-fG~I~sV~---I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~Ik  180 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDP-FGPIKSIN---MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK  180 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHc-cCCEEEEE---EeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceee
Confidence            44679999999999999999999999 99999887   456788999999999999999999999999999999999999


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      |.+..
T Consensus       181 V~rp~  185 (612)
T TIGR01645       181 VGRPS  185 (612)
T ss_pred             ecccc
Confidence            98654

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.

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

Probab=99.70  E-value=1.2e-16  Score=116.94  Aligned_cols=84  Identities=17%  Similarity=0.319  Sum_probs=76.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++|||+|||+++++++|+.+|++ ||.|.+++   ...+..++.++|||||+|.+.++|.+|+..|||..++|+.|.|
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~-FG~I~svr---l~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV  278 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEA-FGEIVKCQ---LARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV  278 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhh-cCCeeEEE---EEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3478999999999999999999999 99999887   4566778899999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      .++.+...
T Consensus       279 ~kAi~pP~  286 (612)
T TIGR01645       279 GKCVTPPD  286 (612)
T ss_pred             EecCCCcc
Confidence            99986543

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.

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=2.5e-17  Score=108.79  Aligned_cols=89  Identities=25%  Similarity=0.389  Sum_probs=83.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ++.+|+|||.+||..+.+.+|..+|.+ ||.|.+.+   ...++.|..+++|+||.|.+..+++.||.+|||..|+-+.|
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~P-FGhivSaK---VFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRL  357 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLP-FGHIVSAK---VFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRL  357 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhcc-ccceeeee---eeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhh
Confidence            577899999999999999999999999 99999887   57788899999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCC
Q 033648          101 IIQFGRNPAAAKP  113 (114)
Q Consensus       101 ~v~~a~~~~~~~~  113 (114)
                      +|++.+++.+.+|
T Consensus       358 KVQLKRPkdanRP  370 (371)
T KOG0146|consen  358 KVQLKRPKDANRP  370 (371)
T ss_pred             hhhhcCccccCCC
Confidence            9999999988775

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

Probab=99.69  E-value=2.1e-16  Score=115.91  Aligned_cols=82  Identities=26%  Similarity=0.438  Sum_probs=74.7

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .+|||+|||.++++++|+++|++ ||.|.+++   .+++..+++++|||||.|.+.++|++|+..+|+..+.|++|+|.|
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~-~G~v~~v~---v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~   76 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKP-FGPVLSVR---VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMW   76 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeec
Confidence            36999999999999999999999 99998886   456777899999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +..+..
T Consensus        77 s~~~~~   82 (562)
T TIGR01628        77 SQRDPS   82 (562)
T ss_pred             cccccc
Confidence            875543

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

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.69  E-value=2.9e-16  Score=85.79  Aligned_cols=70  Identities=37%  Similarity=0.632  Sum_probs=60.3

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      |||+|||+++++++|..+|.. +|.+..+.   ....+. +..+++|||+|.+.++|.+|+..++|..++|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~-~g~v~~v~---~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSR-FGPVEKVR---LIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTT-SSBEEEEE---EEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHh-cCCcceEE---EEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999 99987775   233434 78899999999999999999999999999999874

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 ....

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

Probab=99.68  E-value=4.7e-16  Score=111.52  Aligned_cols=80  Identities=26%  Similarity=0.567  Sum_probs=74.2

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++|||+|||..+++++|+.+|.+ ||.|..+.   .+.+..+|.++|||||+|.+.++|..|+..|||..+.|++|.|
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~-~G~i~~v~---~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v  260 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEP-FGDIEDVQ---LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV  260 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEE
Confidence            3689999999999999999999999 99998886   4566778899999999999999999999999999999999999


Q ss_pred             Eecc
Q 033648          103 QFGR  106 (114)
Q Consensus       103 ~~a~  106 (114)
                      .+|.
T Consensus       261 ~~a~  264 (457)
T TIGR01622       261 GYAQ  264 (457)
T ss_pred             EEcc
Confidence            9976

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.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.67  E-value=5.1e-17  Score=104.69  Aligned_cols=87  Identities=23%  Similarity=0.339  Sum_probs=80.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+..++||||+|...+++.-|...|.+ ||.|..+++   ..+..+++.+||+||+|...|+|.+|+..||+.++.||.|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIP-FGDI~dIqi---PlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grti   82 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIP-FGDIKDIQI---PLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTI   82 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhcccc-ccchhhccc---ccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeE
Confidence            355689999999999999999999999 999999984   4477899999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      +|.+|+|.+..
T Consensus        83 rVN~AkP~kik   93 (298)
T KOG0111|consen   83 RVNLAKPEKIK   93 (298)
T ss_pred             EEeecCCcccc
Confidence            99999987655

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

Probab=99.67  E-value=4.5e-16  Score=114.21  Aligned_cols=83  Identities=30%  Similarity=0.496  Sum_probs=75.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...++|||+||++.+++++|+++|++ ||.|.++++   +.+ .+|.++|||||+|.+.++|.+|+..|||..++|++|.
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~-~G~i~~~~i---~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~  357 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSE-CGEITSAKV---MLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY  357 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHh-cCCeEEEEE---EEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeE
Confidence            45678999999999999999999999 999998863   333 6789999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |.+|..+.
T Consensus       358 V~~a~~k~  365 (562)
T TIGR01628       358 VALAQRKE  365 (562)
T ss_pred             EEeccCcH
Confidence            99998654

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

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

Probab=99.67  E-value=8.8e-16  Score=111.35  Aligned_cols=83  Identities=22%  Similarity=0.304  Sum_probs=75.3

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+..+|||+|||..+++++|+++|.. ||.|..+.   .+.+..+|.++|||||+|.+.++|..|+..|||..++|+.|.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~~~---~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~  368 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLES-FGDLKAFN---LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLH  368 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            34578999999999999999999999 99998876   456677899999999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |.+|...
T Consensus       369 v~~a~~~  375 (509)
T TIGR01642       369 VQRACVG  375 (509)
T ss_pred             EEECccC
Confidence            9998643

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

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=1.7e-16  Score=94.37  Aligned_cols=81  Identities=21%  Similarity=0.327  Sum_probs=70.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ..+++||||||+..++++++.++|++ .|.|..+-..   .++.+-...|||||+|.+.++|+.|++.++|+.+..++|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~-cG~irriiMG---Ldr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir  109 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSK-CGDIRRIIMG---LDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIR  109 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHh-ccchheeEec---cccCCcCccceEEEEEecchhHHHHHHHhccCccccccee
Confidence            56799999999999999999999999 9999876322   2334445669999999999999999999999999999999


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      +.|.-
T Consensus       110 ~D~D~  114 (153)
T KOG0121|consen  110 IDWDA  114 (153)
T ss_pred             eeccc
Confidence            98864

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=5.7e-16  Score=96.54  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=70.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+-.+.||||||+...+..+|+..|.. ||.+..+    |+-.    ...|||||+|.+..+|+.|+..|+|..|.|..+
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~-yG~lrsv----WvAr----nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~   77 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSK-YGPLRSV----WVAR----NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRI   77 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHh-cCcceeE----EEee----cCCCceEEeccCcccHHHHHhhcCCccccCceE
Confidence            355789999999999999999999999 9998765    4322    467999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|+++....
T Consensus        78 rVE~S~G~~   86 (195)
T KOG0107|consen   78 RVELSTGRP   86 (195)
T ss_pred             EEEeecCCc
Confidence            999998654

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=4.8e-16  Score=104.92  Aligned_cols=79  Identities=22%  Similarity=0.268  Sum_probs=70.5

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..+|+|+|||+.+.+.||+.+|.+ ||.|.++++   |.+  ...+||||||+|.+.++|++|=.+|||..+.||+|.|.
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~k-fG~VldVEI---IfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEK-FGKVLDVEI---IFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHh-hCceeeEEE---Eec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            468999999999999999999999 999998874   222  23579999999999999999999999999999999999


Q ss_pred             eccCC
Q 033648          104 FGRNP  108 (114)
Q Consensus       104 ~a~~~  108 (114)
                      .|...
T Consensus       170 ~ATar  174 (376)
T KOG0125|consen  170 NATAR  174 (376)
T ss_pred             ccchh
Confidence            98743

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.64  E-value=2.2e-15  Score=99.96  Aligned_cols=75  Identities=20%  Similarity=0.213  Sum_probs=66.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+.+++++|+++|+. ||.|.++.+   +.+.   ..+|||||+|.+.++|+.|+ .|||..+.|+.|.|.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~-~G~I~~V~I---~~d~---~~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt   75 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSF-SGDIEYVEM---QSEN---ERSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTIT   75 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---eecC---CCCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEE
Confidence            468999999999999999999999 999998863   2232   25689999999999999999 599999999999999


Q ss_pred             ecc
Q 033648          104 FGR  106 (114)
Q Consensus       104 ~a~  106 (114)
                      .+.
T Consensus        76 ~a~   78 (260)
T PLN03120         76 PAE   78 (260)
T ss_pred             ecc
Confidence            987

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.64  E-value=1.9e-15  Score=99.82  Aligned_cols=81  Identities=23%  Similarity=0.393  Sum_probs=73.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+.+|++|+||++..++++++++.|++ ||.|.++++   .      +.+||+||.|.+.|+|.+||..+||.+++|..+
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~-fG~I~EVRv---F------k~qGYaFVrF~tkEaAahAIv~mNntei~G~~V  230 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSP-FGPIQEVRV---F------KDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLV  230 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhccc-CCcceEEEE---e------cccceEEEEecchhhHHHHHHHhcCceeCceEE
Confidence            467899999999999999999999999 999998763   2      367999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      ++.|.|.....
T Consensus       231 kCsWGKe~~~~  241 (321)
T KOG0148|consen  231 RCSWGKEGDDG  241 (321)
T ss_pred             EEeccccCCCC
Confidence            99999976544

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.64  E-value=7.9e-16  Score=98.31  Aligned_cols=82  Identities=29%  Similarity=0.438  Sum_probs=75.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...+.|.|-||...++.++|+.+|++ ||.|..+.   +..+..|+..+|||||.|....+|+.|+.+|+|..++|+.|.
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFek-YG~vgDVy---IPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEK-YGRVGDVY---IPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHH-hCccccee---cccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            44578999999999999999999999 99998886   455788999999999999999999999999999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |++|+=
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            999983

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=7.8e-16  Score=99.79  Aligned_cols=79  Identities=24%  Similarity=0.344  Sum_probs=69.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      -+.||||+|+|.+..+.|++.|+. ||+|.+..   .+.++.+|+++||+||+|.+.++|.+|++. ..-.|+||.-.+.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeq-fGeI~eav---vitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQ-FGEIVEAV---VITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHH-hCceEEEE---EEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            367999999999999999999999 99998876   688999999999999999999999999853 3356899998888


Q ss_pred             eccC
Q 033648          104 FGRN  107 (114)
Q Consensus       104 ~a~~  107 (114)
                      +|.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            7763

>PLN03213 repressor of silencing 3; Provisional

Probab=99.63  E-value=1.5e-15  Score=107.64  Aligned_cols=79  Identities=24%  Similarity=0.437  Sum_probs=70.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCH--HHHHHHHHHhCCcccCCce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV--ELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~--~~a~~a~~~l~g~~~~g~~   99 (114)
                      ....+||||||++.+++++|+..|+. ||.|..+++   +  +.+|  +|||||+|.+.  .++.+|+..|||..+.|+.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSe-FGsVkdVEI---p--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~   79 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSP-MGTVDAVEF---V--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGR   79 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEE---e--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCce
Confidence            44578999999999999999999999 999998873   2  4566  89999999987  7899999999999999999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |+|..|++.
T Consensus        80 LKVNKAKP~   88 (759)
T PLN03213         80 LRLEKAKEH   88 (759)
T ss_pred             eEEeeccHH
Confidence            999999853

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

Probab=99.63  E-value=2.3e-15  Score=110.01  Aligned_cols=79  Identities=25%  Similarity=0.438  Sum_probs=70.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-CceEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-GKPMI  101 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g~~l~  101 (114)
                      ..++|||+|||+++++++|+++|++ ||.|..++   .+++ .+|.++|||||+|.+.++|++|++.||+..+. |+.|.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~-~G~I~~vr---l~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~  131 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEK-AGPIYELR---LMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLG  131 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHh-hCCEEEEE---EEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccc
Confidence            3589999999999999999999999 99998886   3445 78999999999999999999999999999985 78777


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      |..+.
T Consensus       132 V~~S~  136 (578)
T TIGR01648       132 VCISV  136 (578)
T ss_pred             ccccc
Confidence            76553

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.

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=1.9e-17  Score=103.73  Aligned_cols=86  Identities=19%  Similarity=0.411  Sum_probs=77.6

Q ss_pred             cCCCC-CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           17 NYTAG-NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        17 ~~~~~-~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      .|+.. ..++-+||||||+..|+.+|..+|+. ||.+..+.   .+++..||+++||||++|.+..+.-.|+..|||..+
T Consensus        27 SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSq-yGe~vdin---LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki  102 (219)
T KOG0126|consen   27 SWHQEYKDSAYIYIGGLPYELTEGDILCVFSQ-YGEIVDIN---LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI  102 (219)
T ss_pred             chhhhcccceEEEECCCcccccCCcEEEEeec-cCceEEEE---EEecCCCCcccceEEEEecCccceEEEEeccCCcee
Confidence            44443 56788999999999999999999999 99999887   578999999999999999999999999999999999


Q ss_pred             CCceEEEEecc
Q 033648           96 KGKPMIIQFGR  106 (114)
Q Consensus        96 ~g~~l~v~~a~  106 (114)
                      .||.|+|...-
T Consensus       103 ~gRtirVDHv~  113 (219)
T KOG0126|consen  103 LGRTIRVDHVS  113 (219)
T ss_pred             cceeEEeeecc
Confidence            99999998654

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

Probab=99.63  E-value=3e-15  Score=108.20  Aligned_cols=78  Identities=27%  Similarity=0.398  Sum_probs=69.8

Q ss_pred             CCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      +++++|||+|||+ .+++++|+.+|+. ||.|..++++   .+     .+|+|||+|.+.++|..|+..|||..+.|++|
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~-yG~V~~vki~---~~-----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l  343 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCV-YGNVERVKFM---KN-----KKETALIEMADPYQAQLALTHLNGVKLFGKPL  343 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHh-cCCeEEEEEE---eC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceE
Confidence            5778999999998 6999999999999 9999988642   22     36999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|++++..
T Consensus       344 ~v~~s~~~  351 (481)
T TIGR01649       344 RVCPSKQQ  351 (481)
T ss_pred             EEEEcccc
Confidence            99999764

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).

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

Probab=99.62  E-value=4.1e-15  Score=106.66  Aligned_cols=81  Identities=25%  Similarity=0.454  Sum_probs=73.5

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+..+|||+|||..+++++|+++|.+ +|.|..++   .+.+..++.++|||||+|.+.++|.+|+. |+|..+.|++|.
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~-~G~v~~v~---i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~  161 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSK-VGKVRDVQ---CIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPII  161 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeE
Confidence            45679999999999999999999999 99998887   45677789999999999999999999994 999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |+.+..
T Consensus       162 v~~~~~  167 (457)
T TIGR01622       162 VQSSQA  167 (457)
T ss_pred             Eeecch
Confidence            998754

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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=4.3e-15  Score=98.00  Aligned_cols=85  Identities=25%  Similarity=0.478  Sum_probs=80.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..+.|.|.-||..+|+++++.+|.. .|+|.+|+   .++++-+|.+-||+||-|.++++|++|+..|||..+..+.|+|
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~S-iGeiEScK---LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKV  115 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGS-IGEIESCK---LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKV  115 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhc-ccceeeee---eeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEE
Confidence            3467999999999999999999999 99999998   5889999999999999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 033648          103 QFGRNPAAA  111 (114)
Q Consensus       103 ~~a~~~~~~  111 (114)
                      +||++.+++
T Consensus       116 SyARPSs~~  124 (360)
T KOG0145|consen  116 SYARPSSDS  124 (360)
T ss_pred             EeccCChhh
Confidence            999998765

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=8.7e-15  Score=97.78  Aligned_cols=83  Identities=19%  Similarity=0.402  Sum_probs=77.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .|-+||||+.|+.++++..|+..|.. ||.|..+.   .|.+..||+++|||||+|...-+...|-+.-+|.+|+|+.|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~-YG~Ikrir---lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~  174 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEK-YGPIKRIR---LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRIL  174 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHh-cCcceeEE---EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEE
Confidence            55689999999999999999999999 99999887   688889999999999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |.+-...
T Consensus       175 VDvERgR  181 (335)
T KOG0113|consen  175 VDVERGR  181 (335)
T ss_pred             EEecccc
Confidence            9876543

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.61  E-value=3.7e-15  Score=98.50  Aligned_cols=82  Identities=22%  Similarity=0.464  Sum_probs=76.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .-.+||+.|...++.+.|++.|.+ ||.|.+++   .+++..|++++||+||.|...++|+.||..|||..|++|.|+-.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~p-FGevS~ak---virD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTN  137 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAP-FGEVSDAK---VIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTN  137 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhcc-ccccccce---EeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecc
Confidence            346999999999999999999999 99999998   68899999999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      ||.-+.
T Consensus       138 WATRKp  143 (321)
T KOG0148|consen  138 WATRKP  143 (321)
T ss_pred             ccccCc
Confidence            997543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.61  E-value=2.2e-15  Score=106.77  Aligned_cols=82  Identities=22%  Similarity=0.455  Sum_probs=77.9

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      +.+||||+|+++++++|..+|+. .|.|...+   .+.|+.+|+.+||||++|.+.++|..|++.|||.++.||+|+|.|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~-~g~v~s~~---~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSG-VGPVLSFR---LVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhc-cCccceee---ecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeec
Confidence            88999999999999999999999 99998887   577999999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +..++.
T Consensus        95 ~~~~~~  100 (435)
T KOG0108|consen   95 ASNRKN  100 (435)
T ss_pred             ccccch
Confidence            987754

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.60  E-value=4.6e-15  Score=89.13  Aligned_cols=82  Identities=17%  Similarity=0.367  Sum_probs=75.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      -.+..|||+++....+++++...|.. ||.|..+++.+   +..||..+||++|+|.+.+.|++|+..+||..+.|..|.
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~d-yGeiKNihLNL---DRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFAD-YGEIKNIHLNL---DRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhh-cccccceeecc---ccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            33578999999999999999999999 99999887544   678999999999999999999999999999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |.|+=-
T Consensus       146 VDw~Fv  151 (170)
T KOG0130|consen  146 VDWCFV  151 (170)
T ss_pred             EEEEEe
Confidence            998853

>smart00362 RRM_2 RNA recognition motif

Probab=99.60  E-value=1e-14  Score=78.86  Aligned_cols=72  Identities=36%  Similarity=0.621  Sum_probs=62.8

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +|+|+|||..++.++|+.+|.+ ||.+..+.+   ... . +..+++|||+|.+.++|..|+..++|..+.|+.+.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~-~g~v~~~~~---~~~-~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSK-FGPIESVKI---PKD-T-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHh-cCCEEEEEE---ecC-C-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            4899999999999999999999 999987642   222 2 6778999999999999999999999999999998873

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

Probab=99.60  E-value=7.5e-15  Score=106.17  Aligned_cols=77  Identities=25%  Similarity=0.435  Sum_probs=67.8

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh--CCcccCCceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV--NGYVFKGKPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~g~~l  100 (114)
                      |+.+|||+|||+.+++++|+++|++ ||.|..+.+   +      +.+++|||+|.+.++|.+|+..+  ++..++|++|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~-fG~V~~v~i---~------~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l   70 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIP-FGPVSYVMM---L------PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPA   70 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEE---E------CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEE
Confidence            5789999999999999999999999 999988753   1      24689999999999999999875  7788999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|+++..+.
T Consensus        71 ~v~~s~~~~   79 (481)
T TIGR01649        71 FFNYSTSQE   79 (481)
T ss_pred             EEEecCCcc
Confidence            999997543

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.59  E-value=8.8e-15  Score=106.98  Aligned_cols=75  Identities=25%  Similarity=0.453  Sum_probs=67.6

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhc--CCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLF--GSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~--G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ...+|||+||+..+++++|+++|++ |  |.|..+++           .++||||+|.+.++|.+|+..|||..|.|+.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~-f~~G~I~rV~~-----------~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I  299 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSE-FKPGKVERVKK-----------IRDYAFVHFEDREDAVKAMDELNGKELEGSEI  299 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHh-cCCCceEEEEe-----------ecCeEEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            3468999999999999999999999 9  99876641           35699999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|.+|++..
T Consensus       300 ~V~~Akp~~  308 (578)
T TIGR01648       300 EVTLAKPVD  308 (578)
T ss_pred             EEEEccCCC
Confidence            999998754

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.59  E-value=3.3e-15  Score=93.66  Aligned_cols=82  Identities=23%  Similarity=0.340  Sum_probs=75.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      -+...+||||||+..++++.|+++|-. .|.|..++   ..++..++..+||||++|.++|+|+-|++.||+..+.|++|
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iq-agpVv~i~---iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpI   81 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQ-AGPVVNLH---IPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPI   81 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHh-cCceeeee---cchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCcee
Confidence            356789999999999999999999999 99998887   45577788899999999999999999999999999999999


Q ss_pred             EEEecc
Q 033648          101 IIQFGR  106 (114)
Q Consensus       101 ~v~~a~  106 (114)
                      +|..+.
T Consensus        82 rv~kas   87 (203)
T KOG0131|consen   82 RVNKAS   87 (203)
T ss_pred             EEEecc
Confidence            999887

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.58  E-value=1.8e-14  Score=82.93  Aligned_cols=79  Identities=23%  Similarity=0.523  Sum_probs=69.9

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      -...|||.|||..+|.++..++|.+ ||.|..++      ...+-..+|.|||.|++..+|.+|+..|+|+.+.++.|.|
T Consensus        17 vnriLyirNLp~~ITseemydlFGk-yg~IrQIR------iG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~v   89 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGK-YGTIRQIR------IGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVV   89 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhc-ccceEEEE------ecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEE
Confidence            3567999999999999999999999 99997554      3345567899999999999999999999999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      -+-.+.
T Consensus        90 lyyq~~   95 (124)
T KOG0114|consen   90 LYYQPE   95 (124)
T ss_pred             EecCHH
Confidence            887654

>smart00360 RRM RNA recognition motif

Probab=99.58  E-value=1.6e-14  Score=77.74  Aligned_cols=71  Identities=34%  Similarity=0.627  Sum_probs=62.4

Q ss_pred             ecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           29 IKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        29 v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      |+|||..+++++|+.+|.+ ||.+..+.   ......++..+++|||+|.+.++|..|+..+++..++|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~-~g~v~~~~---i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSK-FGKIESVR---LVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHh-hCCEeEEE---EEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6799999999999999999 99998775   23344467889999999999999999999999999999998873

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

Probab=99.58  E-value=1.7e-14  Score=95.70  Aligned_cols=79  Identities=33%  Similarity=0.590  Sum_probs=72.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..+|||+|||..+++++|..+|.. ||.+..+.   ...+..++..+|+|||.|.+.+++..|+..++|..+.|++|.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~-~g~~~~~~---~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKK-FGPVKRVR---LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHh-cCceeEEE---eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEee
Confidence            589999999999999999999999 99998775   34455789999999999999999999999999999999999999


Q ss_pred             ecc
Q 033648          104 FGR  106 (114)
Q Consensus       104 ~a~  106 (114)
                      .+.
T Consensus       191 ~~~  193 (306)
T COG0724         191 KAQ  193 (306)
T ss_pred             ccc
Confidence            964

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=2.4e-14  Score=100.07  Aligned_cols=81  Identities=26%  Similarity=0.398  Sum_probs=73.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc-CCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF-KGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-~g~~l  100 (114)
                      +.+|-||||.||.++.+++|..+|.+ .|.|-+++   .++++.+|.++|||||.|.+.+.|+.|++.||+++| .|+.|
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEk-iG~I~elR---LMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~i  156 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEK-IGKIYELR---LMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLL  156 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHh-ccceeeEE---EeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEe
Confidence            55789999999999999999999999 99998887   466889999999999999999999999999999998 58888


Q ss_pred             EEEecc
Q 033648          101 IIQFGR  106 (114)
Q Consensus       101 ~v~~a~  106 (114)
                      .|+.+-
T Consensus       157 gvc~Sv  162 (506)
T KOG0117|consen  157 GVCVSV  162 (506)
T ss_pred             EEEEee
Confidence            877654

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=2.1e-14  Score=94.79  Aligned_cols=82  Identities=23%  Similarity=0.474  Sum_probs=76.2

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .+.++||.||.++.++.-|+++|++ ||.+..++   .+++..+.+.+||+||.+.+-++|..|+..|||+.+++|.|.|
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgp-FGAv~nVK---virD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQV  352 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGP-FGAVTNVK---VIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQV  352 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCc-ccceeeEE---EEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEE
Confidence            3579999999999999999999999 99999998   5778888999999999999999999999999999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      .|...+
T Consensus       353 sFKtnk  358 (360)
T KOG0145|consen  353 SFKTNK  358 (360)
T ss_pred             EEecCC
Confidence            987654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.55  E-value=2.8e-14  Score=92.14  Aligned_cols=83  Identities=39%  Similarity=0.679  Sum_probs=74.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHH----HHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFF----VFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~----~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      +|..+|||.||+..+..++|+.    +|+. ||.|..      +.-..+.+.+|-|||.|.+.+.|..|+..|+|..+.|
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsq-fG~ild------I~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQ-FGKILD------ISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHh-hCCeEE------EEecCCCCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            4555999999999999998887    9999 998864      4455788999999999999999999999999999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      ++++++||+.+++.
T Consensus        80 K~mriqyA~s~sdi   93 (221)
T KOG4206|consen   80 KPMRIQYAKSDSDI   93 (221)
T ss_pred             chhheecccCccch
Confidence            99999999988653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=6.5e-14  Score=91.89  Aligned_cols=77  Identities=19%  Similarity=0.280  Sum_probs=67.5

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +.+.+|||+||++.+++++|+++|+. ||.|.++++   +.+   +..+++|||+|.+.++++.|+ .|+|..|.+++|.
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~-~G~I~~V~I---~~D---~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~   74 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSH-CGAIEHVEI---IRS---GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVC   74 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHh-cCCeEEEEE---ecC---CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEE
Confidence            35689999999999999999999999 999998863   333   455689999999999999998 7999999999999


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      |..+.
T Consensus        75 It~~~   79 (243)
T PLN03121         75 ITRWG   79 (243)
T ss_pred             EEeCc
Confidence            98754

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.53  E-value=2.1e-13  Score=73.99  Aligned_cols=74  Identities=31%  Similarity=0.612  Sum_probs=64.0

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      +|+|+|||..+++++++.+|.. +|.+..+.    +.....+..+++|||+|.+.++|..|+..+++..++|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~-~g~i~~~~----~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSK-FGKVESVR----IVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHh-cCCEEEEE----EeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999 99987765    22333336689999999999999999999999999999999864

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).

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.52  E-value=4.1e-14  Score=98.61  Aligned_cols=83  Identities=17%  Similarity=0.373  Sum_probs=74.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc-c--CCceE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV-F--KGKPM  100 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~-~--~g~~l  100 (114)
                      .-.+|||.+|..++|.+|+++|++ ||.|.+|.   .++|+.++.++|||||.|.+.++|.+|+.+||... +  ...+|
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~-yg~V~ein---l~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEK-YGNVYEIN---LIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHH-hCceeEEE---eecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            457999999999999999999999 99999987   68899999999999999999999999999999866 3  34689


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|.+|....+
T Consensus       110 qvk~Ad~E~e  119 (510)
T KOG0144|consen  110 QVKYADGERE  119 (510)
T ss_pred             eecccchhhh
Confidence            9999987654

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.49  E-value=9.8e-14  Score=97.03  Aligned_cols=75  Identities=28%  Similarity=0.495  Sum_probs=68.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ..|||.||+..+|++.|+++|.. ||.|..++.           .+-||||-|.+.++|.+|++.+||+.+.|..|.|.+
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~-~G~veRVkk-----------~rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtL  327 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNE-FGKVERVKK-----------PRDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTL  327 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHh-ccceEEeec-----------ccceeEEeecchHHHHHHHHHhcCceecCceEEEEe
Confidence            47999999999999999999999 999987752           356999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 033648          105 GRNPAAA  111 (114)
Q Consensus       105 a~~~~~~  111 (114)
                      ||+....
T Consensus       328 AKP~~k~  334 (506)
T KOG0117|consen  328 AKPVDKK  334 (506)
T ss_pred             cCChhhh
Confidence            9987544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.49  E-value=1.2e-13  Score=87.23  Aligned_cols=81  Identities=25%  Similarity=0.367  Sum_probs=70.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ....+++||+|||.++.+.+++.+|.+ ||.|..+.    +++  .....+||||+|.+..+|+.||..-+|+.++|..|
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyK-yg~i~~ie----LK~--r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rL   75 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYK-YGRIREIE----LKN--RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRL   75 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhh-hcceEEEE----ecc--CCCCCCeeEEEecCccchhhhhhcccccccCcceE
Confidence            355789999999999999999999999 99997664    222  22346899999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|+|+..-
T Consensus        76 RVEfprgg   83 (241)
T KOG0105|consen   76 RVEFPRGG   83 (241)
T ss_pred             EEEeccCC
Confidence            99999865

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=1.3e-13  Score=98.59  Aligned_cols=84  Identities=24%  Similarity=0.445  Sum_probs=75.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh-----CC-cccCC
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV-----NG-YVFKG   97 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-----~g-~~~~g   97 (114)
                      +.+|||.|||+++++++|.+.|++ ||.+.++.   .+.++.|+.++|.|||.|.+...|..||..-     .| ..++|
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fsk-FG~v~ya~---iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G  367 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSK-FGEVKYAI---IVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG  367 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHh-hccceeEE---EEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec
Confidence            479999999999999999999999 99999886   6778999999999999999999999999877     23 66899


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      |.|.|..|-++.++
T Consensus       368 R~Lkv~~Av~RkeA  381 (678)
T KOG0127|consen  368 RLLKVTLAVTRKEA  381 (678)
T ss_pred             cEEeeeeccchHHH
Confidence            99999999887654

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=3.1e-14  Score=97.83  Aligned_cols=77  Identities=23%  Similarity=0.368  Sum_probs=72.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      |++|||.+.+...++.++..|.+ ||.|.++..   .+++.|++++||+||+|.-.|.|+.|++.|||..++||.|+|..
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~P-FGPIKSInM---SWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDP-FGPIKSINM---SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccC-CCCcceeec---ccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            78999999999999999999999 999999984   45888999999999999999999999999999999999999974


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      -
T Consensus       190 P  190 (544)
T KOG0124|consen  190 P  190 (544)
T ss_pred             C
Confidence            3

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.45  E-value=5.6e-13  Score=95.40  Aligned_cols=83  Identities=28%  Similarity=0.444  Sum_probs=74.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+...|.|.|||+.+...+|+.+|+. ||.+..+.+    -....|+..|||||.|....+|..|++.|||.+|+||++-
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~-~G~V~Ei~I----P~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VA  189 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSN-FGKVVEIVI----PRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVA  189 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhh-cceEEEEEc----ccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeE
Confidence            34678999999999999999999999 999987753    2445677789999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |.||-++.
T Consensus       190 VDWAV~Kd  197 (678)
T KOG0127|consen  190 VDWAVDKD  197 (678)
T ss_pred             Eeeecccc
Confidence            99998764

>PF13893 RRM_5: RNA recognition motif

Probab=99.45  E-value=5.8e-13  Score=69.75  Aligned_cols=56  Identities=36%  Similarity=0.710  Sum_probs=47.0

Q ss_pred             HHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           41 FFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        41 l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      |..+|++ ||.|..+.+     .. ..  +++|||+|.+.++|..|+..|||..++|++|+|+||
T Consensus         1 L~~~f~~-fG~V~~i~~-----~~-~~--~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSK-FGEVKKIKI-----FK-KK--RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTT-TS-EEEEEE-----ET-TS--TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCC-cccEEEEEE-----Ee-CC--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            5788999 999987642     11 11  589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.44  E-value=7e-13  Score=72.56  Aligned_cols=63  Identities=29%  Similarity=0.416  Sum_probs=52.2

Q ss_pred             HhHHHHHHh----hhcCCceecccceeEEeccC--CCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           38 PDDFFFVFG----SLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        38 ~~~l~~~f~----~~~G~i~~~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +++|+.+|.    + ||.+..+..  .+.++.+  +.++|++||.|.+.++|..|+..|||..+.|+.|.++
T Consensus         2 ~~~l~~~~~~~~~~-fG~v~~v~~--v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEY-FGEVGKINK--IYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHh-cCCeeEEEE--EEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            456777787    9 999987631  2345545  8899999999999999999999999999999999863

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.44  E-value=2e-13  Score=97.36  Aligned_cols=81  Identities=30%  Similarity=0.498  Sum_probs=72.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .|-..||||||.+++++++|+..|.+ ||.|..+.+   .++..+|.++||+||+|...++|..|+..|||..+.|+.|+
T Consensus       276 ~p~~rl~vgnLHfNite~~lr~ifep-fg~Ie~v~l---~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ik  351 (549)
T KOG0147|consen  276 GPMRRLYVGNLHFNITEDMLRGIFEP-FGKIENVQL---TKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIK  351 (549)
T ss_pred             cchhhhhhcccccCchHHHHhhhccC-cccceeeee---ccccccccccCcceEEEecHHHHHHHHHHhccceecCceEE
Confidence            33344999999999999999999999 999988763   44667999999999999999999999999999999999999


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      |....
T Consensus       352 V~~v~  356 (549)
T KOG0147|consen  352 VSVVT  356 (549)
T ss_pred             EEEee
Confidence            98765

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.41  E-value=6.4e-13  Score=91.00  Aligned_cols=88  Identities=18%  Similarity=0.370  Sum_probs=81.7

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ....+|.+.|||.-|.+-++.++|.-+|+. ||.|.+|.   .+.+.+||.+-.||||+|.+.+++++|.-.|++..|.+
T Consensus       233 Ad~~PPeNVLFVCKLNPVTtDeDLeiIFSr-FG~i~sce---VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD  308 (479)
T KOG0415|consen  233 ADVKPPENVLFVCKLNPVTTDEDLEIIFSR-FGKIVSCE---VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD  308 (479)
T ss_pred             cccCCCcceEEEEecCCcccccchhhHHhh-cccceeee---EEecccccchhheeeeeecchhhHHHHHhhhcceeecc
Confidence            445688999999999999999999999999 99999998   68899999999999999999999999999999999999


Q ss_pred             ceEEEEeccCCC
Q 033648           98 KPMIIQFGRNPA  109 (114)
Q Consensus        98 ~~l~v~~a~~~~  109 (114)
                      +.|+|.|+.+-+
T Consensus       309 rRIHVDFSQSVs  320 (479)
T KOG0415|consen  309 RRIHVDFSQSVS  320 (479)
T ss_pred             ceEEeehhhhhh
Confidence            999999987543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.40  E-value=1.6e-12  Score=83.08  Aligned_cols=84  Identities=20%  Similarity=0.373  Sum_probs=73.8

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhc-CCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLF-GSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~-G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ......+|+..+|..+.+.++...|.+ + |.+...+   .-++++||+++|||||+|.+.+.|.-|-+.||++.+.++.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q-~~g~v~r~r---lsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~l  121 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQ-FGGTVTRFR---LSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHL  121 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhh-cCCeeEEEE---eecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhe
Confidence            355567999999999999999999999 6 6666554   3468889999999999999999999999999999999999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |.|.+-.+.
T Consensus       122 L~c~vmppe  130 (214)
T KOG4208|consen  122 LECHVMPPE  130 (214)
T ss_pred             eeeEEeCch
Confidence            999987765

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=7.7e-13  Score=92.38  Aligned_cols=89  Identities=21%  Similarity=0.370  Sum_probs=81.3

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      .++.+..+||++||.++.+.+|...|.+ ||.|.+.+   ...++.++-+++|+||.|++..+|..||..|||..+++++
T Consensus       420 eGpeGanlfiyhlPqefgdq~l~~~f~p-fG~Vlsak---vfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~Kr  495 (510)
T KOG0144|consen  420 EGPEGANLFIYHLPQEFGDQDLIATFQP-FGGVLSAK---VFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKR  495 (510)
T ss_pred             cCCCccceeeeeCchhhhhHHHHHHhcc-ccceeEEE---EEEecccCHhhhcCcccccchhhhHHHHHHhcchhhcccc
Confidence            3577789999999999999999999999 99998886   5678889999999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |+|++...+....
T Consensus       496 lkVQlk~~~~np~  508 (510)
T KOG0144|consen  496 LKVQLKRDRNNPY  508 (510)
T ss_pred             ceEEeeeccCCCC
Confidence            9999988776544

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.38  E-value=1.5e-12  Score=81.82  Aligned_cols=85  Identities=20%  Similarity=0.411  Sum_probs=74.3

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .-+..+||+||.+.+++..|...|+. ||.+...-  -.+++..+|..++|+||-|.+.+.+.+|+..+||..++.+++.
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsa-fG~l~~~P--~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~it  170 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSA-FGVLISPP--KIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPIT  170 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHh-ccccccCC--cccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceE
Confidence            44588999999999999999999999 99885431  1345667899999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |.++..+.
T Consensus       171 v~ya~k~~  178 (203)
T KOG0131|consen  171 VSYAFKKD  178 (203)
T ss_pred             EEEEEecC
Confidence            99998553

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.37  E-value=1e-12  Score=87.85  Aligned_cols=74  Identities=18%  Similarity=0.394  Sum_probs=67.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ..|||||||...++.+|+.+|.+ ||.|.+|.+           .+.||||-..+...++.|++.|||+.++|..|.|+-
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~-ygkVlECDI-----------vKNYgFVHiEdktaaedairNLhgYtLhg~nInVea   70 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQ-YGKVLECDI-----------VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEA   70 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHh-hCceEeeee-----------ecccceEEeecccccHHHHhhcccceecceEEEEEe
Confidence            35899999999999999999999 999988852           467999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +|+++.
T Consensus        71 SksKsk   76 (346)
T KOG0109|consen   71 SKSKSK   76 (346)
T ss_pred             ccccCC
Confidence            988743

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=1.8e-12  Score=86.04  Aligned_cols=85  Identities=26%  Similarity=0.424  Sum_probs=74.3

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc-cC--Cc
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV-FK--GK   98 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~-~~--g~   98 (114)
                      .....||||-|.....|++++.+|.+ ||.+++|.    +.....|.++||+||.|.++.+|..||..|||.. +-  .-
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~p-fG~~~e~t----vlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASS   91 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQP-FGNIEECT----VLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASS   91 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcc-cCCcceeE----EecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCcc
Confidence            35678999999999999999999999 99999884    5566678999999999999999999999999976 33  45


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|.||.++++.
T Consensus        92 SLVVK~ADTdkER  104 (371)
T KOG0146|consen   92 SLVVKFADTDKER  104 (371)
T ss_pred             ceEEEeccchHHH
Confidence            7999999988753

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.32  E-value=8e-12  Score=90.27  Aligned_cols=82  Identities=18%  Similarity=0.327  Sum_probs=75.2

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .+|||.+|...+...+|+.+|++ ||.|...+   .+.+..+-..+||+||++++.++|.+||..||.+.++|+.|.|+-
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSK-yGKVvGAK---VVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSK-YGKVVGAK---VVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHH-hcceecee---eeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            58999999999999999999999 99998887   567777777899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +|....
T Consensus       482 aKNEp~  487 (940)
T KOG4661|consen  482 AKNEPG  487 (940)
T ss_pred             cccCcc
Confidence            997644

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

Probab=99.32  E-value=8.2e-12  Score=90.75  Aligned_cols=85  Identities=19%  Similarity=0.288  Sum_probs=67.1

Q ss_pred             CCCCeEEecCCCCC--C--------CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           22 NPASVLYIKNLAKD--V--------VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        22 ~~~~~l~v~nlp~~--~--------~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      .++.+|++.|+...  +        ..++|++.|.+ ||.|..+.++....+..++...|++||+|.+.++|.+|+..||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~-~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~ln  485 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSK-YGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMN  485 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHh-cCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcC
Confidence            46778999999632  1        12578999999 9999988643211223345667999999999999999999999


Q ss_pred             CcccCCceEEEEeccC
Q 033648           92 GYVFKGKPMIIQFGRN  107 (114)
Q Consensus        92 g~~~~g~~l~v~~a~~  107 (114)
                      |..|+|+.|.|.|...
T Consensus       486 Gr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       486 GRKFNDRVVVAAFYGE  501 (509)
T ss_pred             CCEECCeEEEEEEeCH
Confidence            9999999999999764

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

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=7.3e-12  Score=87.87  Aligned_cols=77  Identities=29%  Similarity=0.515  Sum_probs=69.2

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEecc
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~  106 (114)
                      +||.||+++++..+|...|+. ||.|.+|+++    ....| ++|| ||+|.+++.|.+|+..+||..+.|++|.|..+.
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~-~g~ilS~kv~----~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSE-FGNILSCKVA----TDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHh-hcCeeEEEEE----EcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            999999999999999999999 9999999742    33444 8999 999999999999999999999999999998887


Q ss_pred             CCCC
Q 033648          107 NPAA  110 (114)
Q Consensus       107 ~~~~  110 (114)
                      .+..
T Consensus       152 ~~~e  155 (369)
T KOG0123|consen  152 RKEE  155 (369)
T ss_pred             chhh
Confidence            6544

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.30  E-value=1.9e-11  Score=85.85  Aligned_cols=78  Identities=22%  Similarity=0.377  Sum_probs=70.1

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      +.+||+|+|+++.+.+|+.++...-|.|.+|+    +....+|+.++||.|+|+++|.+++|++.||.+.+.||+|.|.-
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yve----Ll~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVE----LLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeee----eecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            45999999999999999999996589998886    33457899999999999999999999999999999999999985


Q ss_pred             cc
Q 033648          105 GR  106 (114)
Q Consensus       105 a~  106 (114)
                      ..
T Consensus       121 d~  122 (608)
T KOG4212|consen  121 DH  122 (608)
T ss_pred             cC
Confidence            44

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=3.7e-12  Score=93.24  Aligned_cols=90  Identities=16%  Similarity=0.359  Sum_probs=77.4

Q ss_pred             CcCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           16 KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        16 ~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      +...+...++.|.|.|+|+..+..+++.+|.. ||.+..++++-   ....+.++|||||.|-+..+|.+|+.+|.++.+
T Consensus       605 K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~a-FGqlksvRlPK---K~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHl  680 (725)
T KOG0110|consen  605 KKKSKKKKGTKILVRNIPFEATKREVRKLFTA-FGQLKSVRLPK---KIGKGAHRGFGFVDFLTPREAKNAFDALGSTHL  680 (725)
T ss_pred             cccccccccceeeeeccchHHHHHHHHHHHhc-ccceeeeccch---hhcchhhccceeeeccCcHHHHHHHHhhcccce
Confidence            34444556789999999999999999999999 99999887422   234556789999999999999999999999999


Q ss_pred             CCceEEEEeccCCC
Q 033648           96 KGKPMIIQFGRNPA  109 (114)
Q Consensus        96 ~g~~l~v~~a~~~~  109 (114)
                      .||.|.++||+.+.
T Consensus       681 yGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  681 YGRRLVLEWAKSDN  694 (725)
T ss_pred             echhhheehhccch
Confidence            99999999999875

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.23  E-value=1.5e-11  Score=82.37  Aligned_cols=77  Identities=21%  Similarity=0.337  Sum_probs=70.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++++++|+|+.+.++..+++..|.+ ||.+.+|.+           -++|+||.|.-.++|..|++.|+|.++.|+++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~-ygpviecdi-----------vkdy~fvh~d~~eda~~air~l~~~~~~gk~m  142 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEK-YGPVIECDI-----------VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRM  142 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcc-cCCceeeee-----------ecceeEEEEeeccchHHHHhccccccccccee
Confidence            457789999999999999999999999 999988763           46899999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      +|+++.++-
T Consensus       143 ~vq~stsrl  151 (346)
T KOG0109|consen  143 HVQLSTSRL  151 (346)
T ss_pred             eeeeecccc
Confidence            999988653

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.21  E-value=6.5e-11  Score=83.26  Aligned_cols=76  Identities=29%  Similarity=0.360  Sum_probs=67.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+..|+|+|.|||.++|+..|+.-|.. +|.+.+..+      ...|++++  .|.|.+.++|++|+..|+|..+.||.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre-~G~v~yadi------me~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I  603 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFRE-IGHVLYADI------MENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNI  603 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHh-ccceehhhh------hccCCccc--eEEecCHHHHHHHHHHhccCcccCcee
Confidence            356789999999999999999999999 999987753      24677777  899999999999999999999999999


Q ss_pred             EEEec
Q 033648          101 IIQFG  105 (114)
Q Consensus       101 ~v~~a  105 (114)
                      .|.++
T Consensus       604 ~V~y~  608 (608)
T KOG4212|consen  604 KVTYF  608 (608)
T ss_pred             eeeeC
Confidence            99874

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.19  E-value=6.4e-11  Score=86.94  Aligned_cols=80  Identities=25%  Similarity=0.326  Sum_probs=67.2

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEecc-CCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +.|||.||+++++.+.+...|.+ .|.|.++.+... .++. .-.+.|||||+|.+.++|++|++.|+|+.+.|+.|.|+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k-~G~VlS~~I~kk-kd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSK-QGTVLSIEISKK-KDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHh-cCeEEEEEEecc-ccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            34999999999999999999999 999988753211 1111 12255999999999999999999999999999999999


Q ss_pred             ecc
Q 033648          104 FGR  106 (114)
Q Consensus       104 ~a~  106 (114)
                      ++.
T Consensus       594 ~S~  596 (725)
T KOG0110|consen  594 ISE  596 (725)
T ss_pred             ecc
Confidence            998

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.16  E-value=3.4e-10  Score=75.05  Aligned_cols=86  Identities=28%  Similarity=0.446  Sum_probs=75.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ....+.|+|.|||..+..++|+++|.. ||.+..+    .+.....|.+.|.|-|.|...++|.+|++.|||..++|++|
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~-~~~~~r~----~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~m  154 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAE-FGELKRV----AVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPM  154 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHH-hccceEE----eeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCcee
Confidence            344578999999999999999999999 9976654    45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .+....+.+.+
T Consensus       155 k~~~i~~~~~~  165 (243)
T KOG0533|consen  155 KIEIISSPSQS  165 (243)
T ss_pred             eeEEecCcccc
Confidence            99988766554

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.13  E-value=1.9e-10  Score=85.35  Aligned_cols=76  Identities=22%  Similarity=0.341  Sum_probs=69.3

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ++|||||.|+..+++.+|..+|+. ||.|.++.+         -..++||||.+....+|++|+..|+...+.++.|+|.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~fee-fGeiqSi~l---------i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~  490 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEE-FGEIQSIIL---------IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIA  490 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHh-cccceeEee---------ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEe
Confidence            479999999999999999999999 999998752         1368999999999999999999999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      ||....
T Consensus       491 Wa~g~G  496 (894)
T KOG0132|consen  491 WAVGKG  496 (894)
T ss_pred             eeccCC
Confidence            998654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.12  E-value=3.6e-10  Score=77.29  Aligned_cols=83  Identities=18%  Similarity=0.348  Sum_probs=71.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceec----ccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAA----KSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~----~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ++.|||+|||.++|.+++.++|++ +|.|..-    +....++....|+.+|=|+++|...++...|+..|++..+.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sK-cGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSK-CGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHh-cceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            356999999999999999999999 9988531    11124555567999999999999999999999999999999999


Q ss_pred             EEEEeccC
Q 033648          100 MIIQFGRN  107 (114)
Q Consensus       100 l~v~~a~~  107 (114)
                      |+|+.|+-
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999983

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.12  E-value=7.2e-10  Score=72.08  Aligned_cols=85  Identities=24%  Similarity=0.417  Sum_probs=67.2

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC---CceE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK---GKPM  100 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---g~~l  100 (114)
                      -++|||.+||.++...+|..+|.. |..-..+.+  ....+.....+.+||+.|.+...|.+|+..|||..|+   +..|
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~-f~GYEgslL--K~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRR-FHGYEGSLL--KYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhcc-CCCccceee--eeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            479999999999999999999998 765544432  2222222334589999999999999999999999986   6789


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      ++++||.....
T Consensus       111 hiElAKSNtK~  121 (284)
T KOG1457|consen  111 HIELAKSNTKR  121 (284)
T ss_pred             EeeehhcCccc
Confidence            99999966443

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=99.11  E-value=1.2e-10  Score=85.80  Aligned_cols=86  Identities=26%  Similarity=0.347  Sum_probs=77.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +..++||++||++.++++.|-..|+. ||.+.++++||....-.....+.|+||.|-+..+|++|+..|+|..+.+..++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGr-fgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGR-FGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcc-cCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            44578999999999999999999999 99999999877655555667789999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      +-|+++-
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9999753

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=5.5e-10  Score=76.41  Aligned_cols=76  Identities=30%  Similarity=0.429  Sum_probs=64.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC-cccCCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG-YVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g-~~~~g~~l  100 (114)
                      ....+|||++|...+++.+|+..|.+ ||.|..+.+.         ..+++|||+|.+.+.|+.|....-. ..++|..|
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyq-yGeirsi~~~---------~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQ-YGEIRSIRIL---------PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhh-cCCeeeEEee---------cccccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            33578999999999999999999999 9999876421         1356999999999999998866555 44899999


Q ss_pred             EEEeccC
Q 033648          101 IIQFGRN  107 (114)
Q Consensus       101 ~v~~a~~  107 (114)
                      .|.|+.+
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999998

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.08  E-value=6.5e-10  Score=78.16  Aligned_cols=75  Identities=29%  Similarity=0.430  Sum_probs=67.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ..||||   +++++..|.+.|++ +|.+.+++   ..++. +  +-|||||-|.+.++|++|+..||...+.|+++.+.|
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~-~~~v~s~r---vc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~   71 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSP-AGPVLSIR---VCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMW   71 (369)
T ss_pred             CceecC---CcCChHHHHHHhcc-cCCceeEE---EeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeeh
Confidence            468999   89999999999999 99999887   34555 4  889999999999999999999999999999999999


Q ss_pred             ccCCC
Q 033648          105 GRNPA  109 (114)
Q Consensus       105 a~~~~  109 (114)
                      +.-+.
T Consensus        72 s~rd~   76 (369)
T KOG0123|consen   72 SQRDP   76 (369)
T ss_pred             hccCC
Confidence            87664

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.05  E-value=5.9e-10  Score=77.08  Aligned_cols=80  Identities=18%  Similarity=0.327  Sum_probs=72.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .++||..+.++.++++++.+|.. ||.|..|++   -+....+.++||+|++|.+..+...|+..||-..++|.-|+|-.
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEA-FG~I~~C~L---Ar~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEA-FGEIVKCQL---ARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHh-hcceeeEEe---eccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            58999999999999999999999 999999973   34566778899999999999999999999999999999999987


Q ss_pred             ccCC
Q 033648          105 GRNP  108 (114)
Q Consensus       105 a~~~  108 (114)
                      +-+.
T Consensus       287 ~vTP  290 (544)
T KOG0124|consen  287 CVTP  290 (544)
T ss_pred             ccCC
Confidence            7644

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

Probab=98.95  E-value=2.2e-08  Score=57.85  Aligned_cols=82  Identities=22%  Similarity=0.279  Sum_probs=66.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhc-CCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC----Cc
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLF-GSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK----GK   98 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~-G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~----g~   98 (114)
                      .+||.|.|+|...+.++|.+.+...+ |..+-+.   ...+..++.+.|||||-|.+++.+..-...++|..+.    .+
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~Y---LPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~K   77 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFY---LPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKK   77 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEE---eeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCc
Confidence            36899999999999999998887632 3333333   4567778889999999999999999999999999874    56


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .+.|.+|+-+
T Consensus        78 vc~i~yAriQ   87 (97)
T PF04059_consen   78 VCEISYARIQ   87 (97)
T ss_pred             EEEEehhHhh
Confidence            7888888743

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

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.95  E-value=1.5e-09  Score=71.66  Aligned_cols=78  Identities=23%  Similarity=0.370  Sum_probs=70.0

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+||.|.|...++.+.|-..|.+ |-.-...+   .+++.++|+++||+||.|.+..++.+|+.+|+|..++.++|.+
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~K-fpsf~~ak---viRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKK-FPSFQKAK---VIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHh-ccchhhcc---ccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            3468999999999999999999999 88766665   5789999999999999999999999999999999999999877


Q ss_pred             Ee
Q 033648          103 QF  104 (114)
Q Consensus       103 ~~  104 (114)
                      .-
T Consensus       265 Rk  266 (290)
T KOG0226|consen  265 RK  266 (290)
T ss_pred             hh
Confidence            53

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.95  E-value=5.3e-09  Score=74.31  Aligned_cols=82  Identities=22%  Similarity=0.338  Sum_probs=66.9

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+|||.|||++++.++|+++|.. ||.|....+  .++. ..++..+||||+|.+...++.|+.+ +-..+++++|.|
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~-FG~Ik~~~I--~vr~-~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~V  361 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQ-FGPIKEGGI--QVRS-PGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNV  361 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhh-cccccccce--EEec-cCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEE
Confidence            3456999999999999999999999 999987763  3333 2345559999999999999999965 466789999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      +--++..
T Consensus       362 eek~~~~  368 (419)
T KOG0116|consen  362 EEKRPGF  368 (419)
T ss_pred             Eeccccc
Confidence            9877644

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.92  E-value=1.5e-09  Score=78.00  Aligned_cols=71  Identities=31%  Similarity=0.473  Sum_probs=63.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      -+..+|+|-|||..++.++|...|+. ||+|..++        .+-..++.+||+|.+..+|++|+++|++.++.|+.|.
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~-yGeir~ir--------~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGA-YGEIREIR--------ETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHh-hcchhhhh--------cccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34568999999999999999999999 99998754        3556789999999999999999999999999998887

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.90  E-value=1.9e-09  Score=74.04  Aligned_cols=84  Identities=21%  Similarity=0.325  Sum_probs=71.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..+.+||++|+|.++++.|+..|.. ||.+..|.   .++++.++++++|+||+|.+.+...+++.. .-+.+.|+.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~-~Gev~d~~---vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~   79 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQ-FGEVTDCV---VMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEP   79 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcc-cCceeeEE---EeccCCCCCcccccceecCCCcchheeecc-cccccCCccccc
Confidence            5678999999999999999999988 99999987   455777899999999999998888877642 346689999998


Q ss_pred             EeccCCCCC
Q 033648          103 QFGRNPAAA  111 (114)
Q Consensus       103 ~~a~~~~~~  111 (114)
                      .-|.+..+.
T Consensus        80 k~av~r~~~   88 (311)
T KOG4205|consen   80 KRAVSREDQ   88 (311)
T ss_pred             eeccCcccc
Confidence            888877654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.85  E-value=7.7e-09  Score=71.04  Aligned_cols=83  Identities=24%  Similarity=0.331  Sum_probs=72.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ...+||+.||.++++.+++..|.+ ||.|..+.   .+++..+...++|+||.|.++++..+++ ...-+.++|+.+.|.
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~-~g~v~~~~---~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevk  171 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQ-FGKVADVV---IMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVK  171 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhc-cceeEeeE---EeecccccccccceeeEeccccccceec-ccceeeecCceeeEe
Confidence            458999999999999999999999 99887765   5678889999999999999999999886 456778999999999


Q ss_pred             eccCCCCC
Q 033648          104 FGRNPAAA  111 (114)
Q Consensus       104 ~a~~~~~~  111 (114)
                      .|.++...
T Consensus       172 rA~pk~~~  179 (311)
T KOG4205|consen  172 RAIPKEVM  179 (311)
T ss_pred             eccchhhc
Confidence            99987654

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.79  E-value=1.4e-08  Score=67.24  Aligned_cols=83  Identities=24%  Similarity=0.339  Sum_probs=73.1

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+...+||+|+....+.+++...|.. +|.+..+.   ...+...+..++|+||+|.+.+....++. |+|..+.|+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~-Cg~i~~~t---i~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i  172 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFES-CGGINRVT---VPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAI  172 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeec-cCCcccee---eeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccc
Confidence            355678999999999999999999999 99997665   45677778899999999999999999997 99999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|.+.+..
T Consensus       173 ~vt~~r~~  180 (231)
T KOG4209|consen  173 EVTLKRTN  180 (231)
T ss_pred             eeeeeeee
Confidence            99987754

>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=98.76  E-value=3.1e-08  Score=55.23  Aligned_cols=70  Identities=26%  Similarity=0.426  Sum_probs=46.3

Q ss_pred             CeEEecCCCCCCCHhH----HHHHHhhhcCC-ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           25 SVLYIKNLAKDVVPDD----FFFVFGSLFGS-IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~----l~~~f~~~~G~-i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +.|+|.|||-+.+...    |++++.. +|. +..+             ..+.|++.|.+.+.|.+|.+.|+|-.+.|+.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdN-CGGkVl~v-------------~~~tAilrF~~~~~A~RA~KRmegEdVfG~k   68 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDN-CGGKVLSV-------------SGGTAILRFPNQEFAERAQKRMEGEDVFGNK   68 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHT-TT--EEE---------------TT-EEEEESSHHHHHHHHHHHTT--SSSS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhc-cCCEEEEE-------------eCCEEEEEeCCHHHHHHHHHhhcccccccce
Confidence            4699999999888765    4555555 653 2211             3478999999999999999999999999999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |.|+|....
T Consensus        69 I~v~~~~~~   77 (90)
T PF11608_consen   69 ISVSFSPKN   77 (90)
T ss_dssp             -EEESS--S
T ss_pred             EEEEEcCCc
Confidence            999999543

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

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.72  E-value=1.4e-08  Score=66.18  Aligned_cols=71  Identities=24%  Similarity=0.372  Sum_probs=63.6

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ..+|||+||+...+.+++.+|.. ||.+..+.+           ..+|+||.|.+.-+|..|+..+||..+.|-.+.|++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~-yg~~~d~~m-----------k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~   69 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKG-YGKIPDADM-----------KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEH   69 (216)
T ss_pred             CceeecccCCccchhHHHHHHhh-cccccccee-----------ecccceeccCchhhhhcccchhcCceecceeeeeec
Confidence            35899999999999999999999 999876531           347889999999999999999999999998899999


Q ss_pred             ccC
Q 033648          105 GRN  107 (114)
Q Consensus       105 a~~  107 (114)
                      +..
T Consensus        70 ~r~   72 (216)
T KOG0106|consen   70 ARG   72 (216)
T ss_pred             ccc
Confidence            984

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.65  E-value=2.9e-08  Score=71.67  Aligned_cols=82  Identities=22%  Similarity=0.348  Sum_probs=74.7

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .+.++|++||...++.++.++... ||.+...+   .+.+..+|.++||||-+|.+......|+..|||..++++.|.|+
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~-fg~lk~f~---lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDS-FGPLKAFR---LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHh-cccchhhe---eecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            467999999999999999999999 99998876   46777889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      .|....
T Consensus       365 ~A~~g~  370 (500)
T KOG0120|consen  365 RAIVGA  370 (500)
T ss_pred             hhhccc
Confidence            987543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.61  E-value=2.4e-07  Score=65.07  Aligned_cols=77  Identities=23%  Similarity=0.452  Sum_probs=66.5

Q ss_pred             CCeEEecCCC-CCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           24 ASVLYIKNLA-KDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        24 ~~~l~v~nlp-~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ++.|.|.||. ..+|.+.|..+|+- ||.|.++++   +.+     .+--|+|+|.+...|+.|++.|+|..+.|++|+|
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgv-YGdVqRVki---l~n-----kkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrv  367 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGV-YGDVQRVKI---LYN-----KKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRV  367 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhh-hcceEEEEe---eec-----CCcceeeeecchhHHHHHHHHhhcceecCceEEE
Confidence            5788899987 56899999999999 999999873   222     2367999999999999999999999999999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      .++|...
T Consensus       368 t~SKH~~  374 (492)
T KOG1190|consen  368 TLSKHTN  374 (492)
T ss_pred             eeccCcc
Confidence            9999653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.57  E-value=3e-07  Score=64.60  Aligned_cols=89  Identities=24%  Similarity=0.244  Sum_probs=72.8

Q ss_pred             cCCCCCcCCCC-CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           11 SLPMFKNYTAG-NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        11 ~~~~~~~~~~~-~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      +.|..+++... +|+.++...|+|+++++++++..|.. -|.....       ...-++.+.++++.+.+.|+|-.|+..
T Consensus       400 kkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~-~g~~vka-------fkff~kd~kmal~q~~sveeA~~ali~  471 (492)
T KOG1190|consen  400 KKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQE-PGGQVKA-------FKFFQKDRKMALPQLESVEEAIQALID  471 (492)
T ss_pred             cCcccccccccCCchhheeeccCCcccchhHHHHhhhc-CCceEEe-------eeecCCCcceeecccCChhHhhhhccc
Confidence            34566777665 88899999999999999999999998 6654211       123456788999999999999999999


Q ss_pred             hCCcccCCc-eEEEEeccC
Q 033648           90 VNGYVFKGK-PMIIQFGRN  107 (114)
Q Consensus        90 l~g~~~~g~-~l~v~~a~~  107 (114)
                      ++.+.+++. .|+|+|++.
T Consensus       472 ~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  472 LHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccccCCCCceEEEEeecc
Confidence            999998765 899999885

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.54  E-value=3.8e-08  Score=63.99  Aligned_cols=81  Identities=17%  Similarity=0.151  Sum_probs=68.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +...+|||+|+...++++-|.++|.. .|.|..+.    +...+.++.+ ||||.|.++.+..-|++.+||-.+.+++++
T Consensus         7 e~drtl~v~n~~~~v~eelL~Elfiq-aGPV~kv~----ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q   80 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQ-AGPVYKVG----IPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhc-cCceEEEe----CCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhh
Confidence            34578999999999999999999999 99987654    3333455556 999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      +++-...
T Consensus        81 ~~~r~G~   87 (267)
T KOG4454|consen   81 RTLRCGN   87 (267)
T ss_pred             cccccCC
Confidence            9887654

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.46  E-value=2e-07  Score=60.92  Aligned_cols=66  Identities=23%  Similarity=0.379  Sum_probs=53.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      ..+.+|||.||.+.+++++|+.+|+. |..-..++       .......+.||++|++.+.|..|+..|+|..+
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~-~~gf~~l~-------~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSR-YPGFHILK-------IRARGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHh-CCCceEEE-------EecCCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            34568999999999999999999999 76543222       12333458999999999999999999999876

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.28  E-value=1.3e-06  Score=60.46  Aligned_cols=81  Identities=15%  Similarity=0.263  Sum_probs=64.0

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce-EEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP-MII  102 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~-l~v  102 (114)
                      ..++|||||-|++|.++|.+.+.. .|.-.-..+. .+.++.+|.++|||++...+....++.++.|.-..++|.. ..+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S-~G~~~~~dmK-FFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQS-TGLAQFADMK-FFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHh-hhHHHHhhhh-hhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            357999999999999999998887 7744322211 3557778999999999999999999999999999999975 444


Q ss_pred             Eecc
Q 033648          103 QFGR  106 (114)
Q Consensus       103 ~~a~  106 (114)
                      .+-|
T Consensus       158 ~~NK  161 (498)
T KOG4849|consen  158 SYNK  161 (498)
T ss_pred             ccch
Confidence            4433

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.26  E-value=2e-06  Score=62.34  Aligned_cols=68  Identities=18%  Similarity=0.247  Sum_probs=53.5

Q ss_pred             HHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEeccCC
Q 033648           40 DFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP  108 (114)
Q Consensus        40 ~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~  108 (114)
                      +++..+++ ||.|..|+++....+......-|..||+|.+.++|++|..+|+|.++.+|.+...|...+
T Consensus       425 dvr~ec~k-~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  425 DVRTECAK-FGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHhcc-cCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            46677778 999988875443222333445578899999999999999999999999999999987644

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.18  E-value=3.5e-06  Score=61.74  Aligned_cols=81  Identities=21%  Similarity=0.368  Sum_probs=66.6

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc---
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF---   95 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~---   95 (114)
                      ....+++.|+|.||-.-+|.-+|+.++....|.|...    |+     .+.+..|||.|.+.++|.+...+|||..+   
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~----Wm-----DkIKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF----WM-----DKIKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHH----HH-----HHhhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            3457789999999999999999999999735655443    21     35688999999999999999999999875   


Q ss_pred             CCceEEEEeccCC
Q 033648           96 KGKPMIIQFGRNP  108 (114)
Q Consensus        96 ~g~~l~v~~a~~~  108 (114)
                      +++.|.+.|+..+
T Consensus       510 NPK~L~adf~~~d  522 (718)
T KOG2416|consen  510 NPKHLIADFVRAD  522 (718)
T ss_pred             CCceeEeeecchh
Confidence            6778999998744

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.16  E-value=7.9e-07  Score=64.29  Aligned_cols=78  Identities=23%  Similarity=0.387  Sum_probs=70.7

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..++|+..++...+..+|.++|+. +|.|..+.   .|.+..++.++|.+||+|.+.++...|+ .|.|..+.|-+|.|+
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~-~gkVrdVr---iI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSI-VGKVRDVR---IIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHh-hcCcceeE---eeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            367888889989999999999999 99999886   6888889999999999999999999998 899999999999998


Q ss_pred             ecc
Q 033648          104 FGR  106 (114)
Q Consensus       104 ~a~  106 (114)
                      ...
T Consensus       254 ~sE  256 (549)
T KOG0147|consen  254 LSE  256 (549)
T ss_pred             ccH
Confidence            654

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.14  E-value=4.8e-06  Score=57.63  Aligned_cols=87  Identities=18%  Similarity=0.276  Sum_probs=73.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceeccc----ce-eEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKS----GL-IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~----~~-~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ....++||-+||..++.+.+..+|.+ +|.|..-+.    +. ..+++.|+..++=|.|.|.+...|++|+.-+++..+.
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~q-cg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQ-CGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhh-cceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44568999999999999999999999 998864221    11 2356679999999999999999999999999999999


Q ss_pred             CceEEEEeccCCC
Q 033648           97 GKPMIIQFGRNPA  109 (114)
Q Consensus        97 g~~l~v~~a~~~~  109 (114)
                      +..|+|.+|.-..
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.08  E-value=1.1e-05  Score=55.81  Aligned_cols=78  Identities=19%  Similarity=0.422  Sum_probs=60.1

Q ss_pred             CCeEEecCCCCCCCHhH------HHHHHhhhcCCceecccceeEEeccCCC---cee--EEEEEeCCHHHHHHHHHHhCC
Q 033648           24 ASVLYIKNLAKDVVPDD------FFFVFGSLFGSIDAAKSGLIVKLMQEGR---MRG--QAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~------l~~~f~~~~G~i~~~~~~~~~~~~~~~~---~~g--~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      ..-+||-+||+.+..++      -.++|++ ||.|..+     +.++++..   ..+  -.||.|.+.++|.+||.+.+|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQ-yGkI~KI-----vvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDg  187 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQ-YGKIKKI-----VVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDG  187 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhh-ccceeEE-----EecccccccccccccceEEEEecchHHHHHHHHHhcc
Confidence            35689999999887766      2578888 9998754     33433311   112  339999999999999999999


Q ss_pred             cccCCceEEEEeccC
Q 033648           93 YVFKGKPMIIQFGRN  107 (114)
Q Consensus        93 ~~~~g~~l~v~~a~~  107 (114)
                      ..++||.|+..+..+
T Consensus       188 s~~DGr~lkatYGTT  202 (480)
T COG5175         188 SLLDGRVLKATYGTT  202 (480)
T ss_pred             ccccCceEeeecCch
Confidence            999999999988764

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.07  E-value=4.3e-05  Score=53.56  Aligned_cols=80  Identities=20%  Similarity=0.326  Sum_probs=68.8

Q ss_pred             CCCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ...+++.+.|.+|... +..+.|..+|-- ||.|..+++|.      |  ..|.|.|++.+....++|+..||+..+.|.
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~Cl-YGNV~rvkFmk------T--k~gtamVemgd~~aver~v~hLnn~~lfG~  353 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCL-YGNVERVKFMK------T--KPGTAMVEMGDAYAVERAVTHLNNIPLFGG  353 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhh-cCceeeEEEee------c--ccceeEEEcCcHHHHHHHHHHhccCccccc
Confidence            3567899999999854 667889999999 99999887432      1  357899999999999999999999999999


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      +|.|.++++.
T Consensus       354 kl~v~~SkQ~  363 (494)
T KOG1456|consen  354 KLNVCVSKQN  363 (494)
T ss_pred             eEEEeecccc
Confidence            9999999865

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.06  E-value=2.7e-05  Score=56.00  Aligned_cols=78  Identities=19%  Similarity=0.267  Sum_probs=61.6

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ....|.+.+|||..|+++|..+|+. ++ |..     .+....+|+..|=|||+|.+.++++.|++ .+...+..|-|.|
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~-~~-I~~-----~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEV   80 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSN-CG-IEN-----LEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEV   80 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhc-Cc-eeE-----EEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEE
Confidence            3456888999999999999999988 65 332     23455679999999999999999999995 5666777787888


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      --+...
T Consensus        81 f~~~~~   86 (510)
T KOG4211|consen   81 FTAGGA   86 (510)
T ss_pred             EccCCc
Confidence            766543

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.06  E-value=2.7e-05  Score=50.89  Aligned_cols=78  Identities=22%  Similarity=0.385  Sum_probs=65.1

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-Cc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-GK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g~   98 (114)
                      ..+|...+++.|+|..++.+.+...|.. |..-..+++   +     -..++.|||+|.+...|..|...++|..+- ..
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~q-f~g~keir~---i-----~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~  212 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQ-FPGFKEIRL---I-----PPRSGIAFVEFLSDRQASAAQQALQGFKITKKN  212 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhh-CcccceeEe---c-----cCCCceeEEecchhhhhHHHhhhhccceeccCc
Confidence            3577889999999999999999999998 877766541   1     124689999999999999999999998876 78


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      .+.|.+|+
T Consensus       213 ~m~i~~a~  220 (221)
T KOG4206|consen  213 TMQITFAK  220 (221)
T ss_pred             eEEecccC
Confidence            88888875

>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=98.02  E-value=1.8e-05  Score=46.54  Aligned_cols=71  Identities=21%  Similarity=0.351  Sum_probs=42.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc-----ccCCc
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY-----VFKGK   98 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-----~~~g~   98 (114)
                      ++.|.|.+++..++.++|+..|.. ||.|.++.+       ..  .-.-|||.|.+.+.|+.|+..+...     .+.+.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~-~g~V~yVD~-------~~--G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~   70 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQ-FGEVAYVDF-------SR--GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGK   70 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-S-S--EEEEE---------T--T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSS
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHh-cCCcceEEe-------cC--CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCc
Confidence            367899999999999999999999 998876531       22  2357899999999999999877654     35666


Q ss_pred             eEEEEe
Q 033648           99 PMIIQF  104 (114)
Q Consensus        99 ~l~v~~  104 (114)
                      .+.++.
T Consensus        71 ~~~~~v   76 (105)
T PF08777_consen   71 EVTLEV   76 (105)
T ss_dssp             SEEEE-
T ss_pred             eEEEEE
Confidence            666554

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

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.99  E-value=4.4e-05  Score=52.87  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=61.7

Q ss_pred             CCCCeEEecCCCC----CCC-------HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh
Q 033648           22 NPASVLYIKNLAK----DVV-------PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV   90 (114)
Q Consensus        22 ~~~~~l~v~nlp~----~~~-------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   90 (114)
                      ...++|.+.|+=.    .-+       .++|.+...+ ||.+..+.    +.+   ....|.+-|.|.+.+.|..|++.|
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K-~G~v~~vv----v~d---~hPdGvvtV~f~n~eeA~~ciq~m  334 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEK-FGQVRKVV----VYD---RHPDGVVTVSFRNNEEADQCIQTM  334 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHH-hCCcceEE----Eec---cCCCceeEEEeCChHHHHHHHHHh
Confidence            4457888888732    112       3567788889 99998763    333   246789999999999999999999


Q ss_pred             CCcccCCceEEEEeccCC
Q 033648           91 NGYVFKGKPMIIQFGRNP  108 (114)
Q Consensus        91 ~g~~~~g~~l~v~~a~~~  108 (114)
                      +|..+.||.|..+.....
T Consensus       335 ~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  335 DGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             cCeeecceEEEEEEeCCc
Confidence            999999999999877644

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.98  E-value=8.7e-06  Score=53.34  Aligned_cols=73  Identities=26%  Similarity=0.321  Sum_probs=62.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...+.+.+.|++..+.+.+|...|.+ +|.+....           ...+++||+|++.+++..|+..++|..+.++.|.
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~-~g~~~~~~-----------~~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~  164 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRP-AGEVTYVD-----------ARRNFAFVEFSEQEDAKRALEKLDGKKLNGRRIS  164 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcc-cCCCchhh-----------hhccccceeehhhhhhhhcchhccchhhcCceee
Confidence            34577889999999999999999999 99873221           1568999999999999999999999999999999


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      +...-
T Consensus       165 ~~~~~  169 (216)
T KOG0106|consen  165 VEKNS  169 (216)
T ss_pred             ecccC
Confidence            95443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.93  E-value=6.4e-06  Score=56.37  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=69.3

Q ss_pred             CCeEE-ecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           24 ASVLY-IKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        24 ~~~l~-v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++| +++++..+++++|+..|.. +|.+..++   ...+..++..++++++.|.....+..++.. +...+.++++.+
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~-~~~i~~~r---~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  258 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVS-SGEITSVR---LPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRL  258 (285)
T ss_pred             cccceeecccccccchHHHhhhccC-cCcceeec---cCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccc
Confidence            34455 9999999999999988888 99887765   344667899999999999999999999876 788899999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      ....+...
T Consensus       259 ~~~~~~~~  266 (285)
T KOG4210|consen  259 EEDEPRPK  266 (285)
T ss_pred             ccCCCCcc
Confidence            99887643

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.87  E-value=7.2e-06  Score=54.55  Aligned_cols=74  Identities=20%  Similarity=0.299  Sum_probs=57.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEecc-------CCCce----eEEEEEeCCHHHHHHHHHHhC
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ-------EGRMR----GQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~-------~~~~~----g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..-.+|+++||+.+...-|+++|+. ||.|.++.+  ...+..       .|..+    .=|+|+|.+-..|.++...||
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~-yGeVGRvyl--qpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Ln  149 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQ-YGEVGRVYL--QPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLN  149 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHh-ccccceEEe--cchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhC
Confidence            3457999999999999999999999 999987642  111111       12222    335789999999999999999


Q ss_pred             CcccCCce
Q 033648           92 GYVFKGKP   99 (114)
Q Consensus        92 g~~~~g~~   99 (114)
                      +.+|+|+.
T Consensus       150 n~~Iggkk  157 (278)
T KOG3152|consen  150 NTPIGGKK  157 (278)
T ss_pred             CCccCCCC
Confidence            99999874

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.84  E-value=1.3e-05  Score=53.38  Aligned_cols=64  Identities=25%  Similarity=0.399  Sum_probs=51.5

Q ss_pred             hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEecc
Q 033648           39 DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        39 ~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~  106 (114)
                      +++...|...||.+..++    +.+...-...|-++|.|...++|++|+..|||..+.|++|++.+..
T Consensus        83 Ed~f~E~~~kygEiee~~----Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELN----VCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhh----hhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            456666663399997764    3344455667889999999999999999999999999999999875

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.84  E-value=9.9e-05  Score=53.20  Aligned_cols=78  Identities=22%  Similarity=0.274  Sum_probs=57.8

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +...|.+.+||+.+++++|.++|+. .--+... +  .+.....++..+=|||+|.+.+.|+.|+. -|...++.|-|.|
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaG-L~Iv~~g-i--~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEv  176 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAG-LEIVPDG-I--LLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEV  176 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcC-Ccccccc-e--eeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEe
Confidence            4568999999999999999999987 5444331 1  22233456678999999999999999984 4556677776666


Q ss_pred             Eec
Q 033648          103 QFG  105 (114)
Q Consensus       103 ~~a  105 (114)
                      --+
T Consensus       177 F~S  179 (510)
T KOG4211|consen  177 FRS  179 (510)
T ss_pred             ehh
Confidence            433

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.81  E-value=0.00016  Score=54.36  Aligned_cols=75  Identities=23%  Similarity=0.325  Sum_probs=64.8

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCce-ecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSID-AAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~-~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +.|-+.|+|++++-+++-++|.. |-.+. ++    .++....|...|=|-|.|.+.++|.+|...+++.+|..+.+++.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~d-Y~~~p~sI----~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~  942 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFND-YEPDPNSI----RIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLR  942 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcc-cccCCCce----eEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEE
Confidence            48999999999999999999988 76553 33    35566678888999999999999999999999999999998886


Q ss_pred             e
Q 033648          104 F  104 (114)
Q Consensus       104 ~  104 (114)
                      +
T Consensus       943 i  943 (944)
T KOG4307|consen  943 I  943 (944)
T ss_pred             e
Confidence            4

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.44  E-value=0.00019  Score=55.08  Aligned_cols=78  Identities=18%  Similarity=0.233  Sum_probs=66.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--c
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--K   98 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~   98 (114)
                      ..+.+.+++++|+++.....+..+|.. ||.+..+.         -.+...|++|.|.+...++.|++.|-|..++|  +
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~-fGpir~Id---------y~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~  521 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDR-FGPIRIID---------YRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPR  521 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhc-cCcceeee---------cccCCcceeeecccCccchhhHHHHhcCcCCCCCc
Confidence            456678999999999999999999999 99986542         12355799999999999999999999999987  4


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .+.|.||...
T Consensus       522 r~rvdla~~~  531 (975)
T KOG0112|consen  522 RLRVDLASPP  531 (975)
T ss_pred             ccccccccCC
Confidence            6999998854

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.43  E-value=0.00022  Score=50.89  Aligned_cols=74  Identities=30%  Similarity=0.421  Sum_probs=58.2

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc-cCCceEEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV-FKGKPMIIQ  103 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~-~~g~~l~v~  103 (114)
                      +.+|++||.+..+..+++.+|.. .-......++         -..||+|+.+.+...|.+|++.++|.. +.|+.+.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~-ak~~~~g~fl---------~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~   71 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGD-AKIPGSGQFL---------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVE   71 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcc-ccCCCCccee---------eecceeeccCCchhhhhhhHHhhchhhhhcCceeecc
Confidence            35899999999999999999876 4222222211         135899999999999999999999976 899999988


Q ss_pred             eccCC
Q 033648          104 FGRNP  108 (114)
Q Consensus       104 ~a~~~  108 (114)
                      ..-++
T Consensus        72 ~sv~k   76 (584)
T KOG2193|consen   72 HSVPK   76 (584)
T ss_pred             chhhH
Confidence            76654

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

Probab=97.42  E-value=0.00067  Score=41.91  Aligned_cols=77  Identities=18%  Similarity=0.355  Sum_probs=48.7

Q ss_pred             CCCCCCCeEEecCCCC------CCCH---hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           19 TAGNPASVLYIKNLAK------DVVP---DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~------~~~~---~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ..+||..++.|.=..+      .+.+   .+|.+.|.. ||.+.-++      .     ..+.-+|+|.+.++|.+|+ .
T Consensus        22 ~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~-~GevvLvR------f-----v~~~mwVTF~dg~sALaal-s   88 (146)
T PF08952_consen   22 SQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQ-YGEVVLVR------F-----VGDTMWVTFRDGQSALAAL-S   88 (146)
T ss_dssp             ----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHC-CS-ECEEE------E-----ETTCEEEEESSCHHHHHHH-H
T ss_pred             hcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHh-CCceEEEE------E-----eCCeEEEEECccHHHHHHH-c
Confidence            4467888877775551      2322   357777878 89764322      1     1245689999999999998 7


Q ss_pred             hCCcccCCceEEEEeccCC
Q 033648           90 VNGYVFKGKPMIIQFGRNP  108 (114)
Q Consensus        90 l~g~~~~g~~l~v~~a~~~  108 (114)
                      ++|.+++|+.|+|++..++
T Consensus        89 ~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   89 LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             GCCSEETTEEEEEEE----
T ss_pred             cCCcEECCEEEEEEeCCcc
Confidence            9999999999999987765

; PDB: 1UFW_A 2DNR_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.41  E-value=0.00078  Score=49.68  Aligned_cols=78  Identities=21%  Similarity=0.241  Sum_probs=56.1

Q ss_pred             CCCeEEecCCCCCCC------HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           23 PASVLYIKNLAKDVV------PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      -.+.+.|-|+|---.      ..-|..+|++ +|.+....    +-....|..+||.|++|.+..+|+.|++.|||+.++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk-~gk~vn~~----~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld  131 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSK-AGKIVNMY----YPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLD  131 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHh-hcccccee----eccCccCCeeeEEEEEecChhhHHHHHHhcccceec
Confidence            346788999985322      2346788888 99775433    112234568999999999999999999999999976


Q ss_pred             C-ceEEEEec
Q 033648           97 G-KPMIIQFG  105 (114)
Q Consensus        97 g-~~l~v~~a  105 (114)
                      - +...|..-
T Consensus       132 knHtf~v~~f  141 (698)
T KOG2314|consen  132 KNHTFFVRLF  141 (698)
T ss_pred             ccceEEeehh
Confidence            4 45555543

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.36  E-value=0.00066  Score=46.41  Aligned_cols=66  Identities=21%  Similarity=0.214  Sum_probs=50.0

Q ss_pred             HhHHHHHHhhhcCCceecccceeEEecc-CCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEeccC
Q 033648           38 PDDFFFVFGSLFGSIDAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        38 ~~~l~~~f~~~~G~i~~~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~  107 (114)
                      ++++++.+.+ ||.+..|-+   ..... .-.-....||+|...++|.+|+-.|||..|+||.+...|.+-
T Consensus       300 ede~keEceK-yg~V~~vii---feip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEK-YGKVGNVII---FEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHh-hcceeeEEE---EecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            3567888999 999976631   11111 111235679999999999999999999999999999988763

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.34  E-value=0.001  Score=46.95  Aligned_cols=80  Identities=25%  Similarity=0.360  Sum_probs=61.0

Q ss_pred             CCCCCeEEec--CCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-C
Q 033648           21 GNPASVLYIK--NLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-G   97 (114)
Q Consensus        21 ~~~~~~l~v~--nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g   97 (114)
                      ..++..|.++  |--..+|.+-|..+..+ .|.+.++-    + .+++   .-.|.|+|.+.+.|++|...|||..|. |
T Consensus       117 ~~pN~VLl~TIlNp~YpItvDVly~Icnp-~GkVlRIv----I-fkkn---gVQAmVEFdsv~~AqrAk~alNGADIYsG  187 (494)
T KOG1456|consen  117 ATPNKVLLFTILNPQYPITVDVLYTICNP-QGKVLRIV----I-FKKN---GVQAMVEFDSVEVAQRAKAALNGADIYSG  187 (494)
T ss_pred             CCCCeEEEEEeecCccccchhhhhhhcCC-CCceEEEE----E-Eecc---ceeeEEeechhHHHHHHHhhccccccccc
Confidence            3445555555  44467889999999999 99998763    2 2333   347999999999999999999999975 3


Q ss_pred             -ceEEEEeccCCC
Q 033648           98 -KPMIIQFGRNPA  109 (114)
Q Consensus        98 -~~l~v~~a~~~~  109 (114)
                       ..|+|+|||+..
T Consensus       188 CCTLKIeyAkP~r  200 (494)
T KOG1456|consen  188 CCTLKIEYAKPTR  200 (494)
T ss_pred             ceeEEEEecCcce
Confidence             479999999763

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.32  E-value=0.00035  Score=49.34  Aligned_cols=77  Identities=18%  Similarity=0.262  Sum_probs=60.3

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .|.|.||.+..+.+++..+|.- .|.|..+.+.-.+.+.........|||.|.+...+..|. .|..+.+-|+.|.|--
T Consensus         9 vIqvanispsat~dqm~tlFg~-lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGN-LGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhh-ccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            7999999999999999999999 999998875433333334456789999999999888885 6777777776655543

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

Probab=97.28  E-value=0.00097  Score=34.27  Aligned_cols=52  Identities=19%  Similarity=0.314  Sum_probs=39.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHH
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL   87 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~   87 (114)
                      +.|-|.+.+++.. +.+...|.. ||.|....+         +....+.++.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~-fGeI~~~~~---------~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFAS-FGEIVDIYV---------PESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHh-cCCEEEEEc---------CCCCcEEEEEECCHHHHHhhC
Confidence            4577888887655 445568888 999976542         134678999999999999885

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.25  E-value=0.0029  Score=39.03  Aligned_cols=76  Identities=20%  Similarity=0.250  Sum_probs=54.4

Q ss_pred             CCCCCCCeEEecCCCCCC----CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc
Q 033648           19 TAGNPASVLYIKNLAKDV----VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV   94 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~----~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   94 (114)
                      +..+|-.+|.|.=|..++    +-..+...++. ||.|.++.          -..+.-|.|.|.+..+|..|+.+++. .
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~-fGpI~SVT----------~cGrqsavVvF~d~~SAC~Av~Af~s-~  148 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSV-FGPIQSVT----------LCGRQSAVVVFKDITSACKAVSAFQS-R  148 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHh-cCCcceee----------ecCCceEEEEehhhHHHHHHHHhhcC-C
Confidence            345666778776554443    33456677778 99998763          12456799999999999999999987 5


Q ss_pred             cCCceEEEEecc
Q 033648           95 FKGKPMIIQFGR  106 (114)
Q Consensus        95 ~~g~~l~v~~a~  106 (114)
                      .-|..+++.|-.
T Consensus       149 ~pgtm~qCsWqq  160 (166)
T PF15023_consen  149 APGTMFQCSWQQ  160 (166)
T ss_pred             CCCceEEeeccc
Confidence            566677777643

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.15  E-value=0.0015  Score=47.57  Aligned_cols=64  Identities=19%  Similarity=0.319  Sum_probs=45.3

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccC--CCcee---EEEEEeCCHHHHHHHHHHhC
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRG---QAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~--~~~~g---~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ++.+|||+||+++++++|...|.. ||.+.- .  |..+....  -..+|   |+|+.|.++.+....+.++.
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~-FGs~~V-d--WP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQ-FGSVKV-D--WPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccceeecCCCccccHHHHHhhccc-ccceEe-e--cCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            468999999999999999999999 998731 1  11101111  11345   99999999888777665544

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.10  E-value=0.0014  Score=46.34  Aligned_cols=83  Identities=18%  Similarity=0.268  Sum_probs=63.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++..+|.+.+||...+.+++..+|.. |..-..-+ ...+.....|+..|=|||+|.+++.|.+|....+.+...+|-|
T Consensus       277 ~~~kdcvRLRGLPy~AtvEdIL~Flgd-Fa~~i~f~-gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYi  354 (508)
T KOG1365|consen  277 TRSKDCVRLRGLPYEATVEDILDFLGD-FATDIRFQ-GVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYI  354 (508)
T ss_pred             CCCCCeeEecCCChhhhHHHHHHHHHH-Hhhhcccc-eeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceE
Confidence            445678999999999999999999988 76432210 0023344567778999999999999999999998888878777


Q ss_pred             EEEec
Q 033648          101 IIQFG  105 (114)
Q Consensus       101 ~v~~a  105 (114)
                      .|--+
T Consensus       355 Evfp~  359 (508)
T KOG1365|consen  355 EVFPC  359 (508)
T ss_pred             EEeec
Confidence            76544

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.09  E-value=0.00039  Score=49.57  Aligned_cols=70  Identities=26%  Similarity=0.335  Sum_probs=53.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceeccccee--EEeccCCC--------ceeEEEEEeCCHHHHHHHHHHhC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI--VKLMQEGR--------MRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~--~~~~~~~~--------~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      -++.+|.+-|||-+-.-+.|.++|+. +|.|..+++.-.  +-....+.        .+-+|+|+|...+.|.+|.+.++
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~-~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGT-VGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhc-ccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            47889999999999888999999999 999988763211  00011111        25789999999999999998775


Q ss_pred             C
Q 033648           92 G   92 (114)
Q Consensus        92 g   92 (114)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>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=97.07  E-value=0.0034  Score=36.56  Aligned_cols=80  Identities=19%  Similarity=0.166  Sum_probs=49.4

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEE----eccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK----LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~----~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      .+.|.|-+.|+. ..+.+...|++ ||.|.+..-.+.-.    .........+..|.|.+..+|.+|+ .-||..+.|..
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~-~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSS-FGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSL   82 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHC-CS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHh-cceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcE
Confidence            345788889987 56778888999 99985431000000    0001123468899999999999999 57999998864


Q ss_pred             -EEEEecc
Q 033648          100 -MIIQFGR  106 (114)
Q Consensus       100 -l~v~~a~  106 (114)
                       +-|.+++
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence             4466654

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.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.85  E-value=0.0042  Score=45.34  Aligned_cols=67  Identities=15%  Similarity=0.264  Sum_probs=53.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      +-.|..|+|||+||.-++..+|-.+|..-||.|..+.+   -.+++-...+|-|=|.|++..+--+||.+
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGI---DtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGI---DTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEe---ccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            34778999999999999999999999966999987653   22334456778888999999998888853

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.64  E-value=0.011  Score=42.12  Aligned_cols=64  Identities=27%  Similarity=0.370  Sum_probs=45.9

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      -.+.+.+||++.+..++..+|.+ --.+...........+..|+..|=||+.|..+++|+.|+..
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~-~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGP-PCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCC-CCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence            35788999999999999999974 21121111111233444788889999999999999999854

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.44  E-value=0.0019  Score=49.55  Aligned_cols=78  Identities=13%  Similarity=0.105  Sum_probs=65.7

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ..++|.|.|+.-|.++++.++.+ +|.+.+..+    ...+.|+.+|.+++.|.+..++.+++...+...+.-+.+.|+.
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~-~gn~~~~~~----vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASK-TGNVTSLRL----VTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccc-cCCccccch----hhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccc
Confidence            46999999999999999999999 999987652    2345788999999999999999999888887777777777777


Q ss_pred             ccC
Q 033648          105 GRN  107 (114)
Q Consensus       105 a~~  107 (114)
                      +++
T Consensus       812 snp  814 (881)
T KOG0128|consen  812 SNP  814 (881)
T ss_pred             cCC
Confidence            554

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=96.31  E-value=0.023  Score=36.70  Aligned_cols=62  Identities=15%  Similarity=0.099  Sum_probs=51.9

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ...+.|.+||+.-++.+|+..+.+ .|.++...+    .      .-+++.|+|...|+.+-|+..|+...+.
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmRe-aGdvCfadv----~------rDg~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMRE-AGDVCFADV----Q------RDGVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHh-hCCeeeeee----e------cccceeeeeeehhhHHHHHHhhcccccc
Confidence            357999999999999999999999 999875431    1      1258899999999999999999987754

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.31  E-value=0.0087  Score=40.25  Aligned_cols=63  Identities=25%  Similarity=0.368  Sum_probs=52.9

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      ..|||.||...++.+.+...|+. ||.+...    .++....++..+=++|.|...-.+..|+..+.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~-fg~~e~a----v~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRR-FGPIERA----VAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhh-cCccchh----eeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            78999999999999999999999 9999765    233444567778889999999999999988853

>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=96.25  E-value=0.027  Score=30.23  Aligned_cols=55  Identities=18%  Similarity=0.240  Sum_probs=43.3

Q ss_pred             CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           35 DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        35 ~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .++.++++.-+.+ |+-.       .+....+|-     ||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~-y~~~-------~I~~d~tGf-----YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRK-YRWD-------RIRDDRTGF-----YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhc-CCcc-------eEEecCCEE-----EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677889999988 8753       344545544     89999999999999999999988777654

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

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.23  E-value=0.00026  Score=54.05  Aligned_cols=66  Identities=24%  Similarity=0.367  Sum_probs=54.1

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV   94 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   94 (114)
                      +++|++||+..+.+.++...|.+ +|.+..+++.   ....++..+|.||+.|...+.+.+|+....+..
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~-~~~~e~vqi~---~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~  733 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSP-SGTIEVVQIV---IHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCF  733 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCc-cchhhhHHHH---HHhhccccccceeeEeecCCchhhhhhhhhhhh
Confidence            57899999999999999999999 9988776632   233467889999999999999999986544433

>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=96.22  E-value=0.011  Score=37.96  Aligned_cols=84  Identities=13%  Similarity=0.193  Sum_probs=48.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCc---eecccceeEEecc-CCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSI---DAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i---~~~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .....|.|++||+..++++++..+.+.++.-   ....  ...-... .......|||.|.+.++...-...++|+.+.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~--g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQ--GKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEE--EEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEe--cCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            3456899999999999999888555423322   1111  0000111 12235789999999999999999999987632


Q ss_pred             -----ceEEEEeccC
Q 033648           98 -----KPMIIQFGRN  107 (114)
Q Consensus        98 -----~~l~v~~a~~  107 (114)
                           ....|++|--
T Consensus        83 ~kg~~~~~~VE~Apy   97 (176)
T PF03467_consen   83 SKGNEYPAVVEFAPY   97 (176)
T ss_dssp             TTS-EEEEEEEE-SS
T ss_pred             CCCCCcceeEEEcch
Confidence                 2456777653

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.

>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=96.13  E-value=0.13  Score=30.52  Aligned_cols=68  Identities=21%  Similarity=0.253  Sum_probs=43.6

Q ss_pred             CCeEEecCCCCC-CCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           24 ASVLYIKNLAKD-VVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        24 ~~~l~v~nlp~~-~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ++.+.+--.|+. ++.+.|..+.++ +- .+..++   .++  ....++..+++.|.+.++|......+||..++.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~-~~~~i~~~r---iir--d~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAP-FREDIEHIR---IIR--DGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhc-ccccEEEEE---Eee--CCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344444455554 445556544444 33 333332   222  233477899999999999999999999999754

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

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

Probab=96.06  E-value=0.031  Score=31.41  Aligned_cols=54  Identities=22%  Similarity=0.400  Sum_probs=38.6

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..++++ .|..+...+|.++|++ ||.|. +.   |+       .-.-|||.....+.+..++..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFsp-fG~I~-Vs---Wi-------~dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSP-FGQIY-VS---WI-------NDTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCC-CCCEE-EE---EE-------CTTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhcc-CCcEE-EE---EE-------cCCcEEEEeecHHHHHHHHHHhc
Confidence            345555 9999999999999999 99873 11   21       23469999999999999998876

; 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.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=95.86  E-value=0.019  Score=42.42  Aligned_cols=82  Identities=22%  Similarity=0.225  Sum_probs=54.9

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc---C-C
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF---K-G   97 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~---~-g   97 (114)
                      .+.+++-|.|+|...|...|...-.+..|.-+-+.   ...+-.+....|||||-|.+.+.+..+.+++||+.+   + .
T Consensus       386 ~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlY---LPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~  462 (549)
T KOG4660|consen  386 CPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLY---LPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSE  462 (549)
T ss_pred             CchhhhHhhccCchhhHHhhhhhhccccCccceEE---eccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcce
Confidence            33455666666666666555554333344444343   234445666789999999999999999999999873   3 3


Q ss_pred             ceEEEEecc
Q 033648           98 KPMIIQFGR  106 (114)
Q Consensus        98 ~~l~v~~a~  106 (114)
                      +.+.+.||+
T Consensus       463 Kia~itYAr  471 (549)
T KOG4660|consen  463 KIASITYAR  471 (549)
T ss_pred             eeeeeehhh
Confidence            456777776

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.78  E-value=0.0019  Score=49.87  Aligned_cols=78  Identities=17%  Similarity=0.249  Sum_probs=62.6

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .+.+||+||++..+++.+++..|.. +|.+..+.    +....-+.--.|+|+.|.+...+..|+..+.|..|....+.+
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e-~gkve~VD----iKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDE-SGKVEEVD----IKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhh-hccccccc----cccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            3468999999999999999999999 99998764    333333444579999999999999999999998876556555


Q ss_pred             Eec
Q 033648          103 QFG  105 (114)
Q Consensus       103 ~~a  105 (114)
                      .+.
T Consensus       446 glG  448 (975)
T KOG0112|consen  446 GLG  448 (975)
T ss_pred             ccc
Confidence            555

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.44  E-value=0.14  Score=37.33  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=55.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ++.|.|-.+|..++..++..|..+..-.|..++   .++  ..-..+-.++|.|.+.++|..--..+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~ir---ivR--d~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIR---IVR--DGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeE---Eee--cCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            788999999999999999999887344555554   344  233456788999999999999999999999764

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

Probab=95.11  E-value=0.23  Score=26.34  Aligned_cols=54  Identities=20%  Similarity=0.235  Sum_probs=38.1

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhc-C--CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLF-G--SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV   90 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~-G--~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   90 (114)
                      ..|+|.++. ..+.++++.+|.. | .  ....++   |+-+       .-|-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~-y~~~~~~~~IE---WIdD-------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSE-YFDEEGPFRIE---WIDD-------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHH-hcccCCCceEE---EecC-------CcEEEEECCHHHHHHHHHcC
Confidence            468899986 5778889999988 6 1  222333   3322       23678999999999998764

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.07  E-value=0.028  Score=42.39  Aligned_cols=75  Identities=15%  Similarity=0.163  Sum_probs=62.6

Q ss_pred             cCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           17 NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        17 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ..++-++..++||+|+...+..+-++..+.. +|.|..++.            -.|||-.|..+....+|+..++-..++
T Consensus        33 ~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~-~g~v~s~kr------------~~fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   33 VFQPLPPRDTVFVGNISYLVSQEFWKSILAK-SGFVPSWKR------------DKFGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             cccCCCCCceeEecchhhhhhHHHHHHHHhh-CCcchhhhh------------hhhcccchhhHHHHHHHHHHhcccCCC
Confidence            4556678899999999999999999999999 998865541            129999999999999999999988898


Q ss_pred             CceEEEEe
Q 033648           97 GKPMIIQF  104 (114)
Q Consensus        97 g~~l~v~~  104 (114)
                      |..+.+..
T Consensus       100 ~~kl~~~~  107 (668)
T KOG2253|consen  100 DQKLIENV  107 (668)
T ss_pred             cchhhccc
Confidence            88776654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.96  E-value=0.0063  Score=42.27  Aligned_cols=78  Identities=22%  Similarity=0.417  Sum_probs=55.7

Q ss_pred             CeEEecCCCCCCCHhHH---HHHHhhhcCCceecccceeEEeccC-----CCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           25 SVLYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQE-----GRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l---~~~f~~~~G~i~~~~~~~~~~~~~~-----~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      .-+||-+|+.....+.+   .+.|.. ||.+..+.     +...+     ....+-++|.|...++|..||...+|..++
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgq-ygki~ki~-----~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~d  151 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQ-YGKINKIV-----KNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDD  151 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccc-cccceEEe-----ecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhh
Confidence            45788889877665544   356666 78776542     12211     112345899999999999999999999999


Q ss_pred             CceEEEEeccCC
Q 033648           97 GKPMIIQFGRNP  108 (114)
Q Consensus        97 g~~l~v~~a~~~  108 (114)
                      |+.|++.+..+.
T Consensus       152 g~~lka~~gttk  163 (327)
T KOG2068|consen  152 GRALKASLGTTK  163 (327)
T ss_pred             hhhhHHhhCCCc
Confidence            999888776644

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=94.89  E-value=0.03  Score=42.72  Aligned_cols=79  Identities=15%  Similarity=0.107  Sum_probs=58.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ...+.+|||-.||..++...+..+|..-+-..+.+.    +...-+++.++-|||.|...+.+..|..--+-..++.+.|
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~----lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~i  506 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIE----LTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRII  506 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeE----eccCCcccccchhhheeccccccchhhhcccccccCceEE
Confidence            344578999999999999999999987233333343    3344578888999999999888888765555555677778


Q ss_pred             EEE
Q 033648          101 IIQ  103 (114)
Q Consensus       101 ~v~  103 (114)
                      +|.
T Consensus       507 rv~  509 (944)
T KOG4307|consen  507 RVD  509 (944)
T ss_pred             Eee
Confidence            876

>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=94.87  E-value=0.23  Score=27.06  Aligned_cols=64  Identities=22%  Similarity=0.342  Sum_probs=34.9

Q ss_pred             CCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           34 KDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        34 ~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      ..++..+|..++.. .+.+..-.+. .+.     -...|+||+.... .+..++..|++..+.|+++.|+.|
T Consensus        11 dg~~~~~iv~~i~~-~~gi~~~~IG-~I~-----I~~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICN-EAGIPGRDIG-RID-----IFDNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHT-CTTB-GGGEE-EEE-----E-SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHh-ccCCCHHhEE-EEE-----EeeeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45677888888887 6556443321 111     1345788888654 788899999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.29  E-value=0.055  Score=42.14  Aligned_cols=74  Identities=26%  Similarity=0.331  Sum_probs=57.0

Q ss_pred             EecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc--CCceEEEEec
Q 033648           28 YIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF--KGKPMIIQFG  105 (114)
Q Consensus        28 ~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~a  105 (114)
                      ++-|.+-..+...|-.++++ ||.+.++.    .     =+.-..|.|+|.+.+.|-.|..+++|.++  -|-+.+|.+|
T Consensus       302 ~~~nn~v~~tSssL~~l~s~-yg~v~s~w----t-----lr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSD-YGSVASAW----T-----LRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             hhhcccccchHHHHHHHHHh-hcchhhhe----e-----cccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            33444556677789999999 99987652    1     12346899999999999999999999884  5778999999


Q ss_pred             cCCCCC
Q 033648          106 RNPAAA  111 (114)
Q Consensus       106 ~~~~~~  111 (114)
                      ++...-
T Consensus       372 k~~~~~  377 (1007)
T KOG4574|consen  372 KTLPMY  377 (1007)
T ss_pred             cccccc
Confidence            976543

>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=94.06  E-value=0.11  Score=33.52  Aligned_cols=61  Identities=25%  Similarity=0.318  Sum_probs=41.7

Q ss_pred             HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC--CcccCCceEEEEeccCC
Q 033648           38 PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN--GYVFKGKPMIIQFGRNP  108 (114)
Q Consensus        38 ~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~~g~~l~v~~a~~~  108 (114)
                      ...|+.+|.. ++.+....    ..     ++-+-..|.|.+.+.|.+|...|+  +..+.|..+++.|+...
T Consensus         9 ~~~l~~l~~~-~~~~~~~~----~L-----~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFST-YDPPVQFS----PL-----KSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHT-T-SS-EEE----EE-----TTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHh-cCCceEEE----Ec-----CCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4678889988 88775432    11     133557889999999999999999  99999999999998643

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.79  E-value=0.46  Score=33.02  Aligned_cols=61  Identities=15%  Similarity=0.177  Sum_probs=45.2

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +-|-++|+.- ...+...|.+ +|.|..         +.++....|-+|.|.+..+|++|| ..||..|+|..
T Consensus       200 VTVfGFppg~-~s~vL~~F~~-cG~Vvk---------hv~~~ngNwMhirYssr~~A~KAL-skng~ii~g~v  260 (350)
T KOG4285|consen  200 VTVFGFPPGQ-VSIVLNLFSR-CGEVVK---------HVTPSNGNWMHIRYSSRTHAQKAL-SKNGTIIDGDV  260 (350)
T ss_pred             EEEeccCccc-hhHHHHHHHh-hCeeee---------eecCCCCceEEEEecchhHHHHhh-hhcCeeeccce
Confidence            5566777653 3456778889 998742         234455568999999999999999 57999988864

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.74  E-value=0.26  Score=36.95  Aligned_cols=76  Identities=13%  Similarity=0.242  Sum_probs=51.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhh-hcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC--ccc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGS-LFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG--YVF   95 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~-~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~   95 (114)
                      -+....|.+.++-||..+-.++++.+|.. .+-.+.+|++  .       .. .-=||+|.+..+|+.|.+.|.-  ..|
T Consensus       170 rp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscef--a-------~N-~nWyITfesd~DAQqAykylreevk~f  239 (684)
T KOG2591|consen  170 RPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEF--A-------HN-DNWYITFESDTDAQQAYKYLREEVKTF  239 (684)
T ss_pred             ccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeee--e-------ec-CceEEEeecchhHHHHHHHHHHHHHhh
Confidence            34456688999999999999999999964 1233334431  1       11 1237999999999999877654  336


Q ss_pred             CCceEEEEe
Q 033648           96 KGKPMIIQF  104 (114)
Q Consensus        96 ~g~~l~v~~  104 (114)
                      -|++|...+
T Consensus       240 qgKpImARI  248 (684)
T KOG2591|consen  240 QGKPIMARI  248 (684)
T ss_pred             cCcchhhhh
Confidence            666665543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.96  E-value=0.21  Score=36.64  Aligned_cols=74  Identities=20%  Similarity=0.195  Sum_probs=54.8

Q ss_pred             CeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           25 SVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        25 ~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +.|-+--.|+. .+.++|...|.+ ||.|..|.+.         ...-.|.|+|.+..+|-.|- ..++..|+++.|+|-
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~-fG~i~n~qv~---------~~~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~  441 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQ-FGEIENIQVD---------YSSLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLF  441 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhh-cCcccccccc---------Cchhhheeeeeccccccchh-ccccceecCceeEEE
Confidence            33444444544 356789999999 9999877632         22456889999999986664 678999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      |-++..
T Consensus       442 whnps~  447 (526)
T KOG2135|consen  442 WHNPSP  447 (526)
T ss_pred             EecCCc
Confidence            988743

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=90.68  E-value=1.3  Score=30.78  Aligned_cols=47  Identities=15%  Similarity=0.173  Sum_probs=34.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCH
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV   80 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~   80 (114)
                      +.+|++||+.++...+|+..+.+ .|...-     .+.   .....+-||.-|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~-~~~~pm-----~is---wkg~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRK-RECTPM-----SIS---WKGHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHh-cCCCce-----eEe---eecCCcceeEecCCc
Confidence            56999999999999999999998 776521     111   123467889988553

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=88.74  E-value=0.42  Score=33.04  Aligned_cols=78  Identities=15%  Similarity=0.115  Sum_probs=56.6

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..+++|++++...+.+.+...++.. +|......   .........+++++++.|...+.+..++.........++.+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~-~g~~~~~~---~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~  162 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSE-AGLRVDAR---SSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEK  162 (285)
T ss_pred             ccccccccccccchhhccccccchh-hcCcccch---hhhhccccccccceeeccccHHHHHHHHHhhhccccccccccC
Confidence            4678999999999888877777777 78654443   2333456778999999999999999999654444555555444


Q ss_pred             Ee
Q 033648          103 QF  104 (114)
Q Consensus       103 ~~  104 (114)
                      .+
T Consensus       163 dl  164 (285)
T KOG4210|consen  163 DL  164 (285)
T ss_pred             cc
Confidence            33

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.05  E-value=4.6  Score=29.47  Aligned_cols=55  Identities=25%  Similarity=0.333  Sum_probs=43.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ..|-|.++|...-.++|...|.. |+.- .++++ |+       ...++|..|++...|..|+..
T Consensus       392 HVlEIydfp~efkteDll~~f~~-yq~k-gfdIk-Wv-------DdthalaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  392 HVLEIYDFPDEFKTEDLLKAFET-YQNK-GFDIK-WV-------DDTHALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ceeEeccCchhhccHHHHHHHHH-hhcC-CceeE-Ee-------ecceeEEeecchHHHHHHhhc
Confidence            67999999999999999999999 8754 23332 22       245799999999999999865

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=80.11  E-value=0.075  Score=38.48  Aligned_cols=78  Identities=10%  Similarity=0.212  Sum_probs=61.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ..++.+-|.|+|+...++.+..++.. ||.+..|..  ..++.    -....-++|...+.+..|+..++|..+....++
T Consensus        78 qrsrk~Qirnippql~wevld~Ll~q-yg~ve~~eq--vnt~~----etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k  150 (584)
T KOG2193|consen   78 QRSRKIQIRNIPPQLQWEVLDSLLAQ-YGTVENCEQ--VNTDS----ETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLK  150 (584)
T ss_pred             HHhhhhhHhcCCHHHHHHHHHHHHhc-cCCHhHhhh--hccch----HHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhh
Confidence            34567899999999999999999999 999987752  11111    123345789999999999999999999888888


Q ss_pred             EEecc
Q 033648          102 IQFGR  106 (114)
Q Consensus       102 v~~a~  106 (114)
                      +.|-.
T Consensus       151 ~~YiP  155 (584)
T KOG2193|consen  151 VGYIP  155 (584)
T ss_pred             cccCc
Confidence            87654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	114
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		2e-18
3egn_A	143	C-Terminal Rna Recognition Motif Of The U11U12 65K		5e-15
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		4e-05
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		4e-05
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		4e-05
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		4e-05
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		4e-05
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		4e-05
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		4e-05
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		4e-05
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		4e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		4e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		5e-05
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		5e-05
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		6e-05
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		6e-05

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 87.0 bits (214), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/101 (46%), Positives = 60/101 (59%), Gaps = 4/101 (3%)
Query: 7   EEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQE 66
           EEI  +PMF +Y  G P  VLY+KNL+             SLF      K   I   M  
Sbjct: 8   EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQFRMMT 63
Query: 67  GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           GRMRGQAF+TFP+ E+A +AL+LVNGY   GK ++I+FG+N
Sbjct: 64  GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104

>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN Length = 143

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 66/113 (58%), Gaps = 4/113 (3%)
Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFG-SIDAAKSGLI 60
           G++  EE+ +L +F++Y  G P   +Y+KNLAK           G     S +  +    
Sbjct: 23  GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 82
Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           ++LM+EGRM+GQAF+  P+ + A +AL   NGYV  GKPM++QF R   +A+P
Sbjct: 83  IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR---SARP 132

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 62  SSATNALRSMQGFPFYDKPMRIQYAKTDS 90

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 5   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 59
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 60  SSATNALRSMQGFPFYDKPMRIQYAKTDS 88

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 62  SSATNALRSMQGFPFYDKPMRIQYAKTDS 90

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 3   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 57
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 58  SSATNALRSMQGFPFYDKPMRIQYAKTDS 86

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 63  SSATNALRSMQGFPFYDKPMRIQYAKTDS 91

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 4   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 58
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 59  SSATNALRSMQGFPFYDKPMRIQYAKTDS 87

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 63  SSATNALRSMQGFPFYDKPMRIQYAKTDS 91

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 56
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 57  SSATNALRSMQGFPFYDKPMRIQYAKTDS 85

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
           P   +YI NL +            ++F     ++ G I+ ++  +  +MRGQAFV F  V
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 62  SSATNALRSMQGFPFYDKPMRIQYAKTDS 90

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 49  FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 102
           FG ID     +++K    GR +G  F+TF   E A RAL  +NG+   G+PM +
Sbjct: 29  FGKIDNI---VLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI NL +            ++F         L+ + +   +MRGQAFV F  V  
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 63
Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPA 109
           A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDS 90

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI NL +            ++F         L+ + +   +MRGQAFV F  V  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 64
Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPA 109
           A  AL  + G+ F  KPM IQ+ +  +
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDS 91

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI NL +            ++F         L+ + +   +MRGQAFV F  V  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 64
Query: 83  AHRALNLVNGYVFKGKPMIIQFGRN 107
           A  AL  + G+ F  KPM IQ+ + 
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKT 89

>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein Complex Bound To A Fragment Of U2 Small Nuclear Rna Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23  PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI N+              +LF         + +K M   +MRGQAFV F  +  
Sbjct: 5   PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTM---KMRGQAFVIFKELGS 61
Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPA 109
           +  AL  + G+ F GKPM IQ+ +  +
Sbjct: 62  STNALRQLQGFPFYGKPMRIQYAKTDS 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	114
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-38
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-37
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-26
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-25
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-09
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-09
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-08
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-08
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
2div_A	99	TRNA selenocysteine associated protein; structural	3e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	5e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-06
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	9e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-05
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	5e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	4e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	6e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-04
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	8e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-04

>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 =  122 bits (309), Expect = 6e-38
 Identities = 47/108 (43%), Positives = 62/108 (57%), Gaps = 4/108 (3%)

Query: 6   PEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ 65
            EEI  +PMF +Y  G P  VLY+KNL+  V   D   +F + F          I   M 
Sbjct: 7   GEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLF-ARFQEKKGPP---IQFRMM 62

Query: 66  EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
            GRMRGQAF+TFP+ E+A +AL+LVNGY   GK ++I+FG+N      
Sbjct: 63  TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>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 =  121 bits (304), Expect = 7e-37
 Identities = 42/113 (37%), Positives = 69/113 (61%), Gaps = 3/113 (2%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI- 60
           G++  EE+ +L +F++Y  G P   +Y+KNLAK V   D  ++F   +    +    ++ 
Sbjct: 23  GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIF-GRYVDFSSETQRIMF 81

Query: 61  -VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
            ++LM+EGRM+GQAF+  P+ + A +AL   NGYV  GKPM++QF R+    +
Sbjct: 82  DIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQ 134

>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 = 91.5 bits (228), Expect = 8e-26
 Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 7/94 (7%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI--VKLMQEGRMRGQAFVTFP 78
             P   +YI NL + +  D+      ++F      + G I  + + +  +MRGQAFV F 
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFS-----RFGQILDILVSRSLKMRGQAFVIFK 59

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
            V  A  AL  + G+ F  KPM IQ+ +  +   
Sbjct: 60  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDII 93

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 91.1 bits (226), Expect = 3e-25
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 3/108 (2%)

Query: 2   GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV 61
            K   + + S  +        P+ V+ I N+  +V  +    +  +L  S         +
Sbjct: 7   AKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---I 63

Query: 62  KLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
            +       G+A++ F + E A   +    GY F+G P++I F   P 
Sbjct: 64  VVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 69.1 bits (168), Expect = 2e-15
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 3/90 (3%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI NL + +  D+      ++F         L + + +  +MRGQAFV F  V  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQF---GQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           A  AL  + G+ F  KPM IQ+ +  +   
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDII 94

>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 = 39.9 bits (92), Expect = 5e-05
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 10/95 (10%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
           P  +  +   P  +L++ NL ++        +F + F           V+L+        
Sbjct: 196 PPAQPLSENPPNHILFLTNLPEETNELMLSMLF-NQFPGFKE------VRLVPGRH--DI 246

Query: 73  AFVTFPSVELAHRALNLVNGY-VFKGKPMIIQFGR 106
           AFV F +   A  A + + G+ + +   M I F +
Sbjct: 247 AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>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 = 63.5 bits (155), Expect = 1e-14
 Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 7/93 (7%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
               +LYI+NL   +  ++ + +FG  +G I        +++      RG A+V +  + 
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGK-YGPIRQ------IRVGNTPETRGTAYVVYEDIF 58

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A  A++ ++G+    + +++ +     A +  
Sbjct: 59  DAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKM 91

>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 = 58.5 bits (142), Expect = 1e-12
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           AG   S +++ NL   V       VF S+ G +  A     +   ++G+ RG   VTF  
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVF-SMAGVVVRAD----ILEDKDGKSRGIGTVTFEQ 65

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGR 106
              A +A+++ NG +   +PM ++   
Sbjct: 66  SIEAVQAISMFNGQLLFDRPMHVKMDE 92

>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 = 57.7 bits (140), Expect = 2e-12
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
              S + ++N+       +   +F + FG +   +  L  K+   G  RG  FV F + +
Sbjct: 13  QTTSKILVRNIPFQANQREIRELFST-FGELKTVR--LPKKMTGTGAHRGFGFVDFITKQ 69

Query: 82  LAHRALN-LVNGYVFKGKPMIIQFGR 106
            A +A N L +     G+ +++++  
Sbjct: 70  DAKKAFNALCHSTHLYGRRLVLEWAD 95

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 57.3 bits (139), Expect = 3e-12
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 12/83 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+++    DV   +   +FG  FG +   K            + G AFV F   E A +A
Sbjct: 34  LFVRPFPLDVQESELNEIFGP-FGPMKEVK-----------ILNGFAFVEFEEAESAAKA 81

Query: 87  LNLVNGYVFKGKPMIIQFGRNPA 109
           +  V+G  F  +P+ + + + PA
Sbjct: 82  IEEVHGKSFANQPLEVVYSKLPA 104

>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 = 56.9 bits (138), Expect = 4e-12
 Identities = 26/91 (28%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 14  MFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQA 73
            F           L + NL   V   D   +F   FG++  A     V   + GR  G A
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAE-FGTLKKAA----VHYDRSGRSLGTA 73

Query: 74  FVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
            V F     A +A+   NG    G+PM IQ 
Sbjct: 74  DVHFERKADALKAMKQYNGVPLDGRPMNIQL 104

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 56.6 bits (137), Expect = 5e-12
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 4/82 (4%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +    L  +V       +    +G ++  +   I+   +  +  G A V F S   
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRK-YGEVEEVE---ILLHPRTRKHLGLARVLFTSTRG 60

Query: 83  AHRALNLVNGYVFKGKPMIIQF 104
           A   +  ++     G  +  Q 
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQL 82

>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 = 58.4 bits (141), Expect = 6e-12
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           SVL + NL  + V     F+   ++G +   K   I+        +  A V       A 
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVK---ILF-----NKKENALVQMADGNQAQ 55

Query: 85  RALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A++ +NG+   GKP+ I   ++     P 
Sbjct: 56  LAMSHLNGHKLHGKPIRITLSKHQNVQLPR 85

>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 = 52.2 bits (125), Expect = 1e-09
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P++ L++ N+   V  +D   +F S  G +         K  Q+ R    A +   SVE 
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK------GFKFFQKDR--KMALIQMGSVEE 170

Query: 83  AHRALNLVNGY-VFKGKPMIIQFGRNP 108
           A +AL  ++ + + +   + + F ++ 
Sbjct: 171 AVQALIDLHNHDLGENHHLRVSFSKST 197

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 57.9 bits (140), Expect = 7e-12
 Identities = 24/85 (28%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
                + L + NL   V   D   +F   FG++  A     V   + GR  G A V F  
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAA----VDYDRSGRSLGTADVHFER 138

Query: 80  VELAHRALNLVNGYVFKGKPMIIQF 104
              A +A+    G    G+PM IQ 
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQL 163

>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 = 56.6 bits (137), Expect = 7e-12
 Identities = 24/85 (28%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
                + L + NL   V   D   +F   FG++  A     V   + GR  G A V F  
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAA----VDYDRSGRSLGTADVHFER 85

Query: 80  VELAHRALNLVNGYVFKGKPMIIQF 104
              A +A+    G    G+PM IQ 
Sbjct: 86  RADALKAMKQYKGVPLDGRPMDIQL 110

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 55.5 bits (134), Expect = 1e-11
 Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L I+N+   +  +    +    +G +++       + +          VT+ S + A +A
Sbjct: 18  LQIRNIPPHLQWEVLDSLLVQ-YGVVES------CEQVNTDSETAVVNVTYSSKDQARQA 70

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAK 112
           L+ +NG+  +   + + +  +  AA+
Sbjct: 71  LDKLNGFQLENFTLKVAYIPDEMAAQ 96

>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 = 58.1 bits (140), Expect = 1e-11
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           AG   SVL + NL  + V     F+   ++G +        VK++     +  A V    
Sbjct: 30  AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR------VKILFN--KKENALVQMAD 81

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
              A  A++ +NG+   GKP+ I   ++     P
Sbjct: 82  GNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLP 115

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 5   PPEEILSLPMFKNYTAGNPAS-VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKL 63
            P      P  KN+    P S  L++ N+   V  +D   +F S  G +           
Sbjct: 131 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-------- 182

Query: 64  MQEGRMRGQAFVTFPSVELAHRALNLVNGY-VFKGKPMIIQFGRNP 108
               + R  A +   SVE A +AL  ++ + + +   + + F ++ 
Sbjct: 183 KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 57.0 bits (138), Expect = 2e-11
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 21  GNPASVLYIKNLAKDVVPD---DFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTF 77
           G  A  LY+ N+   +  +   DFF     L G   A   G  V  +Q  + +  AF+ F
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA--PGNPVLAVQINQDKNFAFLEF 58

Query: 78  PSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
            SV+   +A+   +G +F+G+ + I+   + 
Sbjct: 59  RSVDETTQAMAF-DGIIFQGQSLKIRRPHDY 88

>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 = 54.7 bits (132), Expect = 2e-10
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  L   +  D    +  S FG + A     +VK    G  +G AF  +  + +  +A
Sbjct: 117 LFIGGLPNYLNDDQVKELLTS-FGPLKAFN---LVKDSATGLSKGYAFCEYVDINVTDQA 172

Query: 87  LNLVNGYVFKGKPMIIQF 104
           +  +NG     K +++Q 
Sbjct: 173 IAGLNGMQLGDKKLLVQR 190

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.5 bits (134), Expect = 2e-11
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI--VKLMQE---GRMRGQAFVTF 77
             + ++++ L ++V  +     F    G I   K      + L  +   G+++G+A V+F
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQ-IGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 78  PSVELAHRALNLVNGYVFKGKPM 100
                A  A++  +G  F G P+
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPI 87

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 56.4 bits (137), Expect = 2e-11
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ +L  +V  +     F   F S  +     ++  MQ G  RG  FV+F S + A  A
Sbjct: 90  LFVGDLNVNVDDETLRNAF-KDFPSYLSGH---VMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 87  LNLVNGYVFKGKPMIIQF 104
           ++ + G    G+P+ I +
Sbjct: 146 MDSMQGQDLNGRPLRINW 163

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 9/76 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAH 84
           LY+ NL K +  D     F    G I        +K+M +   +    AFV +     A+
Sbjct: 3   LYVGNLDKAITEDILKQYFQV-GGPI------ANIKIMIDKNNKNVNYAFVEYHQSHDAN 55

Query: 85  RALNLVNGYVFKGKPM 100
            AL  +NG   +   +
Sbjct: 56  IALQTLNGKQIENNIV 71

>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 = 56.4 bits (137), Expect = 2e-11
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+  L K +   +   +F S +G I  ++   I+     G  RG  F+ F     A  A
Sbjct: 91  LYVSGLPKTMTQKELEQLF-SQYGRIITSR---ILVDQVTGVSRGVGFIRFDKRIEAEEA 146

Query: 87  LNLVNGYVFKG--KPMIIQF 104
           +  +NG    G  +P+ ++F
Sbjct: 147 IKGLNGQKPSGATEPITVKF 166

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 49.9 bits (120), Expect = 6e-09
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  L +++  ++F  +FGS  G I++ K   +V+    G+  G  FV +   + A +A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGS-IGEIESCK---LVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +N +NG   + K + + + R
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

>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 = 54.9 bits (133), Expect = 2e-11
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 4/93 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +  + + + NL++D    D   +F   FGSI       + K    G+ +G AF++F   E
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRP-FGSISRIY---LAKDKTTGQSKGFAFISFHRRE 68

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A RA+  V+G+ +    + +++ +    + PS
Sbjct: 69  DAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 56.6 bits (137), Expect = 4e-11
 Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ ++ +D+  DD   VF   FG I +A    + +    G+ +G  F+ +   + +  A
Sbjct: 128 IYVASVHQDLSDDDIKSVF-EAFGKIKSAT---LARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 87  LNLVNGYVFKGKPM 100
           ++ +N +   G+ +
Sbjct: 184 VSSMNLFDLGGQYL 197

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 53.5 bits (129), Expect = 4e-10
 Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 4/88 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ ++  ++  D     F   FG I +     +       + +G AFV +   E A  A
Sbjct: 31  VYVGSIYYELGEDTIRQAFAP-FGPIKSID---MSWDSVTMKHKGFAFVEYEVPEAAQLA 86

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           L  +N  +  G+ + +    N   A+P 
Sbjct: 87  LEQMNSVMLGGRNIKVGRPSNIGQAQPI 114

>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 = 55.7 bits (135), Expect = 4e-11
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL + +  D    +F   +GSI       I++    GR RG AFV +   E A  A
Sbjct: 92  LYVTNLPRTITDDQLDTIF-GKYGSIVQKN---ILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 87  LNLVNGYVFKG--KPMIIQF 104
           ++ +N  + +G  +P+ ++ 
Sbjct: 148 ISALNNVIPEGGSQPLSVRL 167

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 53.0 bits (128), Expect = 4e-10
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  L +D+   + + +F +  G I+  +   I++  + G   G AFV F S   + RA
Sbjct: 6   LIVNYLPQDMTDRELYALFRA-IGPINTCR---IMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           + ++NG   + K + + + R
Sbjct: 62  IKVLNGITVRNKRLKVSYAR 81

>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 = 53.8 bits (130), Expect = 6e-11
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSI--DAAKSGLIVKLMQE---GRMRGQAFVTFPSVE 81
           ++++ L ++V  +     F    G I  +      ++ L  +   G+++G+A V+F    
Sbjct: 16  IFVQGLGENVTIESVADYFKQ-IGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A++  +G  F G P+
Sbjct: 75  SAKAAIDWFDGKEFSGNPI 93

>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 = 53.8 bits (130), Expect = 7e-11
 Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 12/89 (13%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           VL+++NLA  V  +     F   FG ++  K           +++  AF+ F   + A +
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQ-FGKLERVK-----------KLKDYAFIHFDERDGAVK 60

Query: 86  ALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           A+  +NG   +G+ + I F + P   +  
Sbjct: 61  AMEEMNGKDLEGENIEIVFAKPPDQKRKE 89

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.3 bits (129), Expect = 8e-11
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 6/89 (6%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
           +  + A  ++++NL  D         F +  G +  A     +K M+ G+ +G   V F 
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKF-NECGHVLYAD----IK-MENGKSKGCGVVKFE 56

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           S E+A RA  ++NG    G+ + ++  RN
Sbjct: 57  SPEVAERACRMMNGMKLSGREIDVRIDRN 85

>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 = 53.0 bits (128), Expect = 8e-11
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPS 79
                +++ NL   V  +  + +F    G +        V +   +EG+ +   FV F  
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQ-AGPLTK------VTICKDREGKPKSFGFVCFKH 66

Query: 80  VELAHRALNLVNGYVFKGKPM 100
            E    A+ L+NG    G+P+
Sbjct: 67  PESVSYAIALLNGIRLYGRPI 87

>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 = 53.4 bits (129), Expect = 9e-11
 Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 10/100 (10%)

Query: 17  NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVT 76
           N T    +  L + NL+     +    VF      I        V   Q G+ +G AF+ 
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEK-ATFIK-------VPQNQNGKSKGYAFIE 59

Query: 77  FPSVELAHRALNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
           F S E A  ALN  N    +G+ + ++    R    + PS
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPS 99

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 53.6 bits (129), Expect = 1e-10
 Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 8/95 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSI--DAAKSGLIVKLMQE---GRMRGQAFVTFPSVE 81
           +Y++ L   V  DD    F    G +  +      ++ +  +   G+ +G A V++    
Sbjct: 18  IYVQGLNDSVTLDDLADFFKQ-CGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 82  LAHRALNLVNGYVFKGKPMIIQFG--RNPAAAKPS 114
            A  A+   +G  F+G  + +     + P  + PS
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 53.0 bits (128), Expect = 1e-10
 Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 8/95 (8%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
           +  + +  L+++NL+     +D   +F + +G +               + +G AFVTF 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSA-YGPLSELH---YPIDSLTKKPKGFAFVTFM 58

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
             E A +A   V+G VF+G+ + +     P+  K 
Sbjct: 59  FPEHAVKAYAEVDGQVFQGRMLHV----LPSTIKK 89

>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 = 55.4 bits (134), Expect = 1e-10
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L + NL   +    F  +    FGS++      +V   + G+ +G  F  +   + A RA
Sbjct: 98  LCVANLPPSLTQQQFEELVRP-FGSLERCF---LVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 87  LNLVNGYVFKGKPMIIQF 104
            + + G     + + + +
Sbjct: 154 KSDLLGKPLGPRTLYVHW 171

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 6/87 (6%)

Query: 27  LYIKNLAKDVVPDDFFF-VFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           L +  L       D       +   S    +    +   Q+G+++G A + + + E+A  
Sbjct: 187 LCVDRLPPGFNDVDALCRALSA-VHSPTFCQ----LACGQDGQLKGFAVLEYETAEMAEE 241

Query: 86  ALNLVNGYVFKGKPMIIQFGRNPAAAK 112
           A    +G    G  + + F       +
Sbjct: 242 AQQQADGLSLGGSHLRVSFCAPGPPGR 268

>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 = 53.4 bits (129), Expect = 7e-10
 Identities = 21/106 (19%), Positives = 36/106 (33%), Gaps = 12/106 (11%)

Query: 4   LPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKL 63
           L PEEI            N    + I+ L  DV   +   +    +             +
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRK-ILIRGLPGDVTNQEVHDLLSD-YELKY-------CFV 53

Query: 64  MQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
               + +G AFVT  + E A  A+N  +    + + + +Q     A
Sbjct: 54  ---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA 96

>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 = 53.1 bits (128), Expect = 1e-10
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 10/86 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y   +A  +        F   FG I        +++  E   +G +FV F + E A  A
Sbjct: 28  VYCGGIASGLTDQLMRQTFSP-FGQIME------IRVFPE---KGYSFVRFSTHESAAHA 77

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAK 112
           +  VNG   +G  +   +G+      
Sbjct: 78  IVSVNGTTIEGHVVKCYWGKESPDMT 103

>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 = 53.1 bits (128), Expect = 1e-10
 Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I +L ++    D   +F   FG++ +AK   +    Q    +   FV++ +   A  A
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMP-FGNVVSAK---VFIDKQTNLSKCFGFVSYDNPVSAQAA 83

Query: 87  LNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
           +  +NG+    K + +Q    +N + + PS
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKNDSKSGPS 113

>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 = 52.9 bits (127), Expect = 1e-10
 Identities = 17/104 (16%), Positives = 37/104 (35%), Gaps = 12/104 (11%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
               ++   + + V++++ L + VV  D        FG+I        V +M     + Q
Sbjct: 4   GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEK-FGTICY------VMMM---PFKRQ 53

Query: 73  AFVTFPSVELAHRALNLV--NGYVFKGKPMIIQFGRNPAAAKPS 114
           A V F +++ A   +           G+     +  +    +P 
Sbjct: 54  ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 52.6 bits (127), Expect = 2e-10
 Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ NL  D+  ++   +F   +G          V +    + +G  F+   +  LA  A
Sbjct: 18  LFVGNLPPDITEEEMRKLFEK-YGKAGE------VFIH---KDKGFGFIRLETRTLAEIA 67

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
              ++    +GK + ++F  + A+   
Sbjct: 68  KVELDNMPLRGKQLRVRFACHSASLTS 94

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I +L ++    D    F   FG++ +AK   +    Q    +   FV+F + + A  A
Sbjct: 43  LFIYHLPQEFTDTDLASTFLP-FGNVISAK---VFIDKQTSLSKCFGFVSFDNPDSAQVA 98

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG+    K + +Q  +
Sbjct: 99  IKAMNGFQVGTKRLKVQLKK 118

>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 = 53.8 bits (130), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
            +Y     A  L+I  L   +  D    +  S FG + A     +VK    G  +G AF 
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTS-FGPLKAFN---LVKDSATGLSKGYAFC 141

Query: 76  TFPSVELAHRALNLVNGYVFKGKPMIIQ 103
            +  + +  +A+  +NG     K +++Q
Sbjct: 142 EYVDINVTDQAIAGLNGMQLGDKKLLVQ 169

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 52.6 bits (127), Expect = 6e-10
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)

Query: 27  LYIKNLAKDVVPD---DFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           LY+ N+   +  +   DFF     L G   A   G  V  +Q  + +  AF+ F SV+  
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA--PGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 84  HRALNLVNGYVFKGKPMIIQFGRNP 108
            +A+   +G +F+G+ + I+   + 
Sbjct: 65  TQAMAF-DGIIFQGQSLKIRRPHDY 88

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 10/83 (12%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           +LY++NL      +     F +        +    VK     ++R  AFV F + E A  
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNN-IKPGAVER----VK-----KIRDYAFVHFSNREDAVE 66

Query: 86  ALNLVNGYVFKGKPMIIQFGRNP 108
           A+  +NG V  G P+ +   +  
Sbjct: 67  AMKALNGKVLDGSPIEVTLAKPV 89

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 5/96 (5%)

Query: 17  NYTAGNPAS-VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
             ++G P   ++ ++N+   V  D+        F         + +K  ++G   G+A V
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEIL----DFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 76  TFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAA 111
            F S + A  A+  +N      + + +  G  P++ 
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>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 = 55.0 bits (133), Expect = 2e-10
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + I+NL+ +++ ++        FGSI+     +     +       AF+ F + + A RA
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKIN--IPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           L + N  +   + + +      A  KP
Sbjct: 271 LQM-NRSLLGNREISVSL----ADKKP 292

>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 = 51.5 bits (124), Expect = 3e-09
 Identities = 11/88 (12%), Positives = 30/88 (34%), Gaps = 4/88 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ N        +   +       +  +     +  ++    R  A++   S E A   
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQD-INVVALSI---RLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +  +NG   +G  ++ +       +K +
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRT 203

>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 = 46.9 bits (112), Expect = 2e-07
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 8/73 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHR 85
           + +KNL K    +  +  F    G I      + V +     +    A + F   + A  
Sbjct: 44  VLVKNLPKSYNQNKVYKYF-KHCGPI------IHVDVADSLKKNFRFARIEFARYDGALA 96

Query: 86  ALNLVNGYVFKGK 98
           A+   +  V + +
Sbjct: 97  AITKTHKVVGQNE 109

>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 = 53.8 bits (130), Expect = 2e-10
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 9/74 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L  KNL+ ++  D+   VF      I          + Q+G+ +G A++ F S   A + 
Sbjct: 102 LLAKNLSFNITEDELKEVFED-ALEI--------RLVSQDGKSKGIAYIEFKSEADAEKN 152

Query: 87  LNLVNGYVFKGKPM 100
           L    G    G+ +
Sbjct: 153 LEEKQGAEIDGRSV 166

>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 = 53.4 bits (129), Expect = 3e-10
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I NL  +    +      S   + +       V  ++ G  R   +V F S E   +A
Sbjct: 16  LFIGNLNPNKSVAELKVAI-SELFAKNDLA----VVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 87  LNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
           L L  G    G  + ++   GR+    + +
Sbjct: 71  LEL-TGLKVFGNEIKLEKPKGRDSKKVRAA 99

>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 = 51.8 bits (125), Expect = 2e-10
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++I  L ++V  D    +F + +G I      + V+ M     +G A+V F + + A +A
Sbjct: 7   VHIGRLTRNVTKDHIMEIFST-YGKIKMID--MPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 87  LNLVNGYVFKGKPMIIQFGRNPA 109
           L  ++G    G+ +       P 
Sbjct: 64  LKHMDGGQIDGQEITATAVLAPW 86

>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 = 52.3 bits (126), Expect = 3e-10
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++IKNL K +     +  F S FG+I + K      +  E   +G  FV F + E A RA
Sbjct: 8   IFIKNLDKSIDNKALYDTF-SAFGNILSCK-----VVCDENGSKGYGFVHFETQEAAERA 61

Query: 87  LNLVNGYVFKGKPM 100
           +  +NG +   + +
Sbjct: 62  IEKMNGMLLNDRKV 75

>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 = 51.5 bits (124), Expect = 5e-10
 Identities = 22/97 (22%), Positives = 33/97 (34%), Gaps = 6/97 (6%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
             +    L + NL     PD    VF   +G +       I +       RG AFV F  
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEK-YGRVGDVY---IPREPHTKAPRGFAFVRFHD 64

Query: 80  VELAHRALNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
              A  A   ++G    G+ + +Q         + PS
Sbjct: 65  RRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 51.6 bits (124), Expect = 5e-10
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++   LA  + P D    F +  G +   +   I+      R +G A+V F  ++    A
Sbjct: 28  VFCMQLAARIRPRDLEDFFSA-VGKVRDVR---IISDRNSRRSKGIAYVEFCEIQSVPLA 83

Query: 87  LNLVNGYVFKGKPMIIQ 103
           + L  G    G P+I+Q
Sbjct: 84  IGL-TGQRLLGVPIIVQ 99

>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 = 51.0 bits (123), Expect = 5e-10
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSI-DAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           ++I NL  ++     +  F S FG I    K   I++    G  +G AF+ F S + +  
Sbjct: 8   IFIGNLDPEIDEKLLYDTF-SAFGVILQTPK---IMRDPDTGNSKGYAFINFASFDASDA 63

Query: 86  ALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           A+  +NG     +P+ +    + A  K S
Sbjct: 64  AIEAMNGQYLCNRPITV----SYAFKKDS 88

>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 = 51.5 bits (124), Expect = 5e-10
 Identities = 17/80 (21%), Positives = 26/80 (32%), Gaps = 5/80 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LYI NL   +   +   +    FG + + +    +     G  RG  F    S E     
Sbjct: 28  LYISNLPLSMDEQELENMLKP-FGQVISTR----ILRDSSGTSRGVGFARMESTEKCEAV 82

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +   NG   K  P +     
Sbjct: 83  IGHFNGKFIKTPPGVSAPTE 102

>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 = 51.0 bits (123), Expect = 6e-10
 Identities = 24/85 (28%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +P   L +  L+      D   VF   +G I       IV   Q  R RG AFV F +V+
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVS---IVYDQQSRRSRGFAFVYFENVD 68

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGR 106
            A  A    NG    G+ + +    
Sbjct: 69  DAKEAKERANGMELDGRRIRVSGPS 93

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 51.7 bits (124), Expect = 7e-10
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
              + L + NL     PD    VF   +G +       I +       RG AFV F    
Sbjct: 45  EGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVY---IPRDRYTKESRGFAFVRFHDKR 100

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGR 106
            A  A++ ++G V  G+ + +Q  R
Sbjct: 101 DAEDAMDAMDGAVLDGRELRVQMAR 125

>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 = 50.8 bits (122), Expect = 8e-10
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 17  NYTAGNPAS-VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
             ++G P   V+ ++N+   V  D+        F         + +K  ++G   G+A V
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEIL----DFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 76  TFPSVELAHRALNLVNGYVFKGKPM 100
            F S + A  A+  +N      + +
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKV 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 = 51.5 bits (123), Expect = 8e-10
 Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 12/97 (12%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
            M  + +AG P+ V++I+ L  DV   +   +    FG +        + ++   + + Q
Sbjct: 20  HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTN------LLML---KGKNQ 69

Query: 73  AFVTFPSVELAHRALNL--VNGYVFKGKPMIIQFGRN 107
           AF+   + E A+  +N       V +G+P+ IQF  +
Sbjct: 70  AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 50.7 bits (122), Expect = 9e-10
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           N  + +Y+  L + V     + +F    G +       + K    G+ +G  FV F S E
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTH---MPKDRVTGQHQGYGFVEFLSEE 68

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A+ +++     GKP+
Sbjct: 69  DADYAIKIMDMIKLYGKPI 87

>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 = 50.7 bits (122), Expect = 9e-10
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+KNL   +  +     F S FG+I +AK   ++  M+ GR +G  FV F S E A +A
Sbjct: 18  LYVKNLDDGIDDERLRKAF-SPFGTITSAK---VM--MEGGRSKGFGFVCFSSPEEATKA 71

Query: 87  LNLVNGYVFKGKPM 100
           +  +NG +   KP+
Sbjct: 72  VTEMNGRIVATKPL 85

>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 = 50.8 bits (122), Expect = 1e-09
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
                  LY+ +L  ++  D    +F   FG I++ +   ++   + GR +G  F+TF  
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEP-FGRIESIQ---LMMDSETGRSKGYGFITFSD 77

Query: 80  VELAHRALNLVNGYVFKGKPM 100
            E A +AL  +NG+   G+PM
Sbjct: 78  SECAKKALEQLNGFELAGRPM 98

>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 = 51.8 bits (124), Expect = 1e-09
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
              + L + NL     PD    VF   +G +       I +       RG AFV F    
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVY---IPRDRYTKESRGFAFVRFHDKR 123

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGR 106
            A  A++ ++G V  G+ + +Q  R
Sbjct: 124 DAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 51.8 bits (125), Expect = 1e-09
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 12/83 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSVELAH 84
           L+I  ++K    +D   +F S FG I+  +      ++   +G  RG AFVTF +  +A 
Sbjct: 98  LFIGMISKKCTENDIRVMF-SSFGQIEECR------ILRGPDGLSRGCAFVTFTTRAMAQ 150

Query: 85  RALNLVNGYVFK---GKPMIIQF 104
            A+  ++          PM+++F
Sbjct: 151 TAIKAMHQAQTMEGCSSPMVVKF 173

>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 = 41.8 bits (99), Expect = 7e-06
 Identities = 11/73 (15%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIV-KLMQEGRMRGQAFVTFPSVELAHR 85
          +++  + +     D   +F   +G++      ++  +     + +G  FVTF + + A  
Sbjct: 6  MFVGQVPRTWSEKDLRELFEQ-YGAVYEIN--VLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 86 ALNLVNGYVFKGK 98
          A N ++       
Sbjct: 63 AQNALHNMKVLPG 75

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 22/94 (23%), Positives = 33/94 (35%), Gaps = 12/94 (12%)

Query: 15  FKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAF 74
           + +      + V++I+ L   VV  D        FG I        V +M     + QA 
Sbjct: 12  YDDPHKTPASPVVHIRGLIDGVVEADLVEALQE-FGPISY------VVVM---PKKRQAL 61

Query: 75  VTFPSVELAHRALNLV--NGYVFKGKPMIIQFGR 106
           V F  V  A  A+N    N     G P  + +  
Sbjct: 62  VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +YIK    D   DD         G +   +    ++       +G  FV F S+E A + 
Sbjct: 14  VYIKGFPTDATLDDIKEWLED-KGQVLNIQ----MRRTLHKAFKGSIFVVFDSIESAKKF 68

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAK 112
           +    G  +K   ++I F  +  A K
Sbjct: 69  VET-PGQKYKETDLLILFKDDYFAKK 93

>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 = 49.9 bits (120), Expect = 1e-09
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 8/87 (9%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ +L+ ++        F + FG I  A+   +VK M  G+ +G  FV+F +   A  A
Sbjct: 9   VFVGDLSPEITTAAIAAAF-APFGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           +  + G    G+ +      N A  KP
Sbjct: 65  IQQMGGQWLGGRQIRT----NWATRKP 87

>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 = 50.8 bits (122), Expect = 1e-09
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ +L+ ++  +D    F + FG I  A+   +VK M  G+ +G  FV+F +   A  A
Sbjct: 18  VFVGDLSPEITTEDIKAAF-APFGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENA 73

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +  + G    G+ +      N A  KP 
Sbjct: 74  IQQMGGQWLGGRQIRT----NWATRKPP 97

>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 = 50.2 bits (121), Expect = 1e-09
 Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 6/97 (6%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
             + +S LY+ +L  ++  D    +F   FG ID      ++K    GR +G  F+TF  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEP-FGKIDNIV---LMKDSDTGRSKGYGFITFSD 56

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFG--RNPAAAKPS 114
            E A RAL  +NG+   G+PM +     R    + PS
Sbjct: 57  SECARRALEQLNGFELAGRPMRVGHVTERLDGGSGPS 93

>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 = 50.0 bits (120), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
            A  L  KNL+ ++  D+   VF      I          + Q+G+ +G A++ F S   
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFED-ALEI--------RLVSQDGKSKGIAYIEFKSEAD 65

Query: 83  AHRALNLVNGYVFKGKPMIIQFGR 106
           A + L    G    G+ + + +  
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 49.7 bits (119), Expect = 1e-09
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 11/87 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + +KNL +D    +   +    +           +K     R +  AFVT  + E A  A
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKD-YD----------LKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           + + + Y F+GK +I+Q     A    
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPTDALLCS 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 = 51.9 bits (125), Expect = 2e-09
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++IKNL K +     +  F S FG+I + K   +V    E   +G  FV F + E A RA
Sbjct: 106 IFIKNLDKSIDNKALYDTF-SAFGNILSCK---VVC--DENGSKGYGFVHFETQEAAERA 159

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           +  +NG +   + + +        ++ 
Sbjct: 160 IEKMNGMLLNDRKVFV----GRFKSRK 182

>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 = 47.7 bits (114), Expect = 6e-08
 Identities = 28/93 (30%), Positives = 41/93 (44%), Gaps = 8/93 (8%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
            P + LY+ +L  DV     +  F    G I + +   + + M   R  G A+V F    
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSP-AGPILSIR---VCRDMITRRSLGYAYVNFQQPA 68

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A RAL+ +N  V KGKP+ I      +   PS
Sbjct: 69  DAERALDTMNFDVIKGKPVRI----MWSQRDPS 97

>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 = 49.9 bits (120), Expect = 2e-09
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 6/74 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I NL  +    +          + +       V  ++ G  R   +V F S E   +A
Sbjct: 20  LFIGNLNPNKSVAELKVAISE-LFAKNDL----AVVDVRTGTNRKFGYVDFESAEDLEKA 74

Query: 87  LNLVNGYVFKGKPM 100
           L L  G    G  +
Sbjct: 75  LEL-TGLKVFGNEI 87

>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 = 50.5 bits (121), Expect = 2e-09
 Identities = 26/92 (28%), Positives = 35/92 (38%), Gaps = 4/92 (4%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
               N    +P   L +  L+      D   VF   +G I       IV   Q  R RG 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVS---IVYDQQSRRSRGF 90

Query: 73  AFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
           AFV F +V+ A  A    NG    G+ + + F
Sbjct: 91  AFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 5/92 (5%)

Query: 11  SLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMR 70
           S          +     +I N+   +   D           I   ++ + V +   G+  
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVL----QFLEGIPVDENAVHVLVDNNGQGL 57

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGKPMII 102
           GQA V F + + A ++  L +     G+   +
Sbjct: 58  GQALVQFKNEDDARKSERL-HRKKLNGREAFV 88

>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 = 49.0 bits (118), Expect = 2e-09
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ +L  +V  +     F   F S  +     ++  MQ G  RG  FV+F S + A  A
Sbjct: 4   LFVGDLNVNVDDETLRNAF-KDFPSYLSGH---VMWDMQTGSSRGYGFVSFTSQDDAQNA 59

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           ++ + G    G+P+ I    N AA   
Sbjct: 60  MDSMQGQDLNGRPLRI----NWAAKLE 82

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 49.6 bits (119), Expect = 3e-09
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 10/80 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
            YI N+       D   +F + FG I         K   E   +G  F+ + + E A   
Sbjct: 30  AYIGNIPHFATEADLIPLFQN-FGFILD------FKHYPE---KGCCFIKYDTHEQAAVC 79

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +  + F+G+ +   +G+
Sbjct: 80  IVALANFPFQGRNLRTGWGK 99

>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 = 49.2 bits (118), Expect = 3e-09
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P+ V+Y+ ++  D   +    +  +  G +   K   ++   Q GR +G AF+ F  +E 
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSN-VGPVINLK---MMFDPQTGRSKGYAFIEFRDLES 56

Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +  A+  +NGY    + +   +  N   +  S
Sbjct: 57  SASAVRNLNGYQLGSRFLKCGYSSNSDISGVS 88

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.6 bits (119), Expect = 3e-09
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ N+       D   +FG  FG I   +   I+    E   +G  FVTF +   A RA
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQ-FGKILDVE---II--FNERGSKGFGFVTFENSADADRA 85

Query: 87  LNLVNGYVFKGKPM 100
              ++G V +G+ +
Sbjct: 86  REKLHGTVVEGRKI 99

>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 = 48.8 bits (117), Expect = 3e-09
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+  L   +   D    F   FG I        + ++Q    +  AF+ F + + A  A
Sbjct: 15  LYVGGLGDTITETDLRNHFYQ-FGEIRT------ITVVQR---QQCAFIQFATRQAAEVA 64

Query: 87  L-NLVNGYVFKGKPMIIQFGR 106
                N  +  G+ + +++GR
Sbjct: 65  AEKSFNKLIVNGRRLNVKWGR 85

>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 = 48.8 bits (117), Expect = 4e-09
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 11/83 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LYI NL+  V  DD   +FG             +    Q     G AFV +P    A RA
Sbjct: 11  LYIGNLSPAVTADDLRQLFGD-RK---------LPLAGQVLLKSGYAFVDYPDQNWAIRA 60

Query: 87  LNLVNGYV-FKGKPMIIQFGRNP 108
           +  ++G V   GK M + +  + 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSK 83

>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 = 48.7 bits (117), Expect = 4e-09
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LYI+ L       D   +    +G I + K    +      + +G  FV F S   A +A
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQP-YGKIVSTK---AILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 87  LNLVNGYVFKGKPM 100
           +  +     + +  
Sbjct: 64  VTALKASGVQAQMA 77

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 49.1 bits (117), Expect = 4e-09
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 12/87 (13%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           +G P+ V++I+ L  DV   +   +    FG +        + ++   + + QAF+   +
Sbjct: 12  SGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTN------LLML---KGKNQAFIEMNT 61

Query: 80  VELAHRALN--LVNGYVFKGKPMIIQF 104
            E A+  +N       V +G+P+ IQF
Sbjct: 62  EEAANTMVNYYTSVTPVLRGQPIYIQF 88

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 50.9 bits (121), Expect = 4e-09
 Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 10/94 (10%)

Query: 21  GNPASVLYIKNLAKDVV-PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           G  + VL +  L +  +  D  F VF  L+G+++       VK M+     G A V    
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVF-CLYGNVEK------VKFMKS--KPGAAMVEMAD 51

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
                RA+  +N     G+ M +   + PA    
Sbjct: 52  GYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPG 85

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 13/79 (16%), Positives = 24/79 (30%), Gaps = 4/79 (5%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           VL+  N   +V  ++FF +     G         +     +        + + S   A  
Sbjct: 125 VLHFFNAPLEVTEENFFEICDE-LGVKRPTS---VKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 86  ALNLVNGYVFKGKPMIIQF 104
            L  +N Y  K       +
Sbjct: 181 TLGFLNHYQMKNPNGPYPY 199

>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 = 48.6 bits (116), Expect = 5e-09
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAK-SGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           LY+ N+   +  +     F +        +  G  V  +Q  + +  AF+ F SV+   +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 86  ALNLVNGYVFKGKPMII 102
           A+   +G +F+G+ + I
Sbjct: 69  AMAF-DGIIFQGQSLKI 84

>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 = 48.4 bits (116), Expect = 7e-09
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 8/91 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++  L K    +D   +F   FG ID       V    +G  +G AFV F S   A  A
Sbjct: 18  LFVGMLNKQQSEEDVLRLF-QPFGVIDECT----VLRGPDGSSKGCAFVKFSSHTEAQAA 72

Query: 87  LNLVNG-YVFKG--KPMIIQFGRNPAAAKPS 114
           ++ ++G     G    ++++F      + PS
Sbjct: 73  IHALHGSQTMPGASSSLVVKFADTDKESGPS 103

>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 = 49.4 bits (118), Expect = 7e-09
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
             +  LY+ NL+     +  + +F    G I       +     +    G  FV + S  
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSK-SGDIKKII---MGLDKMKKTACGFCFVEYYSRA 92

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A+  +NG     + +
Sbjct: 93  DAENAMRYINGTRLDDRII 111

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 48.1 bits (115), Expect = 8e-09
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +    + ++N+A   V D         + S+       ++K  Q  + RG AFV   S  
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSP-YASLAVNNI-RLIKDKQTQQNRGFAFVQLSSAM 64

Query: 82  LAHRALNLVNG----YVFKGKPMIIQFGR 106
            A + L ++          GK + + F +
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 50.5 bits (121), Expect = 8e-09
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ NL  D+  +DF  +F   +G          V +    R RG  F+   S  LA  A
Sbjct: 25  LFVGNLPTDITEEDFKRLFER-YGEPSE------VFIN---RDRGFGFIRLESRTLAEIA 74

Query: 87  LNLVNGYVFKGKPMIIQFGRNPA 109
              ++G + K +P+ I+F  + A
Sbjct: 75  KAELDGTILKSRPLRIRFATHGA 97

>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 = 45.1 bits (107), Expect = 7e-07
 Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
             + L +KNL+  V  +     F S FG ++ A     V +   GR  G+ FV F +   
Sbjct: 95  HGAALTVKNLSPVVSNELLEQAF-SQFGPVEKAV----VVVDDRGRATGKGFVEFAAKPP 149

Query: 83  AHRALNLVNGYVFKGK 98
           A +AL       F   
Sbjct: 150 ARKALERCGDGAFLLT 165

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 48.0 bits (115), Expect = 8e-09
 Identities = 16/98 (16%), Positives = 40/98 (40%), Gaps = 9/98 (9%)

Query: 17  NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVT 76
            Y+       L+I  L      ++   +  +  G++   +   +V   + G+ +G A+V 
Sbjct: 10  RYSTSLEKHKLFISGLPFSCTKEELEEICKA-HGTVKDLR---LVT-NRAGKPKGLAYVE 64

Query: 77  FPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           + +   A +A+  ++G   K   + +      + + PS
Sbjct: 65  YENESQASQAVMKMDGMTIKENIIKV----AISNSGPS 98

>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 = 47.6 bits (114), Expect = 1e-08
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
             S +Y+ NL   +  +D + +F   +G +       I+K     + +G AF+ F   + 
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSK-YGKVVKVT---IMKDKDTRKSKGVAFILFLDKDS 70

Query: 83  AHRALNLVNGYVFKGKPM 100
           A      +N     G+ +
Sbjct: 71  AQNCTRAINNKQLFGRVI 88

>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 = 47.6 bits (114), Expect = 1e-08
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 9/98 (9%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
               P+  L++K L++D   +         F     A+   IV   + G  +G  FV F 
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETL----KESFDGSVRAR---IVTDRETGSSKGFGFVDFN 62

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
           S E A  A   +      G  + + +   +    + PS
Sbjct: 63  SEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPS 100

>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 = 47.6 bits (114), Expect = 1e-08
 Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 7/92 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSVELAH 84
           L+IKNL      +    VF    G+I +    +  K          G  FV +   E A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSK-VGAIKSCT--ISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 85  RALNLVNGYVFKGKPMIIQFG--RNPAAAKPS 114
           +AL  + G+   G  + ++        A+ PS
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERATKPASGPS 96

>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 = 48.2 bits (115), Expect = 2e-08
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  +   V       +F   +G I++ K   IV   +  + RG  FV F S   A +A
Sbjct: 45  LMVNYIPTTVDEVQLRQLFER-YGPIESVK---IVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +  +NG+    K + +         +P 
Sbjct: 101 IAGLNGFNILNKRLKVALAA-SGHQRPG 127

>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 = 47.3 bits (113), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +P    ++ NL  DV  +         F  ++ +   L  +     R++G  +  F  ++
Sbjct: 13  SPPYTAFLGNLPYDVTEESI----KEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLD 68

Query: 82  LAHRALNLVNGYVFKGKPM 100
               AL+L N      K +
Sbjct: 69  SLLSALSL-NEESLGNKRI 86

>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 = 47.3 bits (113), Expect = 2e-08
 Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 7/93 (7%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
               AGN    +Y+ NL  D+   D   VF   +G+I        + L         AFV
Sbjct: 14  IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYK-YGAI------RDIDLKNRRGGPPFAFV 66

Query: 76  TFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
            F     A  A+   +GY + G  + ++F R+ 
Sbjct: 67  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 99

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 47.3 bits (113), Expect = 2e-08
 Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 9/89 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ +L  DV     +  F  ++ S    K    V L Q G  +G  FV F       RA
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGK----VVLDQTGVSKGYGFVKFTDELEQKRA 67

Query: 87  LNLVNGYVFKG-KPMIIQFGRNPAAAKPS 114
           L    G V  G KP+ +    + A  K S
Sbjct: 68  LTECQGAVGLGSKPVRL----SVAIPKAS 92

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 46.9 bits (112), Expect = 3e-08
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +    L++  L+ D        VF   +G I       +VK  +  R RG  FVTF +++
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSK-YGQISEVV---VVKDRETQRSRGFGFVTFENID 65

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A+  +NG    G+ +
Sbjct: 66  DAKDAMMAMNGKSVDGRQI 84

>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 = 46.5 bits (111), Expect = 3e-08
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL++DV       +F    G   + K   ++            FV F     A  A
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQ-IGPCKSCK---MITEHTSND--PYCFVEFYEHRDAAAA 71

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAK 112
           L  +NG    GK + + +   P++ K
Sbjct: 72  LAAMNGRKILGKEVKVNWATTPSSQK 97

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 47.5 bits (113), Expect = 4e-08
 Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 4/90 (4%)

Query: 11  SLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMR 70
           S     +  +     VLY+  LA++V        F   FG I   +   I    +  + R
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQ---IPLDYETEKHR 105

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGKPM 100
           G AFV F   E A  A++ +N     G+ +
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>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 = 46.4 bits (110), Expect = 4e-08
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 12/86 (13%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           G P+ VL+I+ L  +V   +   +    FG +        + ++   + + QAF+   + 
Sbjct: 12  GAPSRVLHIRKLPGEVTETEVIALGLP-FGKVTN------ILML---KGKNQAFLELATE 61

Query: 81  ELAHRALN--LVNGYVFKGKPMIIQF 104
           E A   +N         + +P+ IQ+
Sbjct: 62  EAAITMVNYYSAVTPHLRNQPIYIQY 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.5 bits (111), Expect = 4e-08
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P    Y+ NL  + V  D   +F  L  SI + +   +V+     + +G  +V F  V+ 
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDL--SIRSVR---LVRDKDTDKFKGFCYVEFDEVDS 68

Query: 83  AHRALNLVNGYVFKGKPM 100
              AL   +G +   + +
Sbjct: 69  LKEALTY-DGALLGDRSL 85

>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 = 47.5 bits (113), Expect = 5e-08
 Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 6/94 (6%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
              +L++ ++ ++   D+    F   +G I       +    + G  +G A V + + + 
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIH---LNLDRRTGFSKGYALVEYETHKQ 126

Query: 83  AHRALNLVNGYVFKGKPMIIQF--GRNPAAAKPS 114
           A  A   +NG    G+ + + +   + P   K S
Sbjct: 127 ALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 46.1 bits (110), Expect = 5e-08
 Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 8/90 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ N+       D   +FG  FG I   +  +I     E   +G  FVTF +   A RA
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQ-FGKILDVE--II---FNERGSKGFGFVTFENSADADRA 71

Query: 87  LNLVNGYVFKGKPMIIQFG--RNPAAAKPS 114
              ++G V +G+ + +     R    + PS
Sbjct: 72  REKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>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 = 46.6 bits (111), Expect = 6e-08
 Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
              +L++  + ++   +D    F   +G I       +    + G ++G   V + + + 
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIH---LNLDRRTGYLKGYTLVEYETYKE 76

Query: 83  AHRALNLVNGYVFKGKPMIIQFGR 106
           A  A+  +NG    G+P+ + +  
Sbjct: 77  AQAAMEGLNGQDLMGQPISVDWCF 100

>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 = 46.3 bits (110), Expect = 7e-08
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ N+       D    F S  GSI+      I+     G  +G A++ F        A
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSS-CGSINRIT---ILCDKFSGHPKGYAYIEFAERNSVDAA 94

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           + + +  VF+G+ + +     P     
Sbjct: 95  VAM-DETVFRGRTIKV----LPKRTNM 116

>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 = 45.7 bits (109), Expect = 8e-08
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +P    ++ NL  DV  +         F  ++ +   L  +     R++G  +  F  ++
Sbjct: 17  SPPYTAFLGNLPYDVTEESI----KEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLD 72

Query: 82  LAHRALNLVNGYVFKGKPM 100
               AL+L N      + +
Sbjct: 73  SLLSALSL-NEESLGNRRI 90

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 45.4 bits (107), Expect = 1e-07
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 4/88 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + + N+   +   +   +    F      KS   V+L      + +A V   +++ A  A
Sbjct: 12  VQVSNIDYRLSRKELQQLLQEAFARHGKVKS---VELSPHTDYQLKAVVQMENLQDAIGA 68

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +N ++ Y    K +++      A+   S
Sbjct: 69  VNSLHRYKIGSKKILVSLAT-GASGPSS 95

>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 = 45.4 bits (108), Expect = 1e-07
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 9/93 (9%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  + +++   D   +F   FG I       ++K    G  +G AF+T+   E A +A
Sbjct: 16  LFIGQIPRNLDEKDLKPLF-EEFGKIYELT---VLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 87  LNLVNGYV---FKGKPMIIQF--GRNPAAAKPS 114
            + ++         +P+ ++     +   + PS
Sbjct: 72  QSALHEQKTLPGMNRPIQVKPADSESRGGSGPS 104

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 45.6 bits (108), Expect = 1e-07
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 7/88 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + +KNL +     D   +          +        +      G   + FPS E+   A
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSS-------VNTRDFDGTGALEFPSEEILVEA 83

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           L  +N   F+G  + ++   NP   + S
Sbjct: 84  LERLNNIEFRGSVITVERDDNPPPIRRS 111

>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 = 45.3 bits (107), Expect = 1e-07
 Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 11/102 (10%)

Query: 5   PPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM 64
             ++    P  K         V+++ NL      D         +G I          LM
Sbjct: 6   SGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKN------YILM 59

Query: 65  QEGRMRGQAFVTFPSVELAHRALN--LVNGYVFKGKPMIIQF 104
              RM+ QAF+   + E A   ++  L     F+G+ + +  
Sbjct: 60  ---RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL 98

>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 = 44.8 bits (107), Expect = 1e-07
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
               VLY+  LA++V        F   FG I   +   I    +  + RG AFV F   E
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQ---IPLDYETEKHRGFAFVEFELAE 60

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A++ +N     G+ +
Sbjct: 61  DAAAAIDNMNESELFGRTI 79

>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 = 44.4 bits (106), Expect = 2e-07
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ N+      ++    F    GS++      I+     G  +G A++ F   E    +
Sbjct: 9   IYVGNVDYGATAEELEAHFHG-CGSVNRVT---ILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 87  LNLVNGYVFKGKPM 100
           L L +  +F+G+ +
Sbjct: 65  LAL-DESLFRGRQI 77

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 11/76 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSVELAH 84
           +++  +   +   +    F   +GS+        VK++  + G  +G  FV+F +     
Sbjct: 12  VFVGGIDVRMDETEIRSFFAR-YGSVKE------VKIITDRTGVSKGYGFVSFYNDVDVQ 64

Query: 85  RALNLVNGYVFKGKPM 100
           + +   +   F GK +
Sbjct: 65  KIVE--SQINFHGKKL 78

>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 = 44.8 bits (106), Expect = 2e-07
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 10/81 (12%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           +V+  KNL    +  +    F   FGS+           + EG     A V F     A 
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSR-FGSLGRVL-------LPEGG--ITAIVEFLEPLEAR 60

Query: 85  RALNLVNGYVFKGKPMIIQFG 105
           +A   +    F   P+ +++ 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWA 81

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 45.0 bits (107), Expect = 2e-07
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSVELAH 84
           L+I  L ++        VFG   G I        V L+  +  + RG AF+TF +   A 
Sbjct: 10  LFIGGLNRETNEKMLKAVFGK-HGPISE------VLLIKDRTSKSRGFAFITFENPADAK 62

Query: 85  RALNLVNGYVFKGKPM 100
            A   +NG    GK +
Sbjct: 63  NAAKDMNGKSLHGKAI 78

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
              +L++  + ++   +D    F   +G I       +    + G ++G   V + + + 
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIH---LNLDRRTGYLKGYTLVEYETYKE 77

Query: 83  AHRALNLVNGYVFKGKPM 100
           A  A+  +NG    G+P+
Sbjct: 78  AQAAMEGLNGQDLMGQPI 95

>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 = 44.1 bits (105), Expect = 3e-07
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
               VLY+  LA++V        F   FG I   +   I    +  + RG AFV F   E
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQ---IPLDYETEKHRGFAFVEFELAE 65

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A++ +N     G+ +
Sbjct: 66  DAAAAIDNMNESELFGRTI 84

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.2 bits (105), Expect = 3e-07
 Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 9/96 (9%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
             A+ L++ +L   +  +     F ++  ++ + K   I++    G   G  FV F  + 
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAFATMGETVMSVK---IIRNRLTGIPAGYCFVEFADLA 63

Query: 82  LAHRALNLVNGYVFKGKPMIIQF------GRNPAAA 111
            A + L+ +NG    G     +F         P++ 
Sbjct: 64  TAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSSG 99

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 45.9 bits (108), Expect = 3e-07
 Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 8/94 (8%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE---GRMRGQ 72
             YT       LYI NL      +D      S  G  D  +    +K  +    G+ +G 
Sbjct: 60  VVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS-LGVNDILE----IKFFENRANGQSKGF 114

Query: 73  AFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
           A V   S   + + ++L+      G+  ++    
Sbjct: 115 ALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN 148

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 8/103 (7%)

Query: 5   PPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM 64
            P       ++      N  + +Y+ + +          V  S  G  D  +    +K  
Sbjct: 36  KPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRS-IGVYDVVE----LKFA 90

Query: 65  QE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
           +    G+ +G A V   S    H+ L L+ G V  G+ + ++ 
Sbjct: 91  ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP 133

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 43.7 bits (103), Expect = 5e-07
 Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 9/90 (10%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
                A+ +Y+ NL +D    D         GS+    +            R +AF+ +P
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRE-LGSVPLRLTW--------QGPRRRAFLHYP 64

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
               A +A++ + G       + +   R  
Sbjct: 65  DSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 43.9 bits (103), Expect = 6e-07
 Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 12/96 (12%)

Query: 17  NYTAGNPASVL--YIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAF 74
                  + VL   ++NL   V  D    +F S FG++    +            + QA 
Sbjct: 19  GMAMAGQSPVLRIIVENLFYPVTLDVLHQIF-SKFGTVLKIITF-------TKNNQFQAL 70

Query: 75  VTFPSVELAHRALNLVNGYVF--KGKPMIIQFGRNP 108
           + +     A  A   ++G         + I F +  
Sbjct: 71  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 43.0 bits (102), Expect = 6e-07
 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE---GRMRGQAFVTFPSVELA 83
           LYI NL      +D      S  G  D  +    +K  +    G+ +G A V   S   +
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHS-LGVNDILE----IKFFENRANGQSKGFALVGVGSEASS 58

Query: 84  HRALNLVNGYVFKGKPM 100
            + ++L+      G+  
Sbjct: 59  KKLMDLLPKRELHGQNP 75

>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 = 43.0 bits (102), Expect = 6e-07
 Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 12/89 (13%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           +G  ++ L++ N++      +    F   +G +                ++  AFV    
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEE-YGPVIECD-----------IVKDYAFVHMER 53

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRNP 108
            E A  A+  ++   F+GK M +Q   + 
Sbjct: 54  AEDAVEAIRGLDNTEFQGKRMHVQLSTSR 82

>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 = 43.4 bits (103), Expect = 7e-07
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
              +L++ ++ ++   D+    F   +G I       +    + G  +G A V + + + 
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIH---LNLDRRTGFSKGYALVEYETHKQ 80

Query: 83  AHRALNLVNGYVFKGKPM 100
           A  A   +NG    G+ +
Sbjct: 81  ALAAKEALNGAEIMGQTI 98

>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 = 42.6 bits (101), Expect = 1e-06
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 12/92 (13%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           NP + L++  L  +         F   FGSI        V      +    A++ + S++
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDR-FGSIRTID---HV------KGDSFAYIQYESLD 64

Query: 82  LAHRALNLVNGYVFKGKPMIIQ--FGRNPAAA 111
            A  A   + G+   G    ++  F ++  ++
Sbjct: 65  AAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 41.8 bits (99), Expect = 2e-06
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 12/82 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ N++      +   +F    G +                ++  AFV       A  A
Sbjct: 12  IFVGNVSAACTSQELRSLFER-RGRVIECD-----------VVKDYAFVHMEKEADAKAA 59

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  +NG   KGK + ++     
Sbjct: 60  IAQLNGKEVKGKRINVELSTKG 81

>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 = 43.3 bits (103), Expect = 2e-06
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++  +  DV P +F   F   +G+I  A+   ++     G+ RG  FVT+ S +   R 
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQ-WGTIIDAQ---LMLDKDTGQSRGFGFVTYDSADAVDRV 145

Query: 87  LNLVNGYVFKGKPM 100
                   FK + +
Sbjct: 146 CQN-KFIDFKDRKI 158

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 13/100 (13%)

Query: 13  PMFKNYTAGNPASVL--YIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMR 70
                        VL   I+N    +  D  + V  +  G +         +++   R  
Sbjct: 12  RPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVC-NPVGKVQ--------RIVIFKRNG 62

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGK--PMIIQFGRNP 108
            QA V F SV  A +A   +NG         + I++ R  
Sbjct: 63  IQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 102

>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 = 43.2 bits (101), Expect = 2e-06
 Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 12/96 (12%)

Query: 17  NYTAGNPASVL--YIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAF 74
                  + VL   ++NL   V  D    +F S FG++    +            + QA 
Sbjct: 37  GMAMAGQSPVLRIIVENLFYPVTLDVLHQIF-SKFGTVLKIITF-------TKNNQFQAL 88

Query: 75  VTFPSVELAHRALNLVNGYVF--KGKPMIIQFGRNP 108
           + +     A  A   ++G         + I F +  
Sbjct: 89  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 124

>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 = 44.1 bits (103), Expect = 2e-06
 Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 4/90 (4%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           G+    L++  +  D         F  ++G I       +V   + G+ RG AF+ +   
Sbjct: 99  GDAFKTLFVARVNYDTTESKLRREF-EVYGPIKRIH---MVYSKRSGKPRGYAFIEYEHE 154

Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPAA 110
              H A    +G    G+ +++   R    
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERGRTV 184

>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 = 41.5 bits (98), Expect = 2e-06
 Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 13/90 (14%)

Query: 21  GNPASVLYIKNL-AKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
            +  S L+I NL  K+V  +D F +F S +G I        + +          F+ F +
Sbjct: 19  SHMKSRLFIGNLPLKNVSKEDLFRIF-SPYGHIMQ------INIK-----NAFGFIQFDN 66

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
            +    A+   +  +  GK +I++   + A
Sbjct: 67  PQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 41.6 bits (98), Expect = 3e-06
 Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 13/88 (14%)

Query: 27  LYIKNLAKDVV-PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           ++I NL   +V   D   +F S +G +          +      +G AFV + +   A  
Sbjct: 30  VFIGNLNTALVKKSDVETIF-SKYGRVAG------CSVH-----KGYAFVQYSNERHARA 77

Query: 86  ALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           A+   NG V  G+ + I     P   + 
Sbjct: 78  AVLGENGRVLAGQTLDINMAGEPKPDRS 105

>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 = 41.0 bits (96), Expect = 5e-06
 Identities = 15/95 (15%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 14  MFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM----QEGRM 69
           +++N    + ++      ++   + + +   F  +F  +   K G + ++         +
Sbjct: 9   IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEM-EEKYGEVEEMNVCDNLGDHL 67

Query: 70  RGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
            G  +V F   E A +A+  +N   F G+P+  + 
Sbjct: 68  VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 41.4 bits (97), Expect = 5e-06
 Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 5/80 (6%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
                 +Y+K L  +             F  +D  +  + +     G+  G+ FV F + 
Sbjct: 22  HEAGFCVYLKGLPFEAENKHVI----DFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 81  ELAHRALNLVNGYVFKGKPM 100
                AL   +      + +
Sbjct: 78  ADYKAALCR-HKQYMGNRFI 96

>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 = 40.2 bits (95), Expect = 8e-06
 Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 9/88 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ NL      +    +F   FG +   K   ++   +  + +G  FV     E    A
Sbjct: 4   IYVGNLVYSATSEQVKELFSQ-FGKVFNVK---LIYDRETKKPKGFGFVEMQE-ESVSEA 58

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +  ++   F G+ + +      A  K S
Sbjct: 59  IAKLDNTDFMGRTIRV----TEANPKKS 82

>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 = 40.6 bits (95), Expect = 8e-06
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSL--FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           +++++  L++ +   +          FG I                    A+VT+   E 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 83  AHRALNLVNGYVFKGKPMIIQFG 105
           A RA+  VN  V  G+ +    G
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLG 98

>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 = 41.0 bits (96), Expect = 8e-06
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 5/85 (5%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
            N         + ++ L      ++        F  ++   +G+ + +  EG++ G+AFV
Sbjct: 34  SNSADSANDGFVRLRGLPFGCTKEEIV----QFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 76  TFPSVELAHRALNLVNGYVFKGKPM 100
            F S ELA +AL   +      + +
Sbjct: 90  QFASQELAEKALGK-HKERIGHRYI 113

>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 = 39.9 bits (94), Expect = 9e-06
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 12/82 (14%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I NL ++    +   +F   +G +                ++   FV       A  A
Sbjct: 11  LFIGNLPREATEQEIRSLFEQ-YGKVLECD-----------IIKNYGFVHIEDKTAAEDA 58

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  ++ Y   G  + ++  +N 
Sbjct: 59  IRNLHHYKLHGVNINVEASKNK 80

>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 = 40.3 bits (95), Expect = 9e-06
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
                +++ N+  +   +    +F    G + + +   +V   + G+ +G  F  +   E
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSE-VGPVVSFR---LVYDRETGKPKGYGFCEYQDQE 61

Query: 82  LAHRALNLVNGYVFKGKPM 100
            A  A+  +NG  F G+ +
Sbjct: 62  TALSAMRNLNGREFSGRAL 80

>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 = 41.1 bits (97), Expect = 1e-05
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++  + +D         F   +G I+  +   I+     G+ RG AFVTF   +   + 
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQ-YGKIEVIE---IMTDRGSGKKRGFAFVTFDDHDSVDKI 162

Query: 87  LNLVNGYVFKGKPM 100
           +     +   G   
Sbjct: 163 VIQ-KYHTVNGHNC 175

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ NL       +    F   +G +        V +       G AFV F     A  A
Sbjct: 3   VYVGNLGTGAGKGELERAFSY-YGPLRT------VWIA--RNPPGFAFVEFEDPRDAEDA 53

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  ++G V  G  + ++     
Sbjct: 54  VRGLDGKVICGSRVRVELSTGM 75

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 41.4 bits (96), Expect = 1e-05
 Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 6/92 (6%)

Query: 13  PMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ 72
            +   Y        +YIK    D   DD         G +   +    ++       +G 
Sbjct: 98  EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLED-KGQVLNIQ----MRRTLHKAFKGS 152

Query: 73  AFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
            FV F S+E A + +    G  +K   ++I F
Sbjct: 153 IFVVFDSIESAKKFVET-PGQKYKETDLLILF 183

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 40.3 bits (94), Expect = 1e-05
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
             + +     ++ ++ L      ++    FG     I   K G++     +GR  G AFV
Sbjct: 15  AQFLSKENQVIVRMRGLPFTATAEEVVAFFGQ-HCPITGGKEGILFVTYPDGRPTGDAFV 73

Query: 76  TFPSVELAHRALNLVNGYVFKGKPM 100
            F   E A  AL   +  +   + +
Sbjct: 74  LFACEEYAQNALRK-HKDLLGKRYI 97

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 12/80 (15%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+     D+ P      F S FG+I                 R  AFVT+  +E A +A
Sbjct: 18  LYVYGE--DMTPTLLRGAF-SPFGNIIDLSMD---------PPRNCAFVTYEKMESADQA 65

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG   +   + +   R
Sbjct: 66  VAELNGTQVESVQLKVNIAR 85

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.9 bits (94), Expect = 1e-05
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 13/93 (13%)

Query: 23  PASVLYIKNL-AKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           P S L+I NL  K+V  +D F +F   +G I        + +          F+ F + +
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSP-YGHIMQ------INIK-----NAFGFIQFDNPQ 56

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
               A+   +  +  GK +I++   + A  +  
Sbjct: 57  SVRDAIECESQEMNFGKKLILEVSSSNARPQFD 89

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 39.8 bits (93), Expect = 1e-05
 Identities = 13/86 (15%), Positives = 27/86 (31%), Gaps = 11/86 (12%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
                V++I +  +              FG I          ++       +AF+   + 
Sbjct: 12  VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISN------HLIL---NKINEAFIEMATT 62

Query: 81  ELAHRALNLVNGY--VFKGKPMIIQF 104
           E A  A++       +  GKP+ +  
Sbjct: 63  EDAQAAVDYYTTTPALVFGKPVRVHL 88

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +Y+ NL  +    +    FG  +G + +      V +       G AFV F     A  A
Sbjct: 76  VYVGNLGNNGNKTELERAFGY-YGPLRS------VWVA--RNPPGFAFVEFEDPRDAADA 126

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  ++G    G  + ++     
Sbjct: 127 VRELDGRTLCGCRVRVELSNGE 148

>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 = 39.0 bits (91), Expect = 3e-05
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
            + ++ L      ++        F  ++   +G+ + +  +GR  G+AFV F S E+A +
Sbjct: 17  FVRLRGLPFGCSKEEI----VQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72

Query: 86  ALNLVNGYVFKGKPM 100
           AL   +      + +
Sbjct: 73  ALKK-HKERIGHRYI 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 = 39.1 bits (91), Expect = 4e-05
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 7/85 (8%)

Query: 16  KNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFV 75
           +          ++++ L      +D +  F  L           I     +GR+ G+A V
Sbjct: 38  EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-----NPVRVHIEI-GPDGRVTGEADV 91

Query: 76  TFPSVELAHRALNLVNGYVFKGKPM 100
            F + E A  A++  +    + + +
Sbjct: 92  EFATHEEAVAAMSK-DRANMQHRYI 115

>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 = 38.1 bits (89), Expect = 5e-05
 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
           ++G     + ++    +V   +           +      ++      G   G  FV F 
Sbjct: 5   SSGTTCHTVKLRGAPFNVTEKNVM----EFLAPLKPVAIRIVRN--AHGNKTGYIFVDFS 58

Query: 79  SVELAHRALNLVNGYVFKGKPM 100
           + E   +AL   N     G+ +
Sbjct: 59  NEEEVKQALKC-NREYMGGRYI 79

>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 = 37.5 bits (87), Expect = 1e-04
 Identities = 11/80 (13%), Positives = 20/80 (25%), Gaps = 11/80 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + +  L       D         G +  A          +    G   V F   E    A
Sbjct: 18  VVVSGLPPSGSWQDLKDHM-REAGDVCYA----------DVYRDGTGVVEFVRKEDMTYA 66

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  ++   F+       + R
Sbjct: 67  VRKLDNTKFRSHEGETAYIR 86

>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 = 36.7 bits (85), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  + K    ++       +   +      +      + + RG AFV + S   A  A
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVI--VYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 87  L-NLVNG-YVFKGKPMIIQF 104
              L+ G     G  + + +
Sbjct: 69  RRKLMPGRIQLWGHQIAVDW 88

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKL---MQEGRMRGQAFVTFPSVE 81
          SV+ + N+    V  D      ++   I  +K G I       ++G+ +G  F+ + S  
Sbjct: 16 SVIVVDNVP--QVGPDRLEKLKNVIHKI-FSKFGKITNDFYPEEDGKTKGYIFLEYASPA 72

Query: 82 LAHRALNLVNGYVFKGK 98
           A  A+   +GY    +
Sbjct: 73 HAVDAVKNADGYKLDKQ 89

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 10/94 (10%)

Query: 20  AGNPASVLYIKNL--AKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM-------QEGRMR 70
            G+P  VL + N+   ++++ D+ +          + +K GL+  +         E    
Sbjct: 1   GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRD-ECSKYGLVKSIEIPRPVDGVEVPGC 59

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
           G+ FV F SV    +A+  + G  F  + ++ ++
Sbjct: 60  GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93

>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 = 36.4 bits (84), Expect = 3e-04
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           G    V+ ++ L      +D          +I    +G+     +EGR  G+AFV   S 
Sbjct: 14  GGEGYVVKLRGLPWSCSIEDVQNFLSDC--TIHDGVAGVHFIYTREGRQSGEAFVELESE 71

Query: 81  ELAHRALNLVNGYVFKGKPM 100
           +    AL   +      + +
Sbjct: 72  DDVKLALKK-DRESMGHRYI 90

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 36.0 bits (83), Expect = 4e-04
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           +   ++  + L      +D    F      I   ++G+   L ++G+ RG A +   S 
Sbjct: 8  VDDVFLIRAQGLPWSCTMEDVLNFFSDC--RIRNGENGIHFLLNRDGKRRGDALIEMESE 65

Query: 81 ELAHRALNLVNGY 93
          +   +AL     Y
Sbjct: 66 QDVQKALEKHRMY 78

>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 = 35.5 bits (82), Expect = 6e-04
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
               ++++ L      +D +    + F  ++  +  + +    +GR+ G+A V F + E
Sbjct: 13 TTGHCVHMRGLPYRATENDIY----NFFSPLNPMRVHIEIG--PDGRVTGEADVEFATHE 66

Query: 82 LAHRALNL 89
           A  A+  
Sbjct: 67 DAVAAMAK 74

>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 = 35.5 bits (82), Expect = 6e-04
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
            + +  +    + +D    F  L   +DA     ++K    GR  G   V F S +    
Sbjct: 18  YVSVHGMPFSAMENDVRDFFHGL--RVDAVH---LLK-DHVGRNNGNGLVKFLSPQDTFE 71

Query: 86  ALNLVNGYVFKGKPM 100
           AL   N  +   + +
Sbjct: 72  ALKR-NRMLMIQRYV 85

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 35.1 bits (80), Expect = 8e-04
 Identities = 8/39 (20%), Positives = 14/39 (35%)

Query: 71  GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
             A + F + + A RA   +      G  +I+ F     
Sbjct: 47  CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR 85

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 34.7 bits (80), Expect = 9e-04
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 55 AKSGLIVKL---MQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK 98
          +K G I       ++G+ +G  F+ + S   A  A+   +GY    +
Sbjct: 29 SKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	114
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.93
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.93
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.92
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.9
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.9
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.9
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.9
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.9
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.9
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.9
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.89
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.89
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.89
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.89
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.89
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.89
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.89
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.89
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.89
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.89
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.89
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.89
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2div_A	99	TRNA selenocysteine associated protein; structural	99.88
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.88
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.88
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.88
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.88
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.88
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.88
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.87
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.87
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.87
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.87
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.87
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.87
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.87
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.87
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.86
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.86
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.86
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.86
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.86
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.86
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.86
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.86
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.86
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.86
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.86
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.85
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.85
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.85
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.85
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.85
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.85
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.85
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.85
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.85
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.85
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.85
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.85
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.85
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.85
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.84
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.84
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.84
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.84
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.84
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.84
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.84
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.84
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.84
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.84
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.84
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.84
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.84
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.83
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.83
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.83
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.83
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.83
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.83
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.83
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.83
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.83
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.83
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.83
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.83
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.83
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.83
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.83
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.82
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.82
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.82
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.71
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.81
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.81
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.81
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.8
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.8
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.8
1x5p_A	97	Negative elongation factor E; structure genomics,	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.78
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.78
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.78
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.77
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.77
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.77
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.77
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.76
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.73
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.73
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.73
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.72
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.72
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.68
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.66
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.66
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.66
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.65
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.63
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.58
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.57
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.52
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.38
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.29
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.24
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.18
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.6
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.0
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.53
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.49
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.29
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	97.1
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.9
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.64
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.59
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.57
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.14
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.13

>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=99.93  E-value=2.5e-25  Score=129.01  Aligned_cols=82  Identities=24%  Similarity=0.473  Sum_probs=76.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      -.+++|||+|||+++++++|+++|++ ||.|..++   .+.++.+|.++|||||+|.+.++|.+|+..|||..++|++|.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~-~G~I~~v~---i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~   92 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSS-IGEVESAK---LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK   92 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---EEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEeE---eeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            44688999999999999999999999 99999887   466778899999999999999999999999999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |++|+|
T Consensus        93 V~~AkP   98 (99)
T 4fxv_A           93 VSYARP   98 (99)
T ss_dssp             EEECCB
T ss_pred             EEEeeC
Confidence            999976

>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=99.93  E-value=1.7e-25  Score=137.19  Aligned_cols=108  Identities=40%  Similarity=0.787  Sum_probs=96.7

Q ss_pred             CCCChhhhhcCCCCCcCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceec--ccceeEEeccCCCceeEEEEEeCC
Q 033648            2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAA--KSGLIVKLMQEGRMRGQAFVTFPS   79 (114)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~--~~~~~~~~~~~~~~~g~~fv~f~~   79 (114)
                      ++++.+++..+|..+++.+..++++|||+|||+.+++++|+.+|++ ||.|..+  ++++.+....+|.++|||||+|.+
T Consensus        23 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~  101 (143)
T 3egn_A           23 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGR-YVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN  101 (143)
T ss_dssp             HBCCHHHHHHCGGGTTCCCCSCCSEEEEEEECTTCCHHHHHHHHGG-GCCTTCHHHHHHCEEEEEEETTTEEEEEEECSS
T ss_pred             ccCCHHHHhhcccccccCCCCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCcccccccceeeEEeccCCCcccEEEEEeCC
Confidence            3678899999999889999999999999999999999999999999 9999876  334455556789999999999999


Q ss_pred             HHHHHHHHHHhCCcccCCceEEEEeccCCCC
Q 033648           80 VELAHRALNLVNGYVFKGKPMIIQFGRNPAA  110 (114)
Q Consensus        80 ~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~  110 (114)
                      .++|.+|+..|||..++|+.|.|++|++...
T Consensus       102 ~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~  132 (143)
T 3egn_A          102 EKAAAKALKEANGYVLFGKPMVVQFARSARP  132 (143)
T ss_dssp             HHHHHHHHHHHTTBEETTEECEEEECCCSCC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            9999999999999999999999999987543

>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=99.92  E-value=6.2e-25  Score=130.09  Aligned_cols=107  Identities=43%  Similarity=0.740  Sum_probs=95.1

Q ss_pred             CCCChhhhhcCCCCCcCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHH
Q 033648            2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE   81 (114)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~   81 (114)
                      ++++.++....+......+..++++|||+|||+.+++++|+.+|.+ ||.|..+.+..   +..++.++|||||+|.+.+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~v~~~~~~~---~~~~g~~~g~afV~f~~~~   78 (115)
T 2cpx_A            3 SGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFAR-FQEKKGPPIQF---RMMTGRMRGQAFITFPNKE   78 (115)
T ss_dssp             SCCCCSSSCCCSCCCCCCCCSCCSEEEEECCCTTCCHHHHHHHTHH-HHHSSSSCCEE---EEECSSSCSEEEEECSSHH
T ss_pred             CCCChhhhhhcccccccCCCCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCccceEEEE---EcCCCccceEEEEEECCHH
Confidence            6789999999998888888899999999999999999999999999 99987664322   2238889999999999999


Q ss_pred             HHHHHHHHhCCcccCCceEEEEeccCCCCCC
Q 033648           82 LAHRALNLVNGYVFKGKPMIIQFGRNPAAAK  112 (114)
Q Consensus        82 ~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~~  112 (114)
                      +|.+|+..|||..++|+.|.|++|++.....
T Consensus        79 ~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           79 IAWQALHLVNGYKLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             HHHHHHHHSTTCBCSSCBCEEEECCCCSCCC
T ss_pred             HHHHHHHHhCCCEeCCcEEEEEEccCCCCCC
Confidence            9999999999999999999999999877654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.91  E-value=1.5e-23  Score=123.65  Aligned_cols=83  Identities=16%  Similarity=0.135  Sum_probs=77.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +|.++|||+|||+.+++++|+++|++ ||.|..++   .+.+..++.++|||||+|.+.++|++|+..|||..++|+.|.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~-~G~i~~v~---i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRK-YGEVEEVE---ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHh-cCCeeEEE---EEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            56789999999999999999999999 99999887   466788899999999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |++|...
T Consensus        80 V~~a~~~   86 (110)
T 3s8s_A           80 AQLDIKG   86 (110)
T ss_dssp             EEECSTT
T ss_pred             EEECCCC
Confidence            9999754

>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=99.90  E-value=3.6e-23  Score=116.82  Aligned_cols=84  Identities=21%  Similarity=0.382  Sum_probs=74.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||.++++++|+.+|++ ||.|..++   .+.+..++.++|||||+|.+.++|++|+..|||..++|+.|
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAP-FGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   78 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHh-cCCEeEEE---EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            456789999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|++|+++
T Consensus        79 ~v~~a~~k   86 (87)
T 3bs9_A           79 RTNWATRK   86 (87)
T ss_dssp             EEEEEC--
T ss_pred             EEEecCCC
Confidence            99999875

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=6.9e-23  Score=117.44  Aligned_cols=88  Identities=31%  Similarity=0.500  Sum_probs=79.7

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++++|||+|||+++++++|+++|++ ||.|..+.   .+.+..++.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   77 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEP-FGKIDNIV---LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM   77 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---EECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCEeEEE---EeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Confidence            457789999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCC
Q 033648          101 IIQFGRNPAAAK  112 (114)
Q Consensus       101 ~v~~a~~~~~~~  112 (114)
                      +|++++++....
T Consensus        78 ~V~~a~~~~~~~   89 (95)
T 2dnz_A           78 RVGHVTERLDGG   89 (95)
T ss_dssp             EEEESSCCCCCC
T ss_pred             EEEEcccccCCC
Confidence            999999876553

>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=99.90  E-value=1.3e-22  Score=120.21  Aligned_cols=89  Identities=24%  Similarity=0.368  Sum_probs=80.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+++++++|+++|.+ ||.|..++   .+.+..++.+++||||+|.+.++|++|+..|||..++|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAK---VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGG-GSCCSEEE---EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            456789999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCC
Q 033648          101 IIQFGRNPAAAKP  113 (114)
Q Consensus       101 ~v~~a~~~~~~~~  113 (114)
                      .|++++++...++
T Consensus        98 ~V~~a~~~~~~~~  110 (115)
T 2cpz_A           98 KVQLKRSKNDSKS  110 (115)
T ss_dssp             EEECCCCSCCCCC
T ss_pred             EEEEcCCCCcCCC
Confidence            9999998776543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.90  E-value=1.1e-23  Score=120.35  Aligned_cols=84  Identities=18%  Similarity=0.300  Sum_probs=74.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC-CcccCCceEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN-GYVFKGKPMI  101 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~-g~~~~g~~l~  101 (114)
                      +++|||+|||+++++++|+++|++ || .|.++++   ++++.+|.++|||||+|.+.++|.+|++.++ +..++|++|.
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~-~G~~v~~v~i---~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~   76 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQS-HGVQAREVRL---MRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVS   76 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHH-HTCCCSBCCS---SSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHH-hCCEeEEEEE---EecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEE
Confidence            468999999999999999999999 99 7888874   4577889999999999999999999999875 5679999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |++|+++...
T Consensus        77 V~~a~~~~~~   86 (91)
T 2lxi_A           77 MHYSDPKPKI   86 (91)
T ss_dssp             EECCCSCCCC
T ss_pred             EEEcCCCCCC
Confidence            9999987643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.90  E-value=1.3e-22  Score=117.22  Aligned_cols=85  Identities=20%  Similarity=0.422  Sum_probs=77.2

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCcee--------cccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDA--------AKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~--------~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ..+.++.++|||+|||+++++++|+.+|++ ||.+..        ++   .+.++.+|.++|||||+|.+.++|.+|+..
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~~~~~~~~v~---i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~   82 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQ-IGIIKTNKKTGQPMIN---LYTDRETGKLKGEATVSFDDPPSAKAAIDW   82 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTT-TSCBCEETTTTEESEE---EEECTTTCSEEEEEEEEBSSHHHHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCEeeccccccccEE---EEecCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            345677899999999999999999999999 999987        65   456677899999999999999999999999


Q ss_pred             hCCcccCCceEEEEecc
Q 033648           90 VNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        90 l~g~~~~g~~l~v~~a~  106 (114)
                      |||..+.|+.|.|++|+
T Consensus        83 l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           83 FDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HTTCBSSSSBCEEEECC
T ss_pred             hCCCEeCCcEEEEEecC
Confidence            99999999999999985

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=8.8e-23  Score=119.18  Aligned_cols=86  Identities=16%  Similarity=0.343  Sum_probs=78.6

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...++++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   94 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIH---LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP   94 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhc-cCCeEEEE---EEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcE
Confidence            3456789999999999999999999999 99998886   4567778999999999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|++|+++.
T Consensus        95 l~V~~a~~~~  104 (106)
T 1p27_B           95 ISVDWCFVRG  104 (106)
T ss_dssp             CEEEESEESS
T ss_pred             EEEEeecCCC
Confidence            9999998765

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=2.3e-22  Score=116.30  Aligned_cols=89  Identities=16%  Similarity=0.317  Sum_probs=79.3

Q ss_pred             cCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           17 NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        17 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ......+.++|||+|||+.+++++|+.+|.+ ||.|..+.   .+.+. +|..+|||||+|.+.++|.+|+..|||..++
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~   84 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKA-HGTVKDLR---LVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIK   84 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESS
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCeEEEE---EEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            3445577889999999999999999999999 99998876   33444 8899999999999999999999999999999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |+.|.|+++++...
T Consensus        85 g~~l~v~~a~~~~~   98 (100)
T 2do4_A           85 ENIIKVAISNSGPS   98 (100)
T ss_dssp             SCEEEEEECCCCSC
T ss_pred             CEEEEEEECCCCCC
Confidence            99999999998764

>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=99.90  E-value=6.3e-23  Score=115.33  Aligned_cols=82  Identities=27%  Similarity=0.383  Sum_probs=75.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+++++++|+.+|++ ||.|..+.   .+.+..++..+|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   79 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQ---IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   79 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhc-cCCEEEEE---EEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            467899999999999999999999999 99998886   34567789999999999999999999999999999999999


Q ss_pred             EEEecc
Q 033648          101 IIQFGR  106 (114)
Q Consensus       101 ~v~~a~  106 (114)
                      .|++|+
T Consensus        80 ~v~~ak   85 (85)
T 3mdf_A           80 RVNLAK   85 (85)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999986

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=8.1e-23  Score=118.83  Aligned_cols=89  Identities=25%  Similarity=0.427  Sum_probs=81.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+.+|++ ||.|..+.   .+.+..++.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRP-FGSISRIY---LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTT-TCCEEEEE---EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCeEEEE---EeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            466789999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCC
Q 033648          101 IIQFGRNPAAAKP  113 (114)
Q Consensus       101 ~v~~a~~~~~~~~  113 (114)
                      .|++++++....+
T Consensus        88 ~v~~a~~~~~~~~  100 (103)
T 2cq0_A           88 NVEWAKPSTNSGP  100 (103)
T ss_dssp             EEEESSCCCCSCC
T ss_pred             EEEECCCCCCCCC
Confidence            9999998876654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.89  E-value=2.9e-22  Score=122.18  Aligned_cols=89  Identities=21%  Similarity=0.299  Sum_probs=80.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||.++++++|+.+|++ ||.|..++   .+.+..++.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  112 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFER-YGPIESVK---IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK  112 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHH-HSCEEEEE---EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            33456789999999999999999999999 99998886   456777899999999999999999999999999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++|++....
T Consensus       113 ~l~v~~a~~~~~~  125 (139)
T 1u6f_A          113 RLKVALAASGHQR  125 (139)
T ss_dssp             EEEEEESSCCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999977644

>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=99.89  E-value=1.3e-22  Score=119.13  Aligned_cols=86  Identities=27%  Similarity=0.492  Sum_probs=78.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+.+++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEP-FGRIESIQ---LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTT-TSCEEEEE---EEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            466789999999999999999999999 99998886   45677789999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|++++++.+
T Consensus        99 ~V~~a~~k~d  108 (108)
T 2jrs_A           99 KVGHVTERTD  108 (108)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEEcccCCC
Confidence            9999998753

>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=99.89  E-value=1.4e-22  Score=113.44  Aligned_cols=82  Identities=26%  Similarity=0.411  Sum_probs=75.5

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +.+|||+|||+++++++|+.+|++ ||.|..+.   .+.+..++.++|||||+|.+.++|++|+..|||..++|++|.|+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   76 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKD-FPSYLSGH---VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTT-STTEEEEE---EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            358999999999999999999999 99998886   45567789999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      +|+++.
T Consensus        77 ~a~~~~   82 (83)
T 3md1_A           77 WAAKLE   82 (83)
T ss_dssp             ECCCCC
T ss_pred             ecCcCC
Confidence            998764

>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=99.89  E-value=1.1e-22  Score=117.45  Aligned_cols=87  Identities=24%  Similarity=0.325  Sum_probs=79.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|++ ||.|..+.+   +.+..++..+|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   80 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSA-YGPLSELHY---PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML   80 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEeEEEE---EecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            466789999999999999999999999 999988763   4455688999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|++++++...
T Consensus        81 ~V~~a~~~~~~   91 (99)
T 1whw_A           81 HVLPSTIKKEA   91 (99)
T ss_dssp             EEEECCCCSTT
T ss_pred             EEEEcCCCccc
Confidence            99999988764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.89  E-value=3.2e-23  Score=119.27  Aligned_cols=82  Identities=22%  Similarity=0.412  Sum_probs=72.9

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCc--eecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc----c
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSI--DAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV----F   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i--~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~----~   95 (114)
                      ..-.+|||+|||+.+|+++|+++|++ ||.+  ..++   .++++.+|.++|||||+|.+.++|.+|++.|||..    +
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~-~G~i~v~~v~---i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i   82 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSP-YASLAVNNIR---LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKI   82 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTT-TCCCCGGGEE---CCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHh-hCCccEEEEE---EEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceE
Confidence            45578999999999999999999999 9964  4554   35677889999999999999999999999999974    8


Q ss_pred             CCceEEEEeccC
Q 033648           96 KGKPMIIQFGRN  107 (114)
Q Consensus        96 ~g~~l~v~~a~~  107 (114)
                      +||+|.|+||++
T Consensus        83 ~Gr~i~V~~Aks   94 (95)
T 2lkz_A           83 DGKTIGVDFAKS   94 (95)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEccC
Confidence            999999999986

>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=99.89  E-value=2.2e-23  Score=118.66  Aligned_cols=84  Identities=20%  Similarity=0.237  Sum_probs=70.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcC--CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFG--SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G--~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .+|||+|||+++++++|+++|++ ||  .+.+++   .+.++.+|.++|||||+|.+.++|++|+..|||..++|+.|.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~-~G~~~v~~v~---i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHS-LGVNDILEIK---FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHT-TTCCCCCCEE---EEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHH-hCCCceEEEE---EEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            47999999999999999999999 99  888776   4567789999999999999999999999999999999999999


Q ss_pred             EeccCCCCCC
Q 033648          103 QFGRNPAAAK  112 (114)
Q Consensus       103 ~~a~~~~~~~  112 (114)
                      .++++.....
T Consensus        78 ~~~~~~~~~~   87 (90)
T 3p5t_L           78 TPSNKLEHHH   87 (90)
T ss_dssp             CCC-------
T ss_pred             EECCCCcccc
Confidence            9999876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=1.6e-22  Score=116.55  Aligned_cols=87  Identities=23%  Similarity=0.307  Sum_probs=77.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEecc---CCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ---EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      .+.++|||+|||+++++++|+++|++ ||.|..+.+   +.+..   ++..+|||||+|.+.++|.+|+..|||..++|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSK-VGAIKSCTI---SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH   78 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHT-TSCEEEEEE---EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            56789999999999999999999999 999988863   34444   558899999999999999999999999999999


Q ss_pred             eEEEEeccCCCCCC
Q 033648           99 PMIIQFGRNPAAAK  112 (114)
Q Consensus        99 ~l~v~~a~~~~~~~  112 (114)
                      .|.|+++++.....
T Consensus        79 ~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           79 KLEVRISERATKPA   92 (98)
T ss_dssp             ECEEECSSCSSCCC
T ss_pred             EEEEEEccCCCCCC
Confidence            99999999776543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.7e-22  Score=116.72  Aligned_cols=89  Identities=16%  Similarity=0.299  Sum_probs=79.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+.+|++ ||.|..+.   .+.+..++..+|||||+|.+.++|.+|+. |||..++|+
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~   79 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKK-FGVVTEVV---MIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGK   79 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSS-SSCEEEEE---ECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCe
Confidence            34567789999999999999999999999 99998886   34566788999999999999999999998 999999999


Q ss_pred             eEEEEeccCCCCCC
Q 033648           99 PMIIQFGRNPAAAK  112 (114)
Q Consensus        99 ~l~v~~a~~~~~~~  112 (114)
                      .|.|+++++.....
T Consensus        80 ~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           80 KVEVKRAEPRDSKS   93 (99)
T ss_dssp             BCEEEECCCCCCCC
T ss_pred             EEEEEECCCCcccC
Confidence            99999999876553

>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=99.89  E-value=4.3e-22  Score=116.05  Aligned_cols=88  Identities=25%  Similarity=0.469  Sum_probs=78.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC---
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG---   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g---   97 (114)
                      ..+.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+ .++.++|||||+|.+.++|.+|+..|||..+.|   
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~   86 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQP-FGVIDECT---VLRG-PDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGAS   86 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---EEEC-SSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEC-CCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCC
Confidence            466899999999999999999999999 99998886   2334 478999999999999999999999999999988   


Q ss_pred             ceEEEEeccCCCCCCC
Q 033648           98 KPMIIQFGRNPAAAKP  113 (114)
Q Consensus        98 ~~l~v~~a~~~~~~~~  113 (114)
                      +.|.|.+|+++....+
T Consensus        87 ~~l~V~~a~~~~~~~~  102 (105)
T 2dnh_A           87 SSLVVKFADTDKESGP  102 (105)
T ss_dssp             SCCEEEESCSSCCCSC
T ss_pred             ccEEEEECccCcccCC
Confidence            9999999998876654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.7e-22  Score=117.23  Aligned_cols=90  Identities=23%  Similarity=0.384  Sum_probs=80.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+.+|++ ||.|..++   .+.+..++..++||||+|.+.++|.+|+..|||..++|+
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSK-YGQISEVV---VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR   82 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHH-HSCCCEEE---ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHh-cCCeEEEE---EEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            34567889999999999999999999999 99998876   344566888999999999999999999999999999999


Q ss_pred             eEEEEeccCCCCCC
Q 033648           99 PMIIQFGRNPAAAK  112 (114)
Q Consensus        99 ~l~v~~a~~~~~~~  112 (114)
                      .|.|+++++....+
T Consensus        83 ~l~v~~a~~~~~~~   96 (102)
T 1x5s_A           83 QIRVDQAGKSSDNR   96 (102)
T ss_dssp             CCEEEEEECCCCCC
T ss_pred             EEEEEECCCCCCCC
Confidence            99999999876553

>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=99.89  E-value=9.3e-23  Score=117.25  Aligned_cols=84  Identities=23%  Similarity=0.400  Sum_probs=76.9

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      |+++|||+|||.++++++|+.+|++ ||.|..+++   +.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.|
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   76 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSN-VGPVINLKM---MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC   76 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---CBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHh-cCCEEEEEE---EeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            5789999999999999999999999 999988863   446668899999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      ++|++...
T Consensus        77 ~~a~~~~~   84 (96)
T 2x1f_A           77 GYSSNSDI   84 (96)
T ss_dssp             EECSCSSG
T ss_pred             EEcCCCCC
Confidence            99998754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=2.2e-22  Score=115.28  Aligned_cols=85  Identities=28%  Similarity=0.345  Sum_probs=77.5

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..++..+|||||+|.+.++|.+|+..|||..++|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVS---IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHT-TSCEEEEE---EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHh-cCCeeEEE---EEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34566789999999999999999999999 99998886   456677889999999999999999999999999999999


Q ss_pred             eEEEEeccC
Q 033648           99 PMIIQFGRN  107 (114)
Q Consensus        99 ~l~v~~a~~  107 (114)
                      +|.|++|++
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            999999975

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.89  E-value=4.9e-22  Score=117.61  Aligned_cols=87  Identities=23%  Similarity=0.417  Sum_probs=79.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|.+ ||.|..++   .+.+..++..+|||||+|.+.++|++|+..|||..++|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAP-FGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   87 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            466789999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|.++++....
T Consensus        88 ~V~~a~~~~~~   98 (115)
T 2dgo_A           88 RTNWATRKPPA   98 (115)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999976543

>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=99.89  E-value=1.8e-22  Score=117.68  Aligned_cols=89  Identities=21%  Similarity=0.288  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.+..++..+|||||+|.+.++|.+|+..|||..++|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTHM---PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   85 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            34567789999999999999999999999 999988863   44566899999999999999999999999999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++|+++...
T Consensus        86 ~l~v~~a~~~~~~   98 (105)
T 1x5u_A           86 PIRVNKASAHNKN   98 (105)
T ss_dssp             BCEEEETTTTSCC
T ss_pred             EEEEEECCCCCcC
Confidence            9999999987654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.1e-22  Score=116.76  Aligned_cols=86  Identities=23%  Similarity=0.451  Sum_probs=78.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceec-ccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAA-KSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++++|||+|||+.+++++|+.+|++ ||.|..+ +   .+.+..++..+|||||+|.+.++|++|+..|||..++|+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~~~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSA-FGVILQTPK---IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI   78 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHT-TSCBSSCCE---ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEE---EEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            56789999999999999999999999 9999877 6   34466789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|++|++....
T Consensus        79 ~v~~a~~~~~~   89 (96)
T 1x5t_A           79 TVSYAFKKDSK   89 (96)
T ss_dssp             EEEESCCCCCC
T ss_pred             EEEEecccCCC
Confidence            99999977654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.2e-22  Score=118.17  Aligned_cols=88  Identities=23%  Similarity=0.284  Sum_probs=79.0

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..+.+   +.+..++.++|||||+|.+.++|++|+..|||..++|+.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   84 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEK-YGRVGDVYI---PREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRE   84 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTT-TSCEEEEEC---CBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBC
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---EeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            3466789999999999999999999999 999988763   446667899999999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|++|++....
T Consensus        85 l~V~~a~~~~~~   96 (103)
T 2dnm_A           85 LRVQVARYGRRD   96 (103)
T ss_dssp             CEEEECSSCCSC
T ss_pred             EEEEECCcCCCC
Confidence            999999976544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.4e-22  Score=117.63  Aligned_cols=89  Identities=24%  Similarity=0.314  Sum_probs=80.0

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.+..++..+|||||+|.+.++|++|+..|||..++|+.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   83 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTT-TSCCCCEEC---CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhc-cCCEEEEEE---EecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3467889999999999999999999999 999988863   446678899999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |.|+++++.....
T Consensus        84 l~V~~a~~~~~~~   96 (102)
T 2cqb_A           84 IRVNLAKPMRIKE   96 (102)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999999876553

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=5.3e-22  Score=115.37  Aligned_cols=87  Identities=29%  Similarity=0.462  Sum_probs=77.9

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.+  ++..++||||+|.+.++|.+|+..|||..+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSP-FGTITSAKV---MME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK   83 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTT-TSCEEEEEE---EEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---EcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            33467889999999999999999999999 999988762   333  888999999999999999999999999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++++++...
T Consensus        84 ~l~V~~a~~~~~~   96 (103)
T 2d9p_A           84 PLYVALAQRKEER   96 (103)
T ss_dssp             BCEEEECSSCCCC
T ss_pred             EEEEEEecccccC
Confidence            9999999987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=3.6e-22  Score=116.69  Aligned_cols=90  Identities=18%  Similarity=0.364  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEe-ccCCCceeEEEEEeCCHHHHHHHHHHh-CCcccC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKL-MQEGRMRGQAFVTFPSVELAHRALNLV-NGYVFK   96 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~   96 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.+ ..++..+|||||+|.+.++|.+|+..| ||..+.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~   85 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFST-FGELKTVRL---PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY   85 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHc-cCCeEEEEE---ecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC
Confidence            34567889999999999999999999999 999988763   334 568889999999999999999999999 999999


Q ss_pred             CceEEEEeccCCCCCC
Q 033648           97 GKPMIIQFGRNPAAAK  112 (114)
Q Consensus        97 g~~l~v~~a~~~~~~~  112 (114)
                      |+.|.|++|+++....
T Consensus        86 g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           86 GRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             SCBCEEEECCCCCCCC
T ss_pred             CCEEEEEeCCCCCCCC
Confidence            9999999999876553

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.88  E-value=3.6e-22  Score=118.42  Aligned_cols=82  Identities=27%  Similarity=0.436  Sum_probs=72.7

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++|||+|||+++++++|+++|++ ||.|.++++   +.+  .+.++|||||+|.+.++|++|+..|||..++|+.|.|
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~-~G~v~~v~i---~~d--~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V   77 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSA-FGNILSCKV---VCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV   77 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEEE---EEE--TTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhc-cCCEEEEEE---eec--CCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3568999999999999999999999 999998873   333  3457899999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      .+++++..
T Consensus        78 ~~a~~~~~   85 (115)
T 4f25_A           78 GRFKSRKE   85 (115)
T ss_dssp             EESSCCCC
T ss_pred             EECCCccc
Confidence            99987654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=4.2e-22  Score=115.00  Aligned_cols=87  Identities=20%  Similarity=0.334  Sum_probs=79.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCce-ecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSID-AAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~-~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|. .++   .+.++.++.++|||||+|.+.++|++|+..|||..+.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFAT-MGETVMSVK---IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA   80 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHH-TTCCCCEEE---EEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHH-hCCcceEEE---EeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCC
Confidence            3567899999999999999999999999 99998 886   456777899999999999999999999999999999999


Q ss_pred             e----EEEEeccCCCC
Q 033648           99 P----MIIQFGRNPAA  110 (114)
Q Consensus        99 ~----l~v~~a~~~~~  110 (114)
                      .    |.|++|++...
T Consensus        81 ~~~~~l~v~~a~~~~~   96 (99)
T 2div_A           81 TPAKRFKLNYATYSGP   96 (99)
T ss_dssp             SSCEECCEEETTCCSS
T ss_pred             CcceeEEEeecCCCCC
Confidence            9    99999997754

>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=99.88  E-value=6.7e-22  Score=113.93  Aligned_cols=86  Identities=20%  Similarity=0.303  Sum_probs=78.0

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ..++.++|||+|||+++++++|+.+|.+ ||.|..+.   .+.+..+|..+|||||+|.+.++|++|+..|||..++|+.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~-~G~v~~~~---~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   86 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYG-YQVIPGSV---CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTT-SCCCTTTC---EEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHH-cCCccceE---EEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            3456688999999999999999999999 99998775   4667788999999999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|++++...
T Consensus        87 l~V~~a~~~~   96 (98)
T 2cqp_A           87 VKLVLGSGPS   96 (98)
T ss_dssp             CEEEESSCSS
T ss_pred             EEEEEcCCCC
Confidence            9999998654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=2.3e-22  Score=115.02  Aligned_cols=84  Identities=19%  Similarity=0.360  Sum_probs=75.8

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ...++.++|||+|||+++++++|+++|++ ||.|..++   .+.+..++.+++||||+|.+.++|.+|+..|||..++|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~v~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   86 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSK-YGKVVKVT---IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGR   86 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTT-TSCEEEEE---ECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHh-cCCeEEEE---EEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            33467789999999999999999999999 99998876   344666788999999999999999999999999999999


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      .|.|++|+
T Consensus        87 ~l~v~~ak   94 (94)
T 2e5h_A           87 VIKASIAI   94 (94)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEecC
Confidence            99999986

>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=99.88  E-value=4e-22  Score=117.22  Aligned_cols=88  Identities=20%  Similarity=0.333  Sum_probs=79.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC------Ccc
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN------GYV   94 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------g~~   94 (114)
                      ..+.++|||+|||+++++++|+.+|.+ ||.|..+++   +.+..++..+|||||+|.+.++|.+|+..||      |..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQ-FGDLKYVRV---VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHh-cCCeEEEEE---EecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            466789999999999999999999999 999988863   4566788999999999999999999999999      999


Q ss_pred             cCCceEEEEeccCCCCCC
Q 033648           95 FKGKPMIIQFGRNPAAAK  112 (114)
Q Consensus        95 ~~g~~l~v~~a~~~~~~~  112 (114)
                      ++|+.|.|++++++....
T Consensus        88 ~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SSSCEEEEECCCCCCCCC
T ss_pred             EcCEEEEEEECCCCccCC
Confidence            999999999999876553

>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=99.88  E-value=2.4e-22  Score=118.06  Aligned_cols=87  Identities=16%  Similarity=0.263  Sum_probs=78.6

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...++++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   97 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIH---LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   97 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---CCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            3466789999999999999999999999 99998876   3446678899999999999999999999999999999999


Q ss_pred             EEEEeccCCCC
Q 033648          100 MIIQFGRNPAA  110 (114)
Q Consensus       100 l~v~~a~~~~~  110 (114)
                      |.|++++++..
T Consensus        98 l~V~~a~~~~~  108 (110)
T 1oo0_B           98 IQVDWCFVKGP  108 (110)
T ss_dssp             CEEEESEESSC
T ss_pred             EEEEEcccCCC
Confidence            99999997764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.88  E-value=7.8e-22  Score=114.69  Aligned_cols=87  Identities=18%  Similarity=0.377  Sum_probs=78.1

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      .+..+.++|||+|||+++++++|+.+|++ || |..++   .+.+..++.++|||||+|.+.++|.+|+ .|||..+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~g-i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   83 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKD-LS-IRSVR---LVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDR   83 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTT-SC-EEEEE---EEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHh-CC-ceEEE---EeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCe
Confidence            44567889999999999999999999999 97 88776   4567778999999999999999999999 9999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|+++++....
T Consensus        84 ~l~V~~a~~~~~~   96 (103)
T 2dng_A           84 SLRVDIAEGRKQD   96 (103)
T ss_dssp             ECEEEECCCCCCC
T ss_pred             EEEEEEecCCCCC
Confidence            9999999977654

>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=99.88  E-value=4.5e-22  Score=116.17  Aligned_cols=88  Identities=20%  Similarity=0.299  Sum_probs=78.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc---C
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF---K   96 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~---~   96 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..++   .+.+..++.++|||||+|.+.++|.+|+..|||..+   .
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   84 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEE-FGKIYELT---VLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGM   84 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHH-HSCCCEEE---CCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCC
Confidence            3466789999999999999999999999 99998886   344667899999999999999999999999999997   8


Q ss_pred             CceEEEEeccCCCCC
Q 033648           97 GKPMIIQFGRNPAAA  111 (114)
Q Consensus        97 g~~l~v~~a~~~~~~  111 (114)
                      |+.|.|.+++++...
T Consensus        85 g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           85 NRPIQVKPADSESRG   99 (106)
T ss_dssp             SSCCEEEECCCCSCC
T ss_pred             CceEEEEECCccccc
Confidence            999999999987654

>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=99.88  E-value=2.8e-22  Score=120.36  Aligned_cols=90  Identities=16%  Similarity=0.300  Sum_probs=79.7

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .....+.++|||+|||+.+++++|+.+|++ ||.|..+.+   +.+..++.++|||||+|.+.++|++|+..|||..++|
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   91 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIHL---NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   91 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---CBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            344566789999999999999999999999 999988763   4466688999999999999999999999999999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      +.|.|++|++....
T Consensus        92 ~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           92 QPISVDWCFVRGPP  105 (126)
T ss_dssp             SBCEEEESEESSSC
T ss_pred             eEEEEEEecCCCCC
Confidence            99999999876544

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.88  E-value=1.1e-21  Score=111.73  Aligned_cols=87  Identities=24%  Similarity=0.381  Sum_probs=77.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +..+.++|||+|||+++++++|+.+|++ ||.|..+++   +.  .++..++||||+|.+.++|++|+..|||..++|+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~v~~~~i---~~--~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~   77 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNE-CGHVLYADI---KM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE   77 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHT-TSCEEEEEE---EE--SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---Ec--cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3467889999999999999999999999 999988763   22  47889999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |.|+++++.....
T Consensus        78 l~v~~a~~~~~~~   90 (92)
T 2dgv_A           78 IDVRIDRNASGPS   90 (92)
T ss_dssp             CCCEECSCCSSCC
T ss_pred             EEEEEcCCCCCCC
Confidence            9999999877543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=6.6e-22  Score=116.70  Aligned_cols=87  Identities=22%  Similarity=0.382  Sum_probs=78.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCce--------ecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSID--------AAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~--------~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      ..+.++|||+|||+.+++++|+.+|.+ ||.|.        .++   .+.+..++..+|||||+|.+.++|.+|+..|||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~~~~~~~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQ-CGVVKMNKRTGQPMIH---IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTT-TSCBCBCSSSCCBSEE---CCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHh-cCCEeEccccCccCEE---EEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            466789999999999999999999999 99997        465   344667899999999999999999999999999


Q ss_pred             cccCCceEEEEeccCCCCC
Q 033648           93 YVFKGKPMIIQFGRNPAAA  111 (114)
Q Consensus        93 ~~~~g~~l~v~~a~~~~~~  111 (114)
                      ..+.|+.|.|+++++....
T Consensus        88 ~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CEETTEECEEECSSCCCCS
T ss_pred             CccCCCEEEEEECCCCCCC
Confidence            9999999999999987654

>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=99.87  E-value=4e-22  Score=120.49  Aligned_cols=88  Identities=28%  Similarity=0.377  Sum_probs=79.6

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+++|++ ||.|..++   .+.+..++..+|||||+|.+.++|++|+..|||..++|+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~I~~v~---i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVS---IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTT-TSCEEEEE---EECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34567789999999999999999999999 99998886   455667889999999999999999999999999999999


Q ss_pred             eEEEEeccCCCC
Q 033648           99 PMIIQFGRNPAA  110 (114)
Q Consensus        99 ~l~v~~a~~~~~  110 (114)
                      .|.|++++++..
T Consensus       117 ~l~V~~a~~~~p  128 (129)
T 2kxn_B          117 RIRVDFSITKRP  128 (129)
T ss_dssp             CCEESCCSSSSC
T ss_pred             EEEEEEecCCCC
Confidence            999999988653

>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=99.87  E-value=5.9e-22  Score=113.53  Aligned_cols=83  Identities=19%  Similarity=0.225  Sum_probs=73.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+++++++|+.+|.+ ||.|..+.   .+.+..++..+|||||+|.+.++|++|+..|||..++|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~---~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l   87 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYG-YQVIPGSV---CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTT-SCBCTTCC---EEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCccceE---EEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            345689999999999999999999999 99998776   46677889999999999999999999999999999999999


Q ss_pred             EEEeccC
Q 033648          101 IIQFGRN  107 (114)
Q Consensus       101 ~v~~a~~  107 (114)
                      .|+++++
T Consensus        88 ~v~~a~s   94 (95)
T 2ek1_A           88 KLSGPSS   94 (95)
T ss_dssp             EEECCC-
T ss_pred             EEEeccC
Confidence            9999864

>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=99.87  E-value=1.2e-21  Score=114.47  Aligned_cols=84  Identities=29%  Similarity=0.358  Sum_probs=75.4

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|.+ ||.|..++   .+.+. +|..+|||||+|.+.++|.+|+..|||..++|+
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   98 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAE-FGTLKKAA---VHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR   98 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            33466789999999999999999999999 99998876   34444 899999999999999999999999999999999


Q ss_pred             eEEEEeccC
Q 033648           99 PMIIQFGRN  107 (114)
Q Consensus        99 ~l~v~~a~~  107 (114)
                      .|.|++|++
T Consensus        99 ~l~V~~a~s  107 (107)
T 3ulh_A           99 PMNIQLVTS  107 (107)
T ss_dssp             ECEEEEECC
T ss_pred             EEEEEEeCC
Confidence            999999863

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.87  E-value=1.1e-21  Score=118.27  Aligned_cols=85  Identities=25%  Similarity=0.467  Sum_probs=74.5

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHH----HHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFF----FVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV   94 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~----~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   94 (114)
                      ...+|+++|||+|||+.+++++|+    .+|++ ||.|..+.      ...++.++|||||+|.+.++|..|+..|||..
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~-~G~I~~v~------i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~   96 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASS-QGDILDIV------VDLSDDNSGKAYIVFATQESAQAFVEAFQGYP   96 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHH-HSCEEEEE------ECCCCSSCCCEEEEESSHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhcc-CCCeEEEE------eccCCCcCCEEEEEECCHHHHHHHHHHHCCCE
Confidence            345678999999999999998865    68999 99997653      23478899999999999999999999999999


Q ss_pred             cCCceEEEEeccCCCC
Q 033648           95 FKGKPMIIQFGRNPAA  110 (114)
Q Consensus        95 ~~g~~l~v~~a~~~~~  110 (114)
                      +.|++|.|.+|++++.
T Consensus        97 l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           97 FQGNPLVITFSETPQS  112 (127)
T ss_dssp             CTTSCCEEEECCCCCH
T ss_pred             eCCCEEEEEEccCcch
Confidence            9999999999997653

>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=99.87  E-value=7.7e-22  Score=111.46  Aligned_cols=85  Identities=20%  Similarity=0.304  Sum_probs=74.7

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCC-ceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGR-MRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ...++|||+|||.++++++|+.+|++ ||.|..+.+   +.+..++. .+|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~i---~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   77 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFST-YGKIKMIDM---PVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI   77 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEEE---EeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEE
Confidence            34678999999999999999999999 999988763   34554444 88999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|+++.+...
T Consensus        78 ~v~~a~~~~~   87 (88)
T 4a8x_A           78 TATAVLAPWP   87 (88)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987653

>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=99.87  E-value=1.1e-21  Score=116.44  Aligned_cols=85  Identities=26%  Similarity=0.417  Sum_probs=76.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||.++++++|+.+|++ ||.|..+.   .+.+. +|..+|||||+|.+.++|++|+..|||..+.|+.|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l   78 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGK-HGPISEVL---LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI   78 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHT-SSCCSEEE---EECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            356789999999999999999999999 99998875   23344 88999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|++|++...
T Consensus        79 ~V~~a~~~~~   88 (116)
T 2fy1_A           79 KVEQAKKPSF   88 (116)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEECCCCCC
Confidence            9999996653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.87  E-value=1.4e-22  Score=117.53  Aligned_cols=83  Identities=12%  Similarity=0.171  Sum_probs=75.9

Q ss_pred             CCCCeEEecCCCC------CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           22 NPASVLYIKNLAK------DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~------~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      ..+++|||+|||.      .+++++|+++|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..+
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~-~G~i~~v~---i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~   79 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSK-AGKVVNME---FPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL   79 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHT-TSCEEEEE---CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHh-cCCEeEEE---EEEcCCCCccceEEEEEECCHHHHHHHHHHhCCccc
Confidence            3467899999999      9999999999999 99999887   456778899999999999999999999999999999


Q ss_pred             CC-ceEEEEeccCC
Q 033648           96 KG-KPMIIQFGRNP  108 (114)
Q Consensus        96 ~g-~~l~v~~a~~~  108 (114)
                      .| +.|.|.+|.+.
T Consensus        80 ~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           80 DLKHRLFLYTMKDV   93 (100)
T ss_dssp             SSSCBCEEEESHHH
T ss_pred             CCCeEEEEEECchh
Confidence            99 99999999753

>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=99.87  E-value=9.4e-22  Score=114.53  Aligned_cols=87  Identities=17%  Similarity=0.281  Sum_probs=77.1

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccC-CCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE-GRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .+..+.++|||+|||+.+++++|+.+|.+ || |..+.+   +.+..+ +.++|||||+|.+.++|++|+ .|||..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G-i~~v~i---~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   83 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRG-LN-ISAVRL---PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN   83 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTT-SC-EEEEEC---CBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHH-CC-ceEEEE---ecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC
Confidence            34467789999999999999999999999 99 888763   345555 889999999999999999999 999999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      +.|.|++++++...
T Consensus        84 ~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           84 KRIRVDVADQAQDK   97 (104)
T ss_dssp             EECEEEECCCCCCC
T ss_pred             cEEEEEEccCCCCC
Confidence            99999999987654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.87  E-value=8.3e-22  Score=113.95  Aligned_cols=83  Identities=23%  Similarity=0.331  Sum_probs=72.0

Q ss_pred             cCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc--
Q 033648           17 NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV--   94 (114)
Q Consensus        17 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~--   94 (114)
                      .....+|+.+|||+|||+.+++++|+.+|++ ||.|..+.+   +      +.+|+|||+|.+.++|.+|+..|+|..  
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~-fG~V~~v~i---~------~~kg~AFVef~~~~~A~~Av~~ln~~~~~   83 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEADLVEALQE-FGPISYVVV---M------PKKRQALVEFEDVLGACNAVNYAADNQIY   83 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHHHHHHHGG-GSCEEEEEE---E------TTTTEEEEEESSHHHHHHHHHHHHHSCEE
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHHHHHHHhc-cCCEEEEEE---E------cCCCEEEEEECCHHHHHHHHHHhcCCCce
Confidence            4455688999999999999999999999999 999987752   1      257899999999999999999999976  


Q ss_pred             cCCceEEEEeccCCC
Q 033648           95 FKGKPMIIQFGRNPA  109 (114)
Q Consensus        95 ~~g~~l~v~~a~~~~  109 (114)
                      +.|++|.|+||+++.
T Consensus        84 i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           84 IAGHPAFVNYSTSQK   98 (100)
T ss_dssp             ETTEEEEEEECSCSC
T ss_pred             eCCcEEEEEeccccc
Confidence            789999999999865

>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=99.87  E-value=1.2e-21  Score=112.64  Aligned_cols=84  Identities=12%  Similarity=0.208  Sum_probs=73.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHH----HHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFF----FVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~----~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ..+.++|||+|||+++++++|+    .+|++ ||.|..+++   +.+..+   ++||||+|.+.++|.+|+..|||..++
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~-~G~v~~v~i---~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~   78 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFAR-HGKVKSVEL---SPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIG   78 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHH-HSCEEEEEE---CSCCST---TCCEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccc-cCcEEEEEE---EeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            4567899999999999999999    99999 999988763   223333   789999999999999999999999999


Q ss_pred             CceEEEEeccCCCCC
Q 033648           97 GKPMIIQFGRNPAAA  111 (114)
Q Consensus        97 g~~l~v~~a~~~~~~  111 (114)
                      |+.|.|++|++....
T Consensus        79 gr~l~V~~a~~~~~~   93 (96)
T 2dgx_A           79 SKKILVSLATGASGP   93 (96)
T ss_dssp             TEEEEEEECCCSSCC
T ss_pred             CeEEEEEEcCCCCCC
Confidence            999999999877643

>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=99.87  E-value=2.9e-21  Score=112.20  Aligned_cols=87  Identities=24%  Similarity=0.357  Sum_probs=75.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.+  .+..++||||+|.+.++|.+|+..|||..+.|+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~i---~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   84 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQ-IGPCKSCKM---ITE--HTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKE   84 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHH-HSCEEEEEE---ECC--CCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHh-cCCEeEEEE---Eec--CCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCe
Confidence            3467789999999999999999999999 999988763   223  2336899999999999999999999999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |.|+++++....+
T Consensus        85 l~V~~a~~~~~~~   97 (103)
T 2cqi_A           85 VKVNWATTPSSQK   97 (103)
T ss_dssp             EEEEECCCTTCCC
T ss_pred             EEEEECCCCcccc
Confidence            9999999876554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=121.81  Aligned_cols=82  Identities=20%  Similarity=0.296  Sum_probs=74.7

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcC--CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFG--SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G--~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++|||+|||+++++++|+.+|++ ||  .|..++   .+.+..+|.++|||||+|.+.++|++|+..|||..++|+.|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~-~G~i~v~~v~---i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRS-IGVYDVVELK---FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHH-TTCCCEEEEE---EEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHH-HCCccEEEEE---EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEe
Confidence            4579999999999999999999999 99  888876   46677899999999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|.+|.+.
T Consensus       130 ~V~~a~~~  137 (156)
T 3n9u_C          130 DVRPATRQ  137 (156)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99999753

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=6.3e-21  Score=112.58  Aligned_cols=86  Identities=27%  Similarity=0.389  Sum_probs=76.5

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ....++.++|||+|||+.+++++|+++|.+ ||.|..++   .+.+ .++..++||||+|.+.++|++|+..|||..++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~-~G~i~~~~---i~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   83 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSM-AGVVVRAD---ILED-KDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD   83 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---EEEC-TTCSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEEC-CCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            345577899999999999999999999999 99998875   2333 468899999999999999999999999999999


Q ss_pred             ceEEEEeccCC
Q 033648           98 KPMIIQFGRNP  108 (114)
Q Consensus        98 ~~l~v~~a~~~  108 (114)
                      +.|.|++++..
T Consensus        84 ~~l~v~~a~~~   94 (114)
T 2do0_A           84 RPMHVKMDERA   94 (114)
T ss_dssp             EECEEEECSCC
T ss_pred             CEEEEEEcccC
Confidence            99999999854

>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=99.87  E-value=1.8e-21  Score=113.17  Aligned_cols=84  Identities=17%  Similarity=0.354  Sum_probs=76.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+.+++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~-~G~i~~~~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSE-VGPVVSFR---LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHT-TSCCSEEE---EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHh-cCCeeEEE---EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            34578999999999999999999999 99998886   455667899999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |++|++..
T Consensus        82 v~~a~~~~   89 (104)
T 1p1t_A           82 VDNAASEK   89 (104)
T ss_dssp             EEETTCTT
T ss_pred             EEeCCCcc
Confidence            99999765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=4.7e-21  Score=109.05  Aligned_cols=85  Identities=18%  Similarity=0.276  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+++|++ | .|..++   .+.+ .+|.++|||||+|.+.++|.+|+. |||..++|+
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~-~-~i~~v~---i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr   77 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAP-L-KPVAIR---IVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR   77 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTT-S-CCSEEE---EEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhh-C-CceEEE---EEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCc
Confidence            34566789999999999999999999999 9 787775   3444 788999999999999999999999 999999999


Q ss_pred             eEEEEeccCCCC
Q 033648           99 PMIIQFGRNPAA  110 (114)
Q Consensus        99 ~l~v~~a~~~~~  110 (114)
                      .|.|.+|++...
T Consensus        78 ~i~v~~a~~~~~   89 (91)
T 2dgw_A           78 YIEVFREKSGPS   89 (91)
T ss_dssp             EEEEEEESSCCC
T ss_pred             EEEEEECCcCCC
Confidence            999999988754

>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=99.87  E-value=1.5e-21  Score=111.78  Aligned_cols=83  Identities=23%  Similarity=0.361  Sum_probs=74.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+++|++ ||.|..++   .+.+. ++..+|||||+|.+.++|.+|+..|||..++|+.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~-~G~i~~v~---i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQ-AGPLTKVT---ICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP   86 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---EEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHh-cCCEEEEE---EEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCE
Confidence            3456789999999999999999999999 99998875   23333 5889999999999999999999999999999999


Q ss_pred             EEEEeccC
Q 033648          100 MIIQFGRN  107 (114)
Q Consensus       100 l~v~~a~~  107 (114)
                      |.|++|+.
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999875

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.87  E-value=4.5e-22  Score=118.25  Aligned_cols=82  Identities=24%  Similarity=0.378  Sum_probs=74.1

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+++++++|+++|++ ||.|..++   .+.+..+|..+|||||+|.+.++|++|+..|||..++|+.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLP-FGNVISAK---VFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTT-SCEEEEEE---ECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            455689999999999999999999999 99998876   34466788999999999999999999999999999999999


Q ss_pred             EEEecc
Q 033648          101 IIQFGR  106 (114)
Q Consensus       101 ~v~~a~  106 (114)
                      +|++++
T Consensus       113 ~V~~ak  118 (118)
T 2khc_A          113 KVQLKK  118 (118)
T ss_dssp             CEEEC-
T ss_pred             EEEecC
Confidence            999985

>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=99.86  E-value=4.9e-21  Score=111.24  Aligned_cols=88  Identities=22%  Similarity=0.277  Sum_probs=76.2

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .....+.++|||+|||+++++++|+.+|++ ||.|..+++   +.+.  +..++||||+|.+.++|.+|+..|||..++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~v~~v~i---~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQ-FGKILDVEI---IFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEG   82 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGG-TSCEEEEEE---ECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            344567799999999999999999999999 999988763   2222  3378999999999999999999999999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      +.|.|+++++....
T Consensus        83 ~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           83 RKIEVNNATARVMT   96 (103)
T ss_dssp             EECEEEECCSSCCC
T ss_pred             EEEEEEEcccCCCC
Confidence            99999999977654

>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=99.86  E-value=2.6e-21  Score=120.10  Aligned_cols=87  Identities=24%  Similarity=0.345  Sum_probs=78.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+.+|++ ||.|..+++   +.+..+|.++|||||+|.+.++|.+|+..|||..++|++|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~-~G~v~~~~i---~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  142 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVYI---PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  142 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHH-HSCEEEEEC---CCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---eecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            355789999999999999999999999 999988863   4466789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|++|++....
T Consensus       143 ~v~~a~~~~~~  153 (158)
T 2kn4_A          143 RVQMARYGRPP  153 (158)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEECCCCCCC
Confidence            99999977544

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=4.4e-21  Score=111.20  Aligned_cols=85  Identities=21%  Similarity=0.325  Sum_probs=75.6

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+++|+. |+.+.      .+.+..++.+++||||+|.+.++|.+|+..|||..+.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~~~~~------~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDG-SVRAR------IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTT-CSEEE------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcC-CeEEE------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            3567789999999999999999999998 86442      4556678999999999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|++|+++...
T Consensus        84 l~V~~a~~~~~~   95 (102)
T 2fc8_A           84 VTLDWAKPKGEG   95 (102)
T ss_dssp             CEEEECCCCCSS
T ss_pred             EEEEEecCCCCC
Confidence            999999987654

>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=99.86  E-value=5.6e-21  Score=118.54  Aligned_cols=85  Identities=18%  Similarity=0.235  Sum_probs=78.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||..+++++|+.+|++ ||.|..+.   .+.+..++..++||||+|.+.++|++|+..|||..+.|+.|.
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  112 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSK-SGDIKKII---MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR  112 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            46789999999999999999999999 99998886   456777899999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |++|++...
T Consensus       113 V~~a~~~~~  121 (156)
T 1h2v_Z          113 TDWDAGFKE  121 (156)
T ss_dssp             EEEESCCCT
T ss_pred             EEECCCCCC
Confidence            999987654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=3e-21  Score=112.31  Aligned_cols=88  Identities=25%  Similarity=0.364  Sum_probs=77.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc-cCCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV-FKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~-~~g~   98 (114)
                      ...+.++|||+|||+++++++|+.+|++.||.|..++   .+.+. +|.++|||||+|.+.++|.+|+..|||.. ++|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~---i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK---VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEE---EEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEE---EEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            3467789999999999999999999986599998886   34455 89999999999999999999999999999 9999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|+++++....
T Consensus        81 ~l~v~~a~~~~~~   93 (104)
T 2dhg_A           81 PVRLSVAIPKASR   93 (104)
T ss_dssp             CCCCCBCCCCCSC
T ss_pred             eEEEEEccCCCcC
Confidence            9999999876543

>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=99.86  E-value=2.6e-21  Score=109.52  Aligned_cols=81  Identities=20%  Similarity=0.360  Sum_probs=74.4

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+++|++ ||.|..++   .+.+..++.++|||||+|.+.++|++|+ .|||..+.|+.|.|+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~   80 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHG-CGSVNRVT---ILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVI   80 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGG-GCCEEEEE---EEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEE---EEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEE
Confidence            478999999999999999999999 99998886   4556678999999999999999999999 999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      ++++..
T Consensus        81 ~a~~~~   86 (89)
T 3ucg_A           81 PKRTNR   86 (89)
T ss_dssp             ETTTTS
T ss_pred             EccCCC
Confidence            998754

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.86  E-value=4.2e-21  Score=115.03  Aligned_cols=86  Identities=27%  Similarity=0.317  Sum_probs=77.1

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++++|||+|||+.+++++|+.+|++ ||.|..++   .+.+. +|..+|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~v~---i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  106 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAA---VDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  106 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHT-TSCCSEEE---EECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            456789999999999999999999999 99998876   33444 88899999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|++|.+....
T Consensus       107 ~V~~a~~~~~~  117 (124)
T 2kt5_A          107 DIQLVASQIDL  117 (124)
T ss_dssp             EEEEECCTTCC
T ss_pred             EEEEeCCCCCC
Confidence            99999976544

>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=99.86  E-value=1.9e-21  Score=113.99  Aligned_cols=88  Identities=14%  Similarity=0.136  Sum_probs=76.6

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCC-ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC--CcccC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGS-IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN--GYVFK   96 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~-i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~~   96 (114)
                      ...+.++|||+|||+++++++|+.+|.+ ||. |..+.+.  ..+..+|..+|||||+|.+.++|.+|+..||  +..++
T Consensus         4 ~s~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~~v~~v~i~--~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~   80 (109)
T 2dis_A            4 GSSGNCRLFIGGIPKMKKREEILEEIAK-VTEGVLDVIVY--ASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW   80 (109)
T ss_dssp             CCCCSEEEEEECCCTTSCHHHHHHHHHH-HSTTEEEEECC--SSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT
T ss_pred             cccCCCEEEEeCCCCcCCHHHHHHHHHH-hcCCceEEEEE--ccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec
Confidence            3466789999999999999999999999 998 8877531  1456678899999999999999999999996  58999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |+.|.|.+|+++..
T Consensus        81 g~~l~V~~a~~~~~   94 (109)
T 2dis_A           81 GHQIAVDWAEPEID   94 (109)
T ss_dssp             TBCCEEEESCSSCS
T ss_pred             CCeEEEEEcCCCCC
Confidence            99999999997754

>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=99.86  E-value=1.2e-20  Score=110.74  Aligned_cols=85  Identities=27%  Similarity=0.370  Sum_probs=75.5

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|.+ ||.|..+++      ..++.+++||||+|.+.++|++|+..|||..++|+.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~~~i------~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   90 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYK-YGAIRDIDL------KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR   90 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGG-GSCEEEEEE------CCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE------EECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            3466789999999999999999999999 999987652      335667899999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|+++++....
T Consensus        91 l~V~~a~~~~~~  102 (109)
T 1x4a_A           91 LRVEFPRSGRGT  102 (109)
T ss_dssp             CEEECCCCCCCC
T ss_pred             EEEEEcccCCCC
Confidence            999999987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.86  E-value=9.5e-22  Score=118.97  Aligned_cols=84  Identities=18%  Similarity=0.391  Sum_probs=76.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCcee--cccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc----c
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDA--AKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY----V   94 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~--~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~----~   94 (114)
                      ..+.++|||+|||+++++++|+++|.+ ||.|..  ++   .++++.+|.++|||||+|.+. +|.+|+..|||.    .
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~-~G~v~~~~v~---i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAP-YAVLSSSNVR---VIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGG-GCCCCTTTEE---CCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCcceeeEE---EEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            466789999999999999999999999 999976  65   355777999999999999999 999999999999    9


Q ss_pred             cCCceEEEEeccCCC
Q 033648           95 FKGKPMIIQFGRNPA  109 (114)
Q Consensus        95 ~~g~~l~v~~a~~~~  109 (114)
                      ++|+.|.|++|++..
T Consensus        95 ~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           95 IDGKTINVEFAKGSK  109 (131)
T ss_dssp             GGGCCCCCEECCCSC
T ss_pred             CCCEEEEEEECCCCC
Confidence            999999999998763

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.2e-21  Score=113.11  Aligned_cols=88  Identities=15%  Similarity=0.210  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|.+ ||.|..++   .+.+..++.++|||||+|.+.++|.+|+.. ||..++|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   85 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQ-YGEVVDCV---IMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGR   85 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHT-TSCEEEEE---EEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCE
Confidence            33567789999999999999999999999 99998886   455677899999999999999999999998 99999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|+++++....
T Consensus        86 ~l~V~~a~~~~~~   98 (105)
T 2dh8_A           86 NIDPKPCTPRGMQ   98 (105)
T ss_dssp             EEBCCCSCCSSCC
T ss_pred             EEEEEEccCCCCC
Confidence            9999999977654

>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=99.86  E-value=3.9e-21  Score=120.35  Aligned_cols=87  Identities=16%  Similarity=0.264  Sum_probs=77.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIH---LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhc-CCCEEEEE---EEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            455678999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|.+|++....
T Consensus       145 ~V~~a~~~~~~  155 (165)
T 1rk8_A          145 QVDWCFVKGPK  155 (165)
T ss_dssp             EEEESEECC--
T ss_pred             EEEEecCCCCC
Confidence            99999876543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-21  Score=114.40  Aligned_cols=82  Identities=27%  Similarity=0.437  Sum_probs=71.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC--cccCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG--YVFKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~g   97 (114)
                      ..++.++|||+|||+.+++++|+.+|++ ||.|..+.+   +.      .+|||||+|.+.++|..|+..|++  ..+.|
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~-fG~V~~v~i---~~------~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G   81 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTNLLM---LK------GKNQAFIEMNTEEAANTMVNYYTSVTPVLRG   81 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHH-HCCEEEEEE---ET------TTTEEEEEESSHHHHHHHHHHHTTSCCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---Ec------CCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            3567899999999999999999999999 999988753   11      379999999999999999998874  68999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      ++|.|++|+++...
T Consensus        82 r~l~V~~A~~~~~~   95 (105)
T 1sjq_A           82 QPIYIQFSNHKELK   95 (105)
T ss_dssp             EECCBCCCSSSSCC
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=4e-21  Score=111.25  Aligned_cols=85  Identities=25%  Similarity=0.342  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+.+|.+ ||.|.      .+.+ .++..+|||||+|.+.++|++|+..|||..+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~g~v~------~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   81 (101)
T 2fc9_A           10 TWSGESKTLVLSNLSYSATEETLQEVFEK-ATFIK------VPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR   81 (101)
T ss_dssp             CCSCCCSEEEEESCCTTCCHHHHHHHCSS-CSEEE------CCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCEEE------EEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCe
Confidence            34567899999999999999999999999 99873      1222 6788999999999999999999999999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++++++...
T Consensus        82 ~l~v~~a~~~~~~   94 (101)
T 2fc9_A           82 AIRLELQGPRGSP   94 (101)
T ss_dssp             EEEEEECSSCCCC
T ss_pred             EEEEEEcCCCCCC
Confidence            9999999977654

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.86  E-value=5.8e-21  Score=107.75  Aligned_cols=81  Identities=20%  Similarity=0.291  Sum_probs=73.0

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+. +++..++|+.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~   81 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTK-FGEVVDCT---IKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRV   81 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTT-TSCEEEEE---EEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEE---EeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEE
Confidence            3467789999999999999999999999 99999886   45677789999999999999999999995 5888999999


Q ss_pred             EEEEec
Q 033648          100 MIIQFG  105 (114)
Q Consensus       100 l~v~~a  105 (114)
                      |.|++|
T Consensus        82 i~v~~A   87 (87)
T 3s7r_A           82 IDPKKA   87 (87)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999976

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.1e-21  Score=114.30  Aligned_cols=85  Identities=22%  Similarity=0.330  Sum_probs=76.1

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+.+|.+ ||.|..++   .+.+..++.+++||||+|.+.++|++|+..+++ .+.|+.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEG-FGDIEEAV---VITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHT-TSCEEEEE---ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCeeEEE---EEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            3466789999999999999999999999 99998886   344667889999999999999999999999998 899999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|++|+...
T Consensus        88 l~V~~a~~~~   97 (116)
T 2cqd_A           88 ANVNLAYLGA   97 (116)
T ss_dssp             CEEEESTTTC
T ss_pred             EEEEEcccCC
Confidence            9999997653

>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=99.86  E-value=1.4e-20  Score=111.16  Aligned_cols=84  Identities=21%  Similarity=0.398  Sum_probs=75.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc-----
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF-----   95 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-----   95 (114)
                      ..+.++|||+|||+++++++|+.+|.+ ||.|..++   .+.+. ++.++|||||+|.+.++|.+|+..|||..+     
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~---i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~   96 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKP-FGQVISTR---ILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   96 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTT-TSCEEEEE---EEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcc
Confidence            456789999999999999999999999 99998886   34454 889999999999999999999999999999     


Q ss_pred             ---CCceEEEEeccCCC
Q 033648           96 ---KGKPMIIQFGRNPA  109 (114)
Q Consensus        96 ---~g~~l~v~~a~~~~  109 (114)
                         .+++|.|.||++.+
T Consensus        97 ~~~~~~~l~v~~a~p~~  113 (114)
T 1x5o_A           97 VSAPTEPLLCKFSGPSS  113 (114)
T ss_dssp             SCCCSSCBEEEECCCSC
T ss_pred             ccCCCCceeEEccCCCC
Confidence               68889999999653

>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=99.86  E-value=2.5e-20  Score=108.26  Aligned_cols=85  Identities=18%  Similarity=0.266  Sum_probs=76.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|.+ ||.|..+.   .+.+..++.++|||||+|.+.++|.+|+.  ++..++|+.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l   85 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFST-FGEVLMVQ---VKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWC   85 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGG-GSCEEEEE---EEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEE
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHh-cCCeEEEE---EEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEE
Confidence            466789999999999999999999999 99998886   45667789999999999999999999998  5788999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|++++++...
T Consensus        86 ~v~~a~~~~~~   96 (103)
T 2cqg_A           86 DCKLPNSKQSQ   96 (103)
T ss_dssp             EEECCCTTCCC
T ss_pred             EEEecCCCCcC
Confidence            99999987654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-21  Score=113.58  Aligned_cols=85  Identities=18%  Similarity=0.225  Sum_probs=75.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+.+|++ ||.+.. .   .+.+..+|.++|||||+|.+.++|.+|+. |||..+.|+.|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~-~---~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l   87 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISE-LFAKND-L---AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEI   87 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHH-HHHHHT-C---CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCcce-E---EEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEE
Confidence            456789999999999999999999999 998876 3   34466678899999999999999999998 99999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|.+|+++...
T Consensus        88 ~V~~a~~~~~~   98 (101)
T 1fj7_A           88 KLEKPKGRDGT   98 (101)
T ss_dssp             EEECCSCCCCS
T ss_pred             EEEEcCCCCCC
Confidence            99999987643

>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=99.85  E-value=6.6e-21  Score=113.47  Aligned_cols=84  Identities=26%  Similarity=0.428  Sum_probs=73.0

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC--ccc
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG--YVF   95 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~   95 (114)
                      ....+|+++|||+|||+++++++|+.+|++ ||.|..+.+   +      ..+|||||+|.+.++|.+|+..|++  ..+
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~-fG~V~~v~i---~------~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l   94 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTNLLM---L------KGKNQAFIEMNTEEAANTMVNYYTSVTPVL   94 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTT-TSCCCEEEE---E------GGGTEEEEECSCHHHHHHHHHHHHHHCCCB
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---e------CCCCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            344577899999999999999999999999 999988753   1      1379999999999999999999985  679


Q ss_pred             CCceEEEEeccCCCCC
Q 033648           96 KGKPMIIQFGRNPAAA  111 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~~  111 (114)
                      .|++|.|++|+++...
T Consensus        95 ~Gr~l~V~~a~~k~~~  110 (119)
T 2ad9_A           95 RGQPIYIQFSNHKELK  110 (119)
T ss_dssp             TTBCCEEEECSSSSCC
T ss_pred             CCeEEEEEEccCCCCC
Confidence            9999999999987654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.85  E-value=3.9e-21  Score=113.32  Aligned_cols=84  Identities=19%  Similarity=0.249  Sum_probs=70.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      .+..++|||+|||+++++++|+++|++ || .|..+.+       ..+.++|||||+|.+.++|++|+..|||..++|+.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~-~G~~v~~v~i-------~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~   96 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARE-NSLETTFSSV-------NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSV   96 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHH-HTCCCSEEEC-------SSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHH-hCCeeEEEEE-------EcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            355689999999999999999999999 99 7876642       12357899999999999999999999999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |.|++++.....+
T Consensus        97 i~V~~a~~~p~~r  109 (111)
T 2jvr_A           97 ITVERDDNPPPIR  109 (111)
T ss_dssp             EEEEESCC-----
T ss_pred             EEEEECCCCCCCC
Confidence            9999998765443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.9e-22  Score=112.17  Aligned_cols=82  Identities=20%  Similarity=0.255  Sum_probs=74.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++++|||+|||+++++++|+.+|++ ||.|..++   .+.++.++.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   77 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQP-YGKIVSTK---AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   77 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTT-TSCEEEEE---EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEE---EEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEE
Confidence            467889999999999999999999999 99998886   45566789999999999999999999999999999999999


Q ss_pred             EEEecc
Q 033648          101 IIQFGR  106 (114)
Q Consensus       101 ~v~~a~  106 (114)
                      +++++.
T Consensus        78 ~~~~~~   83 (85)
T 1x4e_A           78 KQSGPS   83 (85)
T ss_dssp             CSSCCC
T ss_pred             eecCCC
Confidence            887654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=6.6e-21  Score=108.25  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=72.3

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..+.+    .       ++||||+|.+.++|++|+..|||..++|+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~~----~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   71 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQ-YGKVLECDI----I-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN   71 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHT-SSCEEEEEE----E-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEEE----E-------CCEEEEEECCHHHHHHHHHHhcCCccCCcE
Confidence            3467889999999999999999999999 999987752    1       689999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|+++++....
T Consensus        72 l~v~~a~~~~~~   83 (90)
T 2dnq_A           72 INVEASKNKSKA   83 (90)
T ss_dssp             CEEECSSCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999977654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.5e-21  Score=112.83  Aligned_cols=82  Identities=22%  Similarity=0.375  Sum_probs=72.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..+.   .+.+.. |.++|||||+|.+.++|.+|+. ++|..++|+.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~-~G~v~~v~---i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~   80 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLED-KGQVLNIQ---MRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETD   80 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHT-SSCEEEEE---EECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTT
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhh-cCCEEEEE---EEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            3456689999999999999999999999 99998886   344444 8899999999999999999998 9999999999


Q ss_pred             EEEEeccC
Q 033648          100 MIIQFGRN  107 (114)
Q Consensus       100 l~v~~a~~  107 (114)
                      |.|.+++.
T Consensus        81 l~V~~~~~   88 (103)
T 1s79_A           81 LLILFKDD   88 (103)
T ss_dssp             CEEEEHHH
T ss_pred             EEEEEchH
Confidence            99998764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.85  E-value=1.6e-21  Score=118.68  Aligned_cols=87  Identities=24%  Similarity=0.345  Sum_probs=77.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+++|++ ||.|..+++   +.+..++..+|||||+|.+.++|++|+..|||..+.|+.|
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~v~i---~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVYI---PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGG-GSCCSEEEC---CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE---EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            355689999999999999999999999 999988763   4456688999999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|+++++....
T Consensus       120 ~V~~a~~~~~~  130 (135)
T 2lea_A          120 RVQMARYGRPP  130 (135)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999977644

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.85  E-value=7.1e-22  Score=114.43  Aligned_cols=84  Identities=17%  Similarity=0.293  Sum_probs=72.1

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEec-cCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM-QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ...+.++|||+|||+++++++|+.+|++ || |..+++   +.+. .+|.++|||||+|.+.++|.+|+ .|||..++|+
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G-i~~v~i---~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRG-LN-ISAVRL---PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCS-SC-EEEEEC---SCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHh-cC-CeEEEE---EecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3466789999999999999999999999 99 988763   3344 47889999999999999999999 9999999999


Q ss_pred             eEEEEeccCCC
Q 033648           99 PMIIQFGRNPA  109 (114)
Q Consensus        99 ~l~v~~a~~~~  109 (114)
                      .|.|++|+++.
T Consensus        89 ~l~V~~a~~~~   99 (100)
T 2j76_E           89 RIRVDVADQAQ   99 (100)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEeccCCC
Confidence            99999998765

>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=99.85  E-value=5.9e-21  Score=114.45  Aligned_cols=85  Identities=13%  Similarity=0.185  Sum_probs=76.2

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      .+..+.++|||+|||+.+++++|+.+|.+ ||.|..+.   .+.+..+|..+|||||+|.+.++|.+|+. +||..++|+
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~v~~~~---~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   94 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKK-LDIVEDSI---YIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   94 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCS-SCBCTTTC---EEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCccceE---EEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            34456789999999999999999999999 99997754   46677899999999999999999999998 999999999


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .|.|.+|..+
T Consensus        95 ~i~V~~a~~~  104 (124)
T 1wel_A           95 FIQVHPITKK  104 (124)
T ss_dssp             CBEEEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999998753

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.85  E-value=1e-20  Score=113.27  Aligned_cols=83  Identities=22%  Similarity=0.342  Sum_probs=75.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||.++++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+ .|||..++|+.|.|+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~  110 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSS-CGSINRIT---ILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVL  110 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHT-TSCEEEEE---EEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEE
Confidence            478999999999999999999999 99998886   4556778999999999999999999999 899999999999999


Q ss_pred             eccCCCCC
Q 033648          104 FGRNPAAA  111 (114)
Q Consensus       104 ~a~~~~~~  111 (114)
                      ++++....
T Consensus       111 ~a~~~~~~  118 (124)
T 2jwn_A          111 PKRTNMPG  118 (124)
T ss_dssp             ESSCCCSS
T ss_pred             ECCCCCCC
Confidence            99976543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=3.9e-21  Score=112.99  Aligned_cols=88  Identities=19%  Similarity=0.262  Sum_probs=74.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..+ |..++|+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~i~~v~---i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~   94 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQ-FGEVKECL---VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSK   94 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---ECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHc-cCCeEEEE---EEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCE
Confidence            34566789999999999999999999999 99998886   3446667999999999999999999999876 5899999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|.++.++...
T Consensus        95 ~l~V~~a~~~~~~  107 (109)
T 2rs2_A           95 TIDPKVAFPRRAQ  107 (109)
T ss_dssp             EEEEEECCCCCCC
T ss_pred             EEEEEEccCCCCC
Confidence            9999999987754

>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=99.85  E-value=7.2e-21  Score=111.03  Aligned_cols=84  Identities=17%  Similarity=0.318  Sum_probs=72.0

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc--ccC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY--VFK   96 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~   96 (114)
                      ...+|+++|||+|||+.+++++|+.+|++ ||.|..+.+    .     ..+|||||+|.+.++|.+|+..|++.  .+.
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~-fG~V~~v~i----~-----~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~   79 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEK-FGTICYVMM----M-----PFKRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTT-TSCEEEEEE----E-----TTTTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEEE----E-----CCCCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            34577899999999999999999999999 999987642    1     13799999999999999999999765  499


Q ss_pred             CceEEEEeccCCCCCC
Q 033648           97 GKPMIIQFGRNPAAAK  112 (114)
Q Consensus        97 g~~l~v~~a~~~~~~~  112 (114)
                      |++|.|++++.+....
T Consensus        80 Gr~l~V~~a~~~~~~~   95 (104)
T 1wex_A           80 GQQAFFNYSTSKRITR   95 (104)
T ss_dssp             SSBCEEEECSSSSCCC
T ss_pred             CEEEEEEEccCccccC
Confidence            9999999999776543

>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=99.85  E-value=3.7e-21  Score=110.55  Aligned_cols=83  Identities=35%  Similarity=0.590  Sum_probs=74.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHH----HHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFF----FVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~----~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      .+++++|||+|||+++++++|+    .+|++ ||.|..+.+.      .+|..+|||||+|.+.++|..|+..|||..++
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~-~G~i~~v~i~------~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   77 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSR-FGQILDILVS------RSLKMRGQAFVIFKEVSSATNALRSMQGFPFY   77 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGG-GSCEEEEECC------HHHHHTTCEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHh-CCCEEEEEEE------cCCCcCcEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            4678999999999999999999    99999 9999876531      36778899999999999999999999999999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |+.|.|++++++..
T Consensus        78 g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           78 DKPMRIQYAKTDSD   91 (97)
T ss_dssp             TEECEEEECSSCCT
T ss_pred             CcEEEEEEccCCCc
Confidence            99999999998764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.2e-21  Score=116.06  Aligned_cols=85  Identities=16%  Similarity=0.243  Sum_probs=76.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+++++++|+.+|.+ ||.|..+.   .+.+..++..+|||||+|.+.++|.+|+.. +|..++|+.|.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~   99 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQ-WGKLTDCV---VMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVE   99 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTS-SCCCSEEE---EECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEE
Confidence            34589999999999999999999999 99998886   455667899999999999999999999988 99999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.+++++...
T Consensus       100 V~~a~~~~~~  109 (116)
T 1x4b_A          100 PKRAVAREES  109 (116)
T ss_dssp             EECCSSCCCC
T ss_pred             EEECCCCccC
Confidence            9999987654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.1e-20  Score=106.58  Aligned_cols=82  Identities=20%  Similarity=0.330  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+.+++++|+.+|++ ||.|..+.+           .++||||+|.+.++|.+|+..|||..+.|+
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~v~~-----------~~~~afV~f~~~~~a~~A~~~l~g~~~~g~   72 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEE-YGPVIECDI-----------VKDYAFVHMERAEDAVEAIRGLDNTEFQGK   72 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHT-TSCCCEEEE-----------CSSEEEEEESCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE-----------ECCEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            34567789999999999999999999999 999987752           144999999999999999999999999999


Q ss_pred             eEEEEeccCCCCCC
Q 033648           99 PMIIQFGRNPAAAK  112 (114)
Q Consensus        99 ~l~v~~a~~~~~~~  112 (114)
                      .|.|+++++.....
T Consensus        73 ~l~V~~a~~~~~~~   86 (92)
T 2dgt_A           73 RMHVQLSTSRLRTA   86 (92)
T ss_dssp             EEEEEESSCCCSCC
T ss_pred             EEEEEEccCCCCCC
Confidence            99999999876543

>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=99.85  E-value=1.2e-20  Score=108.72  Aligned_cols=80  Identities=23%  Similarity=0.355  Sum_probs=70.8

Q ss_pred             CCCCCCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           18 YTAGNPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ....+++++|||+|||+ ++++++|+.+|++ ||.|..+.+           .+|||||+|.+.++|.+|+..|||..++
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~-~G~v~~v~i-----------~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSP-YGHIMQINI-----------KNAFGFIQFDNPQSVRDAIEXESQEMNF   83 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGG-GSCEEEEEE-----------CSSEEEEEESSHHHHHHHHHHHTTSEET
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHh-cCCEEEEEE-----------eCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            44567889999999998 9999999999999 999987652           3799999999999999999999999999


Q ss_pred             CceEEEEeccCCC
Q 033648           97 GKPMIIQFGRNPA  109 (114)
Q Consensus        97 g~~l~v~~a~~~~  109 (114)
                      |+.|.|+++++..
T Consensus        84 g~~l~V~~a~~~~   96 (97)
T 2xnq_A           84 GKKLILEVSSSNA   96 (97)
T ss_dssp             TEECEEEECCCCC
T ss_pred             CEEEEEEecCCCC
Confidence            9999999998753

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.85  E-value=7.7e-21  Score=115.70  Aligned_cols=81  Identities=26%  Similarity=0.353  Sum_probs=73.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|++ ||.|..+++   +.++.++..+|||||+|.+.++|++|+..|||..++|+.|
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~v~i---~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGG-GSCEEEEEC---CCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHh-cCCEEEEEE---eecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            355689999999999999999999999 999988763   4466788999999999999999999999999999999999


Q ss_pred             EEEec
Q 033648          101 IIQFG  105 (114)
Q Consensus       101 ~v~~a  105 (114)
                      .|++|
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99986

>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=99.85  E-value=3.9e-21  Score=111.71  Aligned_cols=81  Identities=16%  Similarity=0.234  Sum_probs=70.4

Q ss_pred             CCCCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc--ccC
Q 033648           20 AGNPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY--VFK   96 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~   96 (114)
                      ...|+++|||+|||+ .+++++|+.+|++ ||.|..+.++         ..++||||+|.+.++|..|+..||+.  .+.
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~-fG~V~~v~i~---------~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEP-FGVISNHLIL---------NKINEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGG-GSCEEEEEEC---------SSSSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHh-cCCEEEEEEE---------cCCCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            346789999999999 9999999999999 9999887531         13589999999999999999999975  499


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |++|.|++|+....
T Consensus        81 Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           81 GKPVRVHLSQKYKR   94 (102)
T ss_dssp             TEECEEEEECCCTT
T ss_pred             CcEEEEEECCCCCC
Confidence            99999999996543

>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=99.85  E-value=3.4e-21  Score=113.50  Aligned_cols=85  Identities=21%  Similarity=0.328  Sum_probs=74.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHH---HHHhhhcCCceecccceeEEeccC---CCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           22 NPASVLYIKNLAKDVVPDDFF---FVFGSLFGSIDAAKSGLIVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~---~~f~~~~G~i~~~~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      .+.++|||+|||+++++++|+   ++|++ ||.|..+.+   +.+..+   +..+|||||+|.+.++|++|+..|||..+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~-~G~i~~v~i---~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGK-FGKIHKVVI---NNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTT-TSCEEEEEE---ECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhc-cCCEEEEEE---ecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            456899999999999999999   99999 999988863   334433   35669999999999999999999999999


Q ss_pred             CCceEEEEeccCCCC
Q 033648           96 KGKPMIIQFGRNPAA  110 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~  110 (114)
                      +|+.|.|++|+++..
T Consensus        89 ~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           89 DGRTLKASLGTTKYC  103 (111)
T ss_dssp             TTEEEEEESCCCCSC
T ss_pred             CCEEEEEEecccccc
Confidence            999999999998763

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.85  E-value=3.1e-21  Score=106.07  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=68.6

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      +|||+|||+++++++|+.+|++ ||.|..+.+   +.++.+|.++|||||+|.+.++|++|+. +||..++|++|.|++|
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 KIFVGGLSVNTTVEDVKHYFEQ-FGKVDDAML---MFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHT-TSCCSEECC---CBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHh-cCCEEEEEE---EecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            4899999999999999999999 999988863   4466688999999999999999999997 9999999999999976

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.84  E-value=8.5e-21  Score=111.39  Aligned_cols=82  Identities=27%  Similarity=0.490  Sum_probs=71.1

Q ss_pred             cCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           17 NYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        17 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ......+.++|||+|||+++++++|+.+|++ ||.|..+.+    .       +|||||+|.+.++|++|+..|||..++
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i~~v~i----~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~   91 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGP-FGPMKEVKI----L-------NGFAFVEFEEAESAAKAIEEVHGKSFA   91 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTT-TSCCCEEEE----E-------TTEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHh-cCCEEEEEE----E-------CCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            3444567899999999999999999999999 999987752    1       789999999999999999999999999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |+.|.|++++++..
T Consensus        92 g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           92 NQPLEVVYSKLPAK  105 (108)
T ss_dssp             TEECEEESCSCCC-
T ss_pred             CeEEEEEEecCCCC
Confidence            99999999998754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.84  E-value=8.8e-21  Score=106.68  Aligned_cols=74  Identities=18%  Similarity=0.178  Sum_probs=67.9

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .+.-|||+||++.+++++|+++|.+ ||.|..+++.         .++|||||+|.+.++|.+|++.|||..+.|++|.|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q-~G~V~~~~l~---------~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V   75 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQ-HGPLVSFHPY---------LNQGIALCKYTTREEANKAQMALNNCVLANTTIFA   75 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHH-HSCEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHh-hCCEEEEEEc---------CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            4667999999999999999999999 9999887631         26899999999999999999999999999999999


Q ss_pred             Eecc
Q 033648          103 QFGR  106 (114)
Q Consensus       103 ~~a~  106 (114)
                      .+|.
T Consensus        76 ~~A~   79 (89)
T 2wbr_A           76 ESPS   79 (89)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            9994

>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=99.84  E-value=2.5e-20  Score=107.19  Aligned_cols=83  Identities=19%  Similarity=0.387  Sum_probs=73.4

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-   96 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-   96 (114)
                      +...++.++|||+|||+++++++|+++|++ ||.|..+.+.       +  .++||||+|.+.++|++|+..|||..+. 
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~v~~~-------~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~   80 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDR-FGSIRTIDHV-------K--GDSFAYIQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHT-TSCEEEEEEC-------S--SSCCEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEe-------C--CCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            455677899999999999999999999999 9999876421       2  2789999999999999999999999999 


Q ss_pred             -CceEEEEeccCCCC
Q 033648           97 -GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 -g~~l~v~~a~~~~~  110 (114)
                       |+.|.|++|+++..
T Consensus        81 ~g~~l~V~~a~~~~~   95 (97)
T 1why_A           81 PDRRLRVDFAKSGPS   95 (97)
T ss_dssp             SSCBCEEEECCCCCC
T ss_pred             CCcEEEEEECCCCCC
Confidence             99999999998764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.2e-20  Score=110.88  Aligned_cols=84  Identities=24%  Similarity=0.284  Sum_probs=73.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||.++++++|+.+|++ ||.|..+++.   .+  .+..+|||||+|.+.++|++|+..|||..++|+.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i~---~~--~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~   98 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQ-FGKILDVEII---FN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRK   98 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGG-TCCCSCEEEC---CB--TTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHh-cCCEEEEEEE---EC--CCCCceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3466789999999999999999999999 9999887632   22  3457899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|++|+++.
T Consensus        99 l~V~~a~~~~  108 (109)
T 2err_A           99 IEVNNATARV  108 (109)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCc
Confidence            9999998763

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=4.6e-20  Score=106.13  Aligned_cols=82  Identities=20%  Similarity=0.351  Sum_probs=71.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      .....++|||+|||+++++++|+.+|++ ||.|. +.   .+    ++..+|||||+|.+.++|++|+..|||..++|+.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~-~G~v~-~~---~~----~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   85 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRE-LGSVP-LR---LT----WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDT   85 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHH-TTCCC-SE---EE----EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHh-cCCEE-EE---EE----cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3455789999999999999999999999 99985 43   22    2467899999999999999999999999999999


Q ss_pred             EEEEeccCCCC
Q 033648          100 MIIQFGRNPAA  110 (114)
Q Consensus       100 l~v~~a~~~~~  110 (114)
                      |.|++++++..
T Consensus        86 l~V~~a~~~~~   96 (97)
T 2e5j_A           86 LRVALARQQRD   96 (97)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEcCCCCC
Confidence            99999998753

>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=99.84  E-value=1e-21  Score=111.50  Aligned_cols=81  Identities=16%  Similarity=0.296  Sum_probs=70.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+++++++|+++|++ ||.|..++   .+.+..+|.++|||||+|.+.+ |.+|+..|||..++|+.|.|++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~   76 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQ-FGKVFNVK---LIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHH-HTCCSEEE---ECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHh-cCCEEEEE---EEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEE
Confidence            57999999999999999999999 99998876   3456667899999999999999 9999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      |.+...
T Consensus        77 a~~~~~   82 (90)
T 2ki2_A           77 ANPKKS   82 (90)
T ss_dssp             C-----
T ss_pred             cCCCCC
Confidence            987653

>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=99.84  E-value=1.5e-20  Score=110.24  Aligned_cols=82  Identities=22%  Similarity=0.333  Sum_probs=73.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||..+++++|+.+|++ ||.|..+++.   .      .++||||+|.+.++|.+|+..|||..++|+.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~-~G~i~~v~i~---~------~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   91 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSP-FGQIMEIRVF---P------EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   91 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHH-HSCEEEEEEE---T------TTTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEEe---C------CCCEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            456789999999999999999999999 9999877531   1      27999999999999999999999999999999


Q ss_pred             EEEeccCCCCCC
Q 033648          101 IIQFGRNPAAAK  112 (114)
Q Consensus       101 ~v~~a~~~~~~~  112 (114)
                      .|.+++++....
T Consensus        92 ~v~~a~~~~~~~  103 (109)
T 1x4g_A           92 KCYWGKESPDMT  103 (109)
T ss_dssp             EEECCCCCCSSC
T ss_pred             EEEecCCCCCCC
Confidence            999999876654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.84  E-value=1.3e-20  Score=110.02  Aligned_cols=82  Identities=18%  Similarity=0.314  Sum_probs=73.4

Q ss_pred             CCCCeEEecCCCCCC------CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           22 NPASVLYIKNLAKDV------VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~------~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      ..+++|||+|||+.+      ++++|+.+|++ ||.|..+.+.     ..+|.++|||||+|.+.++|.+|+..|||..+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~-~G~v~~v~i~-----~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~   86 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSK-FGKITNDFYP-----EEDGKTKGYIFLEYASPAHAVDAVKNADGYKL   86 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGG-GSCEEEEECC-----CBTTBSCCEEEEEECSSSHHHHHHHHCSSEEC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhc-CCCEEEEEee-----CCCCCeeeEEEEEECCHHHHHHHHHHhCCccc
Confidence            456899999999999      77999999999 9999887632     46889999999999999999999999999999


Q ss_pred             CCc-eEEEEeccCCC
Q 033648           96 KGK-PMIIQFGRNPA  109 (114)
Q Consensus        96 ~g~-~l~v~~a~~~~  109 (114)
                      +|+ +|.|.+|....
T Consensus        87 ~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           87 DKQHTFRVNLFTDFD  101 (105)
T ss_dssp             STTCEEEEECSCCCC
T ss_pred             CCCceEEEEEcchHh
Confidence            999 99999997543

>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=99.84  E-value=1.8e-20  Score=108.79  Aligned_cols=82  Identities=22%  Similarity=0.353  Sum_probs=71.3

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC--CcccCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN--GYVFKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~~g   97 (114)
                      ..+|+++|||+|||+.+++++|+.+|++ ||.|..+.+    .     ..+|||||+|.+.++|..|+..|+  +..+.|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~-fG~v~~v~i----~-----~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLP-FGKVTNILM----L-----KGKNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTT-TSCEEEEEE----E-----TTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE----E-----CCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            3467899999999999999999999999 999987642    1     127999999999999999999875  677999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      ++|.|++|+.+...
T Consensus        81 r~l~V~~a~~~~~~   94 (101)
T 2cq1_A           81 QPIYIQYSNHKELK   94 (101)
T ss_dssp             EECEEEECSCSSCC
T ss_pred             cEEEEEEcCcccCc
Confidence            99999999987655

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.84  E-value=1.2e-20  Score=108.20  Aligned_cols=83  Identities=24%  Similarity=0.346  Sum_probs=73.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..      +  ..++.++|||||+|.+.++|.+|+..|||..++|+.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~-~g~v~~------~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   82 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFED-ALEIRL------V--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCS-EEEECC------E--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhh-CCcEEE------e--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            3466789999999999999999999999 997742      2  457889999999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|++++++...
T Consensus        83 l~v~~a~~~~~~   94 (96)
T 1fjc_A           83 VSLYYTGEKGGT   94 (96)
T ss_dssp             EEEEECSSSCCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999877643

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=3.4e-20  Score=105.28  Aligned_cols=80  Identities=16%  Similarity=0.270  Sum_probs=71.4

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..+++           .++||||+|.+.++|.+|+..|||..++|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~~~~-----------~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   72 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFER-RGRVIECDV-----------VKDYAFVHMEKEADAKAAIAQLNGKEVKGKR   72 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHH-HSCEEEEEE-----------CSSCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHc-CCCEEEEEE-----------ECCEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3467789999999999999999999999 999987753           1449999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|+++++....
T Consensus        73 l~v~~a~~~~~~   84 (90)
T 2dnp_A           73 INVELSTKGQKK   84 (90)
T ss_dssp             CEEEESCCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999977543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6.6e-20  Score=105.78  Aligned_cols=81  Identities=25%  Similarity=0.432  Sum_probs=71.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhc--CCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLF--GSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~--G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ....+.++|||+|||+.+++++|+.+|++ |  |.|..+++           .++||||+|.+.++|.+|+..|||..++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~g~g~v~~~~~-----------~~g~afV~f~~~~~A~~A~~~l~g~~~~   77 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNN-IKPGAVERVKK-----------IRDYAFVHFSNREDAVEAMKALNGKVLD   77 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHT-TSTTCEEEEEE-----------CSSEEEEEESSHHHHHHHHHHHSSEEET
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHh-cCCcceEEEEE-----------eCCeEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            34467789999999999999999999999 9  77765531           3679999999999999999999999999


Q ss_pred             CceEEEEeccCCCCC
Q 033648           97 GKPMIIQFGRNPAAA  111 (114)
Q Consensus        97 g~~l~v~~a~~~~~~  111 (114)
                      |+.|.|++|++....
T Consensus        78 g~~l~v~~a~~~~~~   92 (99)
T 2cpd_A           78 GSPIEVTLAKPVDKD   92 (99)
T ss_dssp             TEEEEEECCCCCCCC
T ss_pred             CcEEEEEECCCCCCC
Confidence            999999999987643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=4.6e-21  Score=105.81  Aligned_cols=76  Identities=20%  Similarity=0.291  Sum_probs=69.8

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+++++++|+.+|++ ||.+..+.   .+.++.+|.++|||||+|.+.++|++|+..++ ..++|+.|.|++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~-~G~v~~v~---i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQ-FGEVKECL---VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTT-TSCCCCEE---EECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEE---EecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEe
Confidence            47999999999999999999999 99998876   35566788999999999999999999999999 999999999998


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      |
T Consensus        76 a   76 (77)
T 1uaw_A           76 A   76 (77)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=99.84  E-value=4.4e-20  Score=107.29  Aligned_cols=79  Identities=27%  Similarity=0.474  Sum_probs=71.1

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+.+|.+ ||.|..+++           .++||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~-~G~i~~v~~-----------~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   75 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQ-FGKLERVKK-----------LKDYAFIHFDERDGAVKAMEEMNGKDLEGENI   75 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHH-HSCEEEEEE-----------CSSCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEE-----------ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEE
Confidence            456789999999999999999999999 999987652           25699999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|+++++....
T Consensus        76 ~v~~a~~~~~~   86 (103)
T 2dgu_A           76 EIVFAKPPDQK   86 (103)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEcCCCccc
Confidence            99999977544

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.8e-20  Score=105.66  Aligned_cols=76  Identities=18%  Similarity=0.232  Sum_probs=67.1

Q ss_pred             CCCCe-EEecCCCCCCCHhH----HHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           22 NPASV-LYIKNLAKDVVPDD----FFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        22 ~~~~~-l~v~nlp~~~~~~~----l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      +|+.+ |||+|||..+++++    |+++|++ || .|..+          ++   |+|||.|.+.++|.+|++.|||..+
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~-yGG~Vl~V----------tg---G~AfV~F~~~esA~~A~~~l~G~~l   71 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDN-CGGKVLSI----------TG---CSAILRFINQDSAERAQKRMENEDV   71 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHT-TTCCEEEC----------CT---TCEEEEESSHHHHHHHHHHHTTCCS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHH-cCCeeEEE----------ec---CEEEEEECCHHHHHHHHHHhcCCcc
Confidence            56666 99999999999887    5589999 94 88654          33   9999999999999999999999999


Q ss_pred             CCceEEEEeccCCCCC
Q 033648           96 KGKPMIIQFGRNPAAA  111 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~~  111 (114)
                      .||+|+|++|+.+++.
T Consensus        72 ~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           72 FGNRIIVSFTPKNREL   87 (96)
T ss_dssp             SSSCCEEESSCCSCCC
T ss_pred             CCceEEEEecCCCcce
Confidence            9999999999988765

>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=99.84  E-value=1e-20  Score=124.10  Aligned_cols=81  Identities=21%  Similarity=0.239  Sum_probs=74.0

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcC--CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFG--SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G--~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..++|||+|||+++++++|+.+|.+ ||  .|..++   .+.++.+++++|||||+|.+.++|.+||..|||..|.|+.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~-~G~~~v~~v~---i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHS-LGVNDILEIK---FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHT-TTCCCEEEEE---EEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHH-HCCcceEEEE---EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEe
Confidence            4578999999999999999999999 99  898886   46677899999999999999999999999999999999999


Q ss_pred             EEEeccC
Q 033648          101 IIQFGRN  107 (114)
Q Consensus       101 ~v~~a~~  107 (114)
                      .|.+|++
T Consensus       143 ~V~~a~~  149 (229)
T 3q2s_C          143 VVTPVNK  149 (229)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            9999874

>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=99.83  E-value=5.2e-20  Score=107.89  Aligned_cols=82  Identities=12%  Similarity=0.102  Sum_probs=72.0

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC-
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG-   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g-   97 (114)
                      .+..+.++|||+|||+++++++|+.+|.+ ||.|..+++   +.+       +||||+|.+.++|++|+..|||..+.| 
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~~i---~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~   78 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMRE-AGDVCYADV---YRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSH   78 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGG-GSCEEEEEE---ETT-------TEEEEEESSHHHHHHHHHHSSSEEEECT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEeEEEE---ecC-------CEEEEEECCHHHHHHHHHHHCcCCccCC
Confidence            33466789999999999999999999999 999987753   111       899999999999999999999999999 


Q ss_pred             ----ceEEEEeccCCCCC
Q 033648           98 ----KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ----~~l~v~~a~~~~~~  111 (114)
                          +.|.|++|++....
T Consensus        79 ~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           79 EGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             TSCEEEEEEEESSCCSCC
T ss_pred             cCcceEEEEEeCCCCCCC
Confidence                99999999987644

>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=99.83  E-value=8.3e-21  Score=112.16  Aligned_cols=80  Identities=24%  Similarity=0.403  Sum_probs=73.2

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+.+|.. ||.|..++   .+.+..++..+|||||+|.+.++|++|+ .|||..++|+.|.|+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSA-VGKVRDVR---IISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---ECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHh-CCCEeEEE---EEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            479999999999999999999999 99998886   3446667899999999999999999999 999999999999999


Q ss_pred             eccCC
Q 033648          104 FGRNP  108 (114)
Q Consensus       104 ~a~~~  108 (114)
                      ++++.
T Consensus       100 ~a~~~  104 (114)
T 2cq4_A          100 ASQAE  104 (114)
T ss_dssp             EHHHH
T ss_pred             ecCCC
Confidence            99854

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.83  E-value=1.6e-20  Score=107.90  Aligned_cols=79  Identities=24%  Similarity=0.376  Sum_probs=69.9

Q ss_pred             CCCCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ..++.++|||+|||+ .+++++|+.+|++ ||.|..+.+           .+|||||+|.+.++|..|+..|||..+.|+
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~-~G~v~~v~i-----------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   73 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSP-YGHIMQINI-----------KNAFGFIQFDNPQSVRDAIECESQEMNFGK   73 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTT-TCCCCEEEE-----------ETTEEEEEESCHHHHHHHHHHHTCSSCBTT
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHh-cCCEEEEEE-----------eCCEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            457789999999998 9999999999999 999987752           268999999999999999999999999999


Q ss_pred             eEEEEeccCCCC
Q 033648           99 PMIIQFGRNPAA  110 (114)
Q Consensus        99 ~l~v~~a~~~~~  110 (114)
                      .|.|+++++...
T Consensus        74 ~l~V~~a~~~~~   85 (96)
T 2kvi_A           74 KLILEVSSSNAR   85 (96)
T ss_dssp             TBCEEEEECCCC
T ss_pred             EEEEEEcCcCCC
Confidence            999999987654

>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=99.83  E-value=3.2e-20  Score=105.93  Aligned_cols=80  Identities=28%  Similarity=0.424  Sum_probs=70.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCC-ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC-cccCCc
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGS-IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG-YVFKGK   98 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~-i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g-~~~~g~   98 (114)
                      ..+.++|||+|||+++++++|+.+|++ ||. +..+.    +      ..++||||+|.+.++|++|+..||| ..++|+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~vv~~~~----~------~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~   73 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGD-RKLPLAGQV----L------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGK   73 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHH-TTCCCSSCE----E------EETTEEEECCSCHHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHH-cCCceEEEE----E------cCCCEEEEEECCHHHHHHHHHHccCCeeECCE
Confidence            466789999999999999999999999 999 54442    2      2578999999999999999999999 999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++++++...
T Consensus        74 ~l~v~~a~~~~~~   86 (93)
T 2cqh_A           74 IMEVDYSVSKKLR   86 (93)
T ss_dssp             ECEEEECCCCCCC
T ss_pred             EEEEEEccCcccc
Confidence            9999999987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.83  E-value=3.5e-20  Score=110.29  Aligned_cols=81  Identities=17%  Similarity=0.206  Sum_probs=71.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCC---ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGS---IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~---i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ..+.++|||+|||+++++++|+++|++ ||.   |..++   .+.+. .|+++|||||+|.+.++|++|+. +||..++|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~~~~v~~v~---i~~~~-~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g   87 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSD-CTIHDGVAGVH---FIYTR-EGRQSGEAFVELESEDDVKLALK-KDRESMGH   87 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTT-SCBTTGGGGEE---EEECS-SSCEEEEEEEEBSSHHHHHHHGG-GTTEEETT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHH-cCCccCceeEE---EEECC-CCCCCeEEEEEECCHHHHHHHHh-cCCCeECC
Confidence            456789999999999999999999999 998   66665   34444 48999999999999999999998 99999999


Q ss_pred             ceEEEEeccC
Q 033648           98 KPMIIQFGRN  107 (114)
Q Consensus        98 ~~l~v~~a~~  107 (114)
                      +.|.|.++..
T Consensus        88 r~i~V~~a~~   97 (118)
T 2db1_A           88 RYIEVFKSHR   97 (118)
T ss_dssp             EEEEEEEECH
T ss_pred             eEEEEEECCH
Confidence            9999999863

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.83  E-value=5.7e-20  Score=119.06  Aligned_cols=86  Identities=30%  Similarity=0.438  Sum_probs=76.4

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +..|.++|||+|||+++++++|+++|++ ||.|.+++   .+.+..++.++|||||+|.+.++|.+|+..+|+..+.|+.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~-~G~I~~v~---i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSP-AGPILSIR---VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHh-hCCEEEEE---EecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            3467789999999999999999999999 99999887   4667889999999999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.+.++....
T Consensus        87 i~~~~~~~~~   96 (213)
T 4f02_A           87 VRIMWSQRDP   96 (213)
T ss_dssp             CEEEECCCCT
T ss_pred             cccccccccc
Confidence            9999987543

>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=99.83  E-value=3e-20  Score=113.14  Aligned_cols=82  Identities=16%  Similarity=0.178  Sum_probs=72.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCC---ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGS---IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~---i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ..+.++|||+|||+++++++|+++|++ ||.   |..++   .+.+.. |+++|||||+|.+.++|++|+. +||..++|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~-~G~v~~v~~v~---i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g  114 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSD-CTIHDGAAGVH---FIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGH  114 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTT-CCCSSSSTTEE---EEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCcCceeEEE---EEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECC
Confidence            355689999999999999999999999 998   66665   344554 9999999999999999999998 99999999


Q ss_pred             ceEEEEeccCC
Q 033648           98 KPMIIQFGRNP  108 (114)
Q Consensus        98 ~~l~v~~a~~~  108 (114)
                      +.|.|.++..+
T Consensus       115 r~i~V~~a~~~  125 (136)
T 2hgl_A          115 RYIEVFKSHRT  125 (136)
T ss_dssp             SEEEEEECCHH
T ss_pred             EEEEEEECChH
Confidence            99999998643

>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=99.83  E-value=4.2e-20  Score=108.54  Aligned_cols=80  Identities=25%  Similarity=0.392  Sum_probs=71.3

Q ss_pred             CCCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      +..+.++|||+|||+. +++++|+.+|.+ ||.|..+.+           .++||||+|.+.++|++|+..|||..++|+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~-~G~v~~v~i-----------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   90 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSK-YGRVAGCSV-----------HKGYAFVQYSNERHARAAVLGENGRVLAGQ   90 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGG-GSCCSEEEE-----------ETTEEEEECSSSHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHh-CCCeEEEEE-----------eCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            3455689999999999 999999999999 999987642           579999999999999999999999999999


Q ss_pred             eEEEEeccCCCCC
Q 033648           99 PMIIQFGRNPAAA  111 (114)
Q Consensus        99 ~l~v~~a~~~~~~  111 (114)
                      .|.|++++.....
T Consensus        91 ~l~V~~a~~~~~~  103 (110)
T 1wf1_A           91 TLDINMAGEPKPD  103 (110)
T ss_dssp             ECCEEESCCCCSC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999865543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.83  E-value=1.4e-20  Score=108.94  Aligned_cols=77  Identities=21%  Similarity=0.379  Sum_probs=69.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ..+++|||+|||.++++++|+.+|++ ||.|..+++    .     ..+|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~-~G~i~~~~~----~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   94 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQN-FGFILDFKH----Y-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLR   94 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHT-TSCCSEEEE----E-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHh-CCCEEEEEE----e-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            45689999999999999999999999 999987752    1     4679999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |.+|+++
T Consensus        95 V~~a~~~  101 (101)
T 2la4_A           95 TGWGKER  101 (101)
T ss_dssp             CCBCCCC
T ss_pred             EEeccCC
Confidence            9999864

>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=99.83  E-value=5.7e-20  Score=108.66  Aligned_cols=83  Identities=19%  Similarity=0.462  Sum_probs=73.4

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +..++++|||+|||+.+++++|+.+|++ ||.|..+.+   +   ..+..+|||||+|.+.++|.+|+..|||..++|+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~v~i---~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   76 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGK-YGPIRQIRV---G---NTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRY   76 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEEE---E---CSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---e---eCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            3467789999999999999999999999 999987752   2   34566899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|.+++++.
T Consensus        77 l~v~~a~~~~   86 (115)
T 3lqv_A           77 LVVLYYNANR   86 (115)
T ss_dssp             CEEEECCHHH
T ss_pred             EEEEEecCCh
Confidence            9999998643

>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=99.83  E-value=4.9e-20  Score=106.33  Aligned_cols=81  Identities=20%  Similarity=0.348  Sum_probs=72.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|.+ ||.|..+.+    .     ..++||||+|.+.++|.+|+..|||..++|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~v~~----~-----~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEK-YGKAGEVFI----H-----KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTST-TCCCSEEEE----E-----TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhh-cCCeEEEEE----e-----cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            466789999999999999999999999 999987652    1     247999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|+++++....
T Consensus        82 ~v~~a~~~~~~   92 (99)
T 2cpj_A           82 RVRFACHSASL   92 (99)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999987643

>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=99.83  E-value=5.8e-20  Score=114.29  Aligned_cols=86  Identities=23%  Similarity=0.473  Sum_probs=77.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +++++|||+|||+++++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|+|..++|+.|.
T Consensus         1 ~~~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~   76 (168)
T 1b7f_A            1 ASNTNLIVNYLPQDMTDRELYALFRA-IGPINTCR---IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK   76 (168)
T ss_dssp             -CCSEEEEECCCTTCCHHHHHHHHHT-TSCEEEEE---CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEE---EEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEE
Confidence            36789999999999999999999999 99998886   345667889999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.++++....
T Consensus        77 v~~~~~~~~~   86 (168)
T 1b7f_A           77 VSYARPGGES   86 (168)
T ss_dssp             EEECCCCSST
T ss_pred             EEecCCCccc
Confidence            9999976543

>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=99.83  E-value=5e-20  Score=107.31  Aligned_cols=86  Identities=17%  Similarity=0.209  Sum_probs=74.5

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCcee-cccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDA-AKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~-~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ....+.++|||+|||+.+++++|+++|.+ ||.|.. +.+   +.+ .+|+++|||||+|.+.++|++|+.. |+..++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~v~~~v~i---~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g   83 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSG-LEIVPNGMTL---PVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGH   83 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTT-CCEEEEEEEC---CBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCcceeEEE---EEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCC
Confidence            33466789999999999999999999999 999875 542   233 6889999999999999999999987 9999999


Q ss_pred             ceEEEEeccCCCC
Q 033648           98 KPMIIQFGRNPAA  110 (114)
Q Consensus        98 ~~l~v~~a~~~~~  110 (114)
                      +.|.|..+.....
T Consensus        84 r~i~v~~~~~~~~   96 (104)
T 1wg5_A           84 RYIEIFKSSRAEV   96 (104)
T ss_dssp             SCCEEEEECTTTS
T ss_pred             cEEEEEECCHHHH
Confidence            9999999986653

>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=99.83  E-value=4.4e-20  Score=107.33  Aligned_cols=84  Identities=15%  Similarity=0.235  Sum_probs=72.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+++|.+ ||.+ .++   .+.+. +++++|||||+|.+.++|++|+ .+|+..++|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~~-~v~---i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~   83 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSP-LNPM-RVH---IEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRY   83 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCS-CCCS-EEE---EEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHH-cCce-EEE---EEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcE
Confidence            3456789999999999999999999999 9954 665   34444 8999999999999999999999 57999999999


Q ss_pred             EEEEeccCCCC
Q 033648          100 MIIQFGRNPAA  110 (114)
Q Consensus       100 l~v~~a~~~~~  110 (114)
                      |.|..+.+...
T Consensus        84 i~V~~~~~~~~   94 (102)
T 1wez_A           84 VELFLNSTAGT   94 (102)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999886654

>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=99.83  E-value=3.8e-20  Score=103.92  Aligned_cols=77  Identities=22%  Similarity=0.392  Sum_probs=68.9

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh-CCcccCCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV-NGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~g~   98 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..+++.         ..+|||||+|.+.++|.+|+..| +|..++|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~-~G~i~~~~~~---------~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~   77 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQ-FGEIRTITVV---------QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGR   77 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHT-TSCEEEEEEE---------GGGTEEEEEESSHHHHHHHHHTTTTTCEETTE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHh-CCCEeEEEEE---------CCCCEEEEEECCHHHHHHHHHHhcCCeeECCC
Confidence            3466789999999999999999999999 9999877531         14799999999999999999999 99999999


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      .|.|++|+
T Consensus        78 ~l~v~~ak   85 (85)
T 2ytc_A           78 RLNVKWGR   85 (85)
T ss_dssp             ECCEEECC
T ss_pred             EEEEEecC
Confidence            99999985

>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=99.83  E-value=1.1e-19  Score=112.76  Aligned_cols=84  Identities=26%  Similarity=0.495  Sum_probs=76.7

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ++++|||+|||+++++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..+.|++|.|
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~v~---~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v   76 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGS-IGEIESCK---LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHh-cCCeEEEE---EEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEE
Confidence            4689999999999999999999999 99998886   4556668999999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      .++.+...
T Consensus        77 ~~~~~~~~   84 (167)
T 1fxl_A           77 SYARPSSA   84 (167)
T ss_dssp             EECCCCCG
T ss_pred             EecCCCcc
Confidence            99987654

>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=99.82  E-value=4e-20  Score=109.18  Aligned_cols=85  Identities=19%  Similarity=0.256  Sum_probs=73.7

Q ss_pred             CCCCCCeEEe--cCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc--
Q 033648           20 AGNPASVLYI--KNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF--   95 (114)
Q Consensus        20 ~~~~~~~l~v--~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~--   95 (114)
                      ...|+.+|||  +||++++++++|+++|++ ||.|..+.+.       +  .+|||||+|.+.++|++|+..|||..+  
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~-fG~v~~v~i~-------~--~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEK-CGLVDALLMP-------P--NKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHH-HSCEEEEECC-------T--TCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHh-cCCeEEEEEe-------C--CCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            3467789999  779999999999999999 9999776421       1  378999999999999999999999988  


Q ss_pred             ---CCceEEEEeccCCCCCCCC
Q 033648           96 ---KGKPMIIQFGRNPAAAKPS  114 (114)
Q Consensus        96 ---~g~~l~v~~a~~~~~~~~~  114 (114)
                         .|++|.|.|++.....+|+
T Consensus        91 ~lg~g~~l~v~~a~~~p~~~~~  112 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKVQWSGPS  112 (114)
T ss_dssp             TTSCEEECEEEEESCCCCSSCC
T ss_pred             ccCCCcEEEEEecccCcccCCC
Confidence               6899999999988777663

>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=99.82  E-value=2e-20  Score=110.65  Aligned_cols=83  Identities=16%  Similarity=0.186  Sum_probs=73.3

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCc-eecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSI-DAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i-~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ...+.++|||+|||+.+++++|+++|.+ ||.+ ..++   .+.+. +|..+|||||+|.+.++|.+|+.. ||..++|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~g~v~~~v~---i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr   84 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEG-IPVDENAVH---VLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGR   84 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTT-SCCCSTTEE---ECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHh-CCCcCCeEE---EEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCe
Confidence            3466789999999999999999999999 9998 6665   23444 899999999999999999999977 99999999


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .|.|.+|.++
T Consensus        85 ~i~v~~a~~~   94 (114)
T 2cpy_A           85 EAFVHVVTLE   94 (114)
T ss_dssp             EEEEEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999999754

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.82  E-value=3.3e-20  Score=107.36  Aligned_cols=77  Identities=19%  Similarity=0.277  Sum_probs=69.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+++++++|+.+|++ ||.|..+.+   +.+     .+|||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~i---~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   71 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSY-YGPLRTVWI---ARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVEL   71 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHH-HCCCSEEEE---ESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---eeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEE
Confidence            57999999999999999999999 999987752   111     689999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +++...
T Consensus        72 a~~~~~   77 (101)
T 2hvz_A           72 STGMPR   77 (101)
T ss_dssp             SSSCCC
T ss_pred             ccCCCC
Confidence            987653

>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=99.82  E-value=4.2e-20  Score=108.89  Aligned_cols=78  Identities=19%  Similarity=0.226  Sum_probs=69.9

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...++|||+|||+.+++++|+.+|++ ||.|..+.+.         ..++||||+|.+.++|++|+..|||..+.|++|.
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~v~i~---------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   77 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSR-FGSLGRVLLP---------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHT-TSCEEEEECC---------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEEe---------CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEE
Confidence            44679999999999999999999999 9999876531         2678999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |+||+...
T Consensus        78 V~~a~~~~   85 (111)
T 1whx_A           78 LEWAPIGV   85 (111)
T ss_dssp             EEEEETTT
T ss_pred             EEECCCCc
Confidence            99998653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.82  E-value=1.3e-20  Score=105.14  Aligned_cols=73  Identities=21%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             CCeEEecCCCCCC------CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           24 ASVLYIKNLAKDV------VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        24 ~~~l~v~nlp~~~------~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      +++|||+|||+.+      ++++|+.+|++ ||.|..+.+.     ..+|.++|||||+|.+.++|.+|+..|||..++|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~-~G~i~~v~i~-----~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g   74 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSK-FGKITNDFYP-----EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   74 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHT-TCCEEEEECC-----CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhh-cCCeEEEEec-----CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCC
Confidence            3689999999999      67999999999 9999887531     4688999999999999999999999999999999


Q ss_pred             c-eEEE
Q 033648           98 K-PMII  102 (114)
Q Consensus        98 ~-~l~v  102 (114)
                      + +|+|
T Consensus        75 ~~~l~V   80 (81)
T 2krb_A           75 QHTFRV   80 (81)
T ss_dssp             SSCCCC
T ss_pred             ceeEEe
Confidence            9 8876

>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=99.82  E-value=1.7e-20  Score=110.58  Aligned_cols=81  Identities=17%  Similarity=0.235  Sum_probs=70.8

Q ss_pred             CCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC--cccCC
Q 033648           21 GNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG--YVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~g   97 (114)
                      .+|+++|||+|||++ +++++|+.+|++ ||.|..+.+    .     +.+|||||+|.+.++|..|+..||+  ..+.|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~-fG~V~~v~i----~-----~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEP-YGKIKNYIL----M-----RMKSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTT-TSCCSEEEE----E-----TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHh-cCCEEEEEE----e-----cCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            567899999999998 999999999999 999987752    1     3579999999999999999998865  55999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      ++|.|++|+.....
T Consensus        92 r~l~V~~a~~~~~~  105 (112)
T 1x4f_A           92 RCVKVDLSEKYKKL  105 (112)
T ss_dssp             SCCEEEEECSCSSS
T ss_pred             EEEEEEECcccccc
Confidence            99999999876654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.82  E-value=2.6e-19  Score=110.96  Aligned_cols=84  Identities=25%  Similarity=0.422  Sum_probs=76.7

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||..+++++|+.+|++ ||.|..+.   .+.+..+|.++|+|||+|.+.++|.+|+..|||..++|++
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  158 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKD-FPSYLSGH---VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTT-STTEEEEE---EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhc-cCCeeEEE---EEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            3466789999999999999999999999 99998886   4556678999999999999999999999999999999999


Q ss_pred             EEEEeccC
Q 033648          100 MIIQFGRN  107 (114)
Q Consensus       100 l~v~~a~~  107 (114)
                      |.|.||+.
T Consensus       159 i~v~~a~~  166 (166)
T 3md3_A          159 LRINWAAK  166 (166)
T ss_dssp             CEEEESCC
T ss_pred             EEEEecCC
Confidence            99999863

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=8.5e-20  Score=104.67  Aligned_cols=85  Identities=16%  Similarity=0.252  Sum_probs=71.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|.+ ||.|..++.  .+.+..    .+.|||+|.+.++|.+|+..|||..++|+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~v~~~~~--i~~~~~----~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~   83 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQ-YGVVESCEQ--VNTDSE----TAVVNVTYSSKDQARQALDKLNGFQLENFT   83 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHH-HSCEEEEEE--ECCSSS----SEEEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHh-cCCeEEEEE--eecCCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3456789999999999999999999999 999987631  122222    233999999999999999999999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|.+|+++.++
T Consensus        84 l~V~~a~~~~~~   95 (96)
T 2e44_A           84 LKVAYIPDEMAA   95 (96)
T ss_dssp             CEEEECCCCCSC
T ss_pred             EEEEEcCccccc
Confidence            999999988543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.82  E-value=2.5e-19  Score=115.53  Aligned_cols=86  Identities=20%  Similarity=0.408  Sum_probs=78.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||..+++++|+++|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~v~---i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~  198 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEA-FGKIKSAT---LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR  198 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTT-SSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhc-cCCeeEEE---EEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEE
Confidence            45579999999999999999999999 99998886   455667899999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.+|++....
T Consensus       199 V~~a~~~~~~  208 (216)
T 2qfj_A          199 VGKAVTPPMP  208 (216)
T ss_dssp             EEECSSCSST
T ss_pred             EEEecCCCCC
Confidence            9999987654

>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=99.82  E-value=1.1e-19  Score=112.11  Aligned_cols=81  Identities=19%  Similarity=0.270  Sum_probs=72.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..+.+..        .++|||||+|.+.++|..|+..|||..++|++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~-~G~i~~v~i~~--------~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  139 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGY-YGPLRSVWVAR--------NPPGFAFVEFEDPRDAADAVRELDGRTLCGCR  139 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHH-HSCEEEEEECS--------SSCSEEEEEESSHHHHHHHHHHHSSSCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-hCCEEEEEEee--------CCCcEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            3466789999999999999999999999 99998775321        15899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|++++++.
T Consensus       140 l~v~~a~~~~  149 (150)
T 2i2y_A          140 VRVELSNGEK  149 (150)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEcCCCC
Confidence            9999998764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=7.7e-22  Score=116.99  Aligned_cols=87  Identities=21%  Similarity=0.422  Sum_probs=77.7

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCcee--------cccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDA--------AKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~--------~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      ..+.++|||+|||..+++++|+.+|++ ||.|..        +.   .+.+..++..+|||||+|.+.++|.+|+..|||
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~~~~~~~~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   79 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQ-IGIIKTNKKTGQPMIN---LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   79 (116)
Confidence            356789999999999999999999999 999977        55   345667889999999999999999999999999


Q ss_pred             cccCCceEEEEeccCCCCC
Q 033648           93 YVFKGKPMIIQFGRNPAAA  111 (114)
Q Consensus        93 ~~~~g~~l~v~~a~~~~~~  111 (114)
                      ..+.|+.|.|++|+++...
T Consensus        80 ~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           80 KEFSGNPIKVSFATRRADF   98 (116)
Confidence            9999999999999977543

>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=99.81  E-value=7.9e-20  Score=103.43  Aligned_cols=78  Identities=26%  Similarity=0.385  Sum_probs=69.9

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ..+++|||+|||+++++++|+.+|++ | .|..+++     +    ..+|||||+|.+.++|++|+..|||..++|++|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~-~v~~~~i-----~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   71 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKD-Y-DLKYCYV-----D----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLI   71 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCS-S-CCCCEEE-----E----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhh-C-CeEEEEE-----e----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEE
Confidence            45688999999999999999999999 9 8877652     1    5789999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |++|+.+..
T Consensus        72 V~~a~~~~~   80 (88)
T 1wg1_A           72 VQLQPTDAL   80 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCce
Confidence            999987653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=8.1e-20  Score=115.68  Aligned_cols=83  Identities=28%  Similarity=0.332  Sum_probs=74.9

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .++++|||+|||+.+++++|+++|++ ||.|..+.+   +.+. ++.++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~-~G~I~~v~i---~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~  160 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAAV---DYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD  160 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHH-TSCCSEEEE---CCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            45689999999999999999999999 999988762   3344 888999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |++|....
T Consensus       161 V~~a~~~~  168 (177)
T 2f3j_A          161 IQLVASQI  168 (177)
T ss_dssp             EEEESSGG
T ss_pred             EEEecCCC
Confidence            99998654

>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=99.81  E-value=2.3e-20  Score=102.53  Aligned_cols=75  Identities=17%  Similarity=0.263  Sum_probs=67.8

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      +|||+|||+++++++|+.+|++ ||.+..+.+   +.+..+|.++|||||+|.+.++|.+|+.. ++..++|+.|.|++|
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 KIFVGGLSPDTPEEKIREYFGG-FGEVESIEL---PMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHH-HSCCSEECC---CCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEE---EecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            5899999999999999999999 999988863   44666789999999999999999999974 999999999999876

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.81  E-value=5.3e-19  Score=112.60  Aligned_cols=85  Identities=25%  Similarity=0.375  Sum_probs=77.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~-~G~v~~~~---~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  187 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTS-FGPLKAFN---LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL  187 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHT-BSCEEEEE---EEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHH-cCCccEEE---EeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            56789999999999999999999999 99998876   455666899999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |++|+++..
T Consensus       188 v~~a~~~~~  196 (198)
T 2yh0_A          188 VQRASVGAK  196 (198)
T ss_dssp             EEESCCCCC
T ss_pred             EEECCCCCC
Confidence            999998753

>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=99.80  E-value=4.3e-19  Score=110.78  Aligned_cols=83  Identities=24%  Similarity=0.354  Sum_probs=75.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +..+.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|+|||+|.+.++|.+|+..|||..++|+.
T Consensus        90 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  165 (172)
T 2g4b_A           90 PLPGAHKLFIGGLPNYLNDDQVKELLTS-FGPLKAFN---LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK  165 (172)
T ss_dssp             CCTTTTCEEEECCCTTCCHHHHHHHHHT-TSCEEEEE---EEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEEcCCCcCCHHHHHHHHHh-cCCceEEE---EEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeE
Confidence            3455789999999999999999999999 99998886   4556668999999999999999999999999999999999


Q ss_pred             EEEEecc
Q 033648          100 MIIQFGR  106 (114)
Q Consensus       100 l~v~~a~  106 (114)
                      |.|++|.
T Consensus       166 l~V~~As  172 (172)
T 2g4b_A          166 LLVQRAS  172 (172)
T ss_dssp             CEEEECC
T ss_pred             EEEEeCC
Confidence            9999973

>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=99.80  E-value=2.9e-19  Score=126.60  Aligned_cols=84  Identities=19%  Similarity=0.380  Sum_probs=77.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+.+++++|..+|.+ ||.|..+.   ++.+..+|.++|||||+|.+.++|.+||..|||..|+|+.|.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~-~G~I~~v~---i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~  175 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEV-YGPIKRIH---MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  175 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHH-cCCeeEEE---eeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEE
Confidence            45689999999999999999999999 99998886   455667899999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |.+|++..
T Consensus       176 V~~a~~~~  183 (437)
T 3pgw_S          176 VDVERGRT  183 (437)
T ss_pred             EEEeCCCC
Confidence            99998654

>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=99.80  E-value=5.3e-20  Score=107.72  Aligned_cols=83  Identities=13%  Similarity=0.128  Sum_probs=72.5

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCC---ceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGS---IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~---i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      .....++|||+|||+++++++|+.+|+. ||.   |..+++   +.+.. |.++|||||+|.+.++|++|+. +||..++
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~g~~~~v~~v~i---~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~   80 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSD-CRIRNGENGIHF---LLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMG   80 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTT-SCBTTTTTTEEC---CCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHh-cCCcCCcceEEE---EECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeC
Confidence            3466789999999999999999999999 998   666653   33444 8899999999999999999998 9999999


Q ss_pred             CceEEEEeccCC
Q 033648           97 GKPMIIQFGRNP  108 (114)
Q Consensus        97 g~~l~v~~a~~~  108 (114)
                      |+.|.|.++.++
T Consensus        81 gr~i~V~~a~~~   92 (107)
T 2lmi_A           81 QRYVEVYEINNE   92 (107)
T ss_dssp             SSCCCCEECCHH
T ss_pred             CeEEEEEECCHH
Confidence            999999998743

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4.1e-19  Score=101.57  Aligned_cols=80  Identities=14%  Similarity=0.185  Sum_probs=69.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ....+|||+|||+++++++|+.+|++ ||.|..+     +.+..++.   ||||+|.+.++|.+|+. |||..++|+.|.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~-~G~v~~v-----~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~   75 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLA-FGPVASV-----VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLR   75 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGG-TSCEEEE-----EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHh-cCCeEEE-----EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEE
Confidence            45679999999999999999999999 9999764     34555555   99999999999999999 999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |+++......
T Consensus        76 V~~a~~~~~~   85 (94)
T 2e5g_A           76 VRPREQKEFQ   85 (94)
T ss_dssp             CBCSCCSCCC
T ss_pred             EEECCcCCCC
Confidence            9999866543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.2e-19  Score=106.65  Aligned_cols=79  Identities=18%  Similarity=0.202  Sum_probs=68.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ....+|||+|||+.+++++|+++|++ | .|..+.+   +.+ ..|+++|||||+|.+.++|++|+ .+||..++||.|.
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~-~-~v~~v~i---~~d-~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~   86 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHG-L-RVDAVHL---LKD-HVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVE   86 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTT-S-CCCEEEE---CCC-TTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhcc-C-CeeEEEE---EEC-CCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEE
Confidence            34578999999999999999999999 9 7777653   334 35889999999999999999999 7999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |..+..
T Consensus        87 V~~a~~   92 (109)
T 2dnn_A           87 VSPATE   92 (109)
T ss_dssp             EEECCH
T ss_pred             EEECCc
Confidence            988763

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.1e-18  Score=100.28  Aligned_cols=80  Identities=24%  Similarity=0.335  Sum_probs=70.8

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|+  ++++++|+.+|.+ ||.|..+.+         +..+|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~-~G~i~~v~i---------~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   79 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSP-FGNIIDLSM---------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQL   79 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTT-TSCEEEEEE---------ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhh-CCCEEEEEe---------cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            456789999996  8999999999999 999987752         2567999999999999999999999999999999


Q ss_pred             EEEeccCCCCCC
Q 033648          101 IIQFGRNPAAAK  112 (114)
Q Consensus       101 ~v~~a~~~~~~~  112 (114)
                      .|++|+++....
T Consensus        80 ~v~~a~~~~~~~   91 (97)
T 1x5p_A           80 KVNIARKQPMLD   91 (97)
T ss_dssp             EEECCSSCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999999876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.79  E-value=6.8e-20  Score=106.22  Aligned_cols=81  Identities=16%  Similarity=0.275  Sum_probs=72.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+++++++|+.+|++ ||.|..+.   .+.+. +|..+|||||+|.+.++|++|+.  +|..++|+.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~   79 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFAR-YGSVKEVK---IITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLK   79 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---EEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-CCCeEEEE---EEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEE
Confidence            45689999999999999999999999 99998886   34455 89999999999999999999997  99999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |.++.+..
T Consensus        80 v~~a~~~~   87 (102)
T 2xs2_A           80 LGPAIRKQ   87 (102)
T ss_dssp             EEEEEECC
T ss_pred             EEECCcCc
Confidence            99997553

>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=99.79  E-value=8.2e-19  Score=111.57  Aligned_cols=85  Identities=19%  Similarity=0.274  Sum_probs=75.2

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ...+.++|||+|||+++++++|+.+|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+.. ++..+.|+.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~   83 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQ-WGTLTDCV---VMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRV   83 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEE---EEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEE
Confidence            3456789999999999999999999999 99998886   456677899999999999999999999976 999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|.++....
T Consensus        84 l~v~~~~~~~   93 (196)
T 1l3k_A           84 VEPKRAVSRE   93 (196)
T ss_dssp             CEEEECCC--
T ss_pred             eeeecccCcc
Confidence            9999998654

>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=99.79  E-value=1.6e-18  Score=108.08  Aligned_cols=78  Identities=18%  Similarity=0.191  Sum_probs=68.2

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--ceEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--KPMI  101 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~~l~  101 (114)
                      ..+|||+||++.+++++|+++|++ ||.|..+.+    ..   ...++||||+|.+.++|+.|+..|||..+.|  +.|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~-fG~V~~V~i----~~---k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSK-FGTVLKIIT----FT---KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHH-HSCEEEEEE----EE---SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHh-cCCEEEEEE----Ee---CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            356899999999999999999999 999988752    21   2357899999999999999999999999965  9999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |+||+++.
T Consensus       118 V~~Ak~~~  125 (164)
T 1sjr_A          118 IDFSKLTS  125 (164)
T ss_dssp             EEECSSSS
T ss_pred             EEEecCCc
Confidence            99999764

>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=99.78  E-value=7e-19  Score=113.64  Aligned_cols=78  Identities=23%  Similarity=0.330  Sum_probs=70.1

Q ss_pred             CCCCeEEecCCC-CCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLA-KDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp-~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++++|||+||| +.+++++|+.+|++ ||.|.+++++.        ..+|||||+|.+.++|+.|++.|||..+.|++|
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~-~G~v~~v~i~~--------~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l   72 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCL-YGNVEKVKFMK--------SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKM   72 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTT-TSCEEEEEECT--------TSTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHh-cCCeEEEEEec--------CCCCEEEEEECCHHHHHHHHHHhCCCEECCceE
Confidence            578899999999 89999999999999 99998876321        247999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|.+++..
T Consensus        73 ~v~~s~~~   80 (205)
T 3tyt_A           73 NVCVSKQP   80 (205)
T ss_dssp             EEEECSCS
T ss_pred             EEEEccCC
Confidence            99999754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=7.9e-19  Score=105.16  Aligned_cols=81  Identities=20%  Similarity=0.310  Sum_probs=70.1

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCc----eecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSI----DAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i----~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ..+..+|||+|||+++++++|+++|++ ||.|    ..+.   .+.+ .+|+++|||||+|.+.++|++|+.. |+..++
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~-~g~v~g~v~~v~---i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~   93 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQ-HCPITGGKEGIL---FVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLG   93 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHT-TSCCTTGGGGEE---EEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-hCCccCCcceEE---EEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeC
Confidence            356789999999999999999999999 9975    4554   3344 6899999999999999999999986 999999


Q ss_pred             CceEEEEeccC
Q 033648           97 GKPMIIQFGRN  107 (114)
Q Consensus        97 g~~l~v~~a~~  107 (114)
                      ||.|.|..+..
T Consensus        94 gR~i~V~~a~~  104 (123)
T 2dha_A           94 KRYIELFRSTA  104 (123)
T ss_dssp             SCEECCEEECH
T ss_pred             CeEEEEEECCH
Confidence            99999988763

>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=99.78  E-value=1.6e-18  Score=110.21  Aligned_cols=86  Identities=16%  Similarity=0.251  Sum_probs=72.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+.. +|..++|+.|.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~---i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~  176 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQ-YGKIEVIE---IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCE  176 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTT-TSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhc-CCCeEEEE---EeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEE
Confidence            45589999999999999999999999 99998886   455667899999999999999999999976 89999999999


Q ss_pred             EEeccCCCCCC
Q 033648          102 IQFGRNPAAAK  112 (114)
Q Consensus       102 v~~a~~~~~~~  112 (114)
                      |.+|.++...+
T Consensus       177 v~~a~~k~~~~  187 (196)
T 1l3k_A          177 VRKALSKQEMA  187 (196)
T ss_dssp             EEECC------
T ss_pred             EEecCChhHhc
Confidence            99999876543

>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=99.78  E-value=3.8e-19  Score=110.56  Aligned_cols=81  Identities=23%  Similarity=0.366  Sum_probs=73.4

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +.++|||+|||+.+++++|+.+|++ ||.|..+.+   +.+..+|.++|||||+|.+.++|.+|+. ++|..++|++|.|
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~i---~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V  160 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQ-WGTIIDAQL---MLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEI  160 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHT-TSCCSEEEC---CCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEE
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHh-CccEEEEEE---EEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEE
Confidence            4578999999999999999999999 999988763   3455688999999999999999999997 8999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      .+|+++
T Consensus       161 ~~a~pk  166 (167)
T 2cjk_A          161 KRAEPR  166 (167)
T ss_dssp             EECCCC
T ss_pred             eecCCC
Confidence            999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.78  E-value=2.7e-18  Score=111.19  Aligned_cols=80  Identities=28%  Similarity=0.444  Sum_probs=71.8

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+|||+|||+.+++++|+.+|++ ||.|..+++   +.+  .+.++|||||+|.+.++|.+|+..|||..++|++|.|
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~-~G~i~~~~i---~~d--~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V  175 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSA-FGNILSCKV---VCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV  175 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGG-GSCEEEEEE---EEE--TTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccccceECCcccccHHHHHHHHHhh-cCCeEEEEe---ecc--CCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4568999999999999999999999 999998863   333  3457999999999999999999999999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      .+|+++
T Consensus       176 ~~a~~~  181 (213)
T 4f02_A          176 GRFKSR  181 (213)
T ss_dssp             EECCCH
T ss_pred             EEcCCC
Confidence            999865

>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=99.78  E-value=4.4e-18  Score=105.74  Aligned_cols=81  Identities=30%  Similarity=0.540  Sum_probs=73.4

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--c
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--K   98 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~   98 (114)
                      ..+.++|||+|||..+++++|+.+|++ ||.|..+.   .+.+..+|.++|+|||+|.+.++|.+|+..|||..+.|  +
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~  161 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGK-YGSIVQKN---ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ  161 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTS-SSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhc-CCcEEEEE---EEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCe
Confidence            356789999999999999999999999 99998876   35566688999999999999999999999999999988  9


Q ss_pred             eEEEEec
Q 033648           99 PMIIQFG  105 (114)
Q Consensus        99 ~l~v~~a  105 (114)
                      +|.|.||
T Consensus       162 ~l~V~~A  168 (168)
T 1b7f_A          162 PLSVRLA  168 (168)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEeC
Confidence            9999986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.77  E-value=3.7e-18  Score=102.86  Aligned_cols=77  Identities=17%  Similarity=0.219  Sum_probs=67.1

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeE-EEEEeCCHHHHHHHHHHhCCcccCC--ceE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ-AFVTFPSVELAHRALNLVNGYVFKG--KPM  100 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~g~~~~g--~~l  100 (114)
                      --.|||+||++.+++++|+.+|++ ||.|..+.+   +.     +.+++ |||+|.+.++|..|+..|||..+.|  +.|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~-yG~V~~V~i---~~-----~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~L   98 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSK-FGTVLKIIT---FT-----KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   98 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTT-SSCEEEEEE---EE-----ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhC-cCCEEEEEE---Ec-----CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEE
Confidence            346789999999999999999999 999988752   22     13577 9999999999999999999999988  899


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      +|+||+++.
T Consensus        99 rI~~ak~~~  107 (130)
T 3zzy_A           99 RIDFSKLTS  107 (130)
T ss_dssp             EEEECSCSS
T ss_pred             EEEecCCCc
Confidence            999999764

>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=99.77  E-value=1.3e-18  Score=103.00  Aligned_cols=78  Identities=13%  Similarity=0.128  Sum_probs=64.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce--
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP--   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~--   99 (114)
                      ...++|||+|||+++++++|+++|.+ ||.|..+.+.      ..    +||||+|.+.++|++|+..|||..++|+.  
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~~~i~------~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMRE-AGDVCYADVY------RD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGG-GSCEEEEEEC------TT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEEe------cC----CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            45689999999999999999999999 9999877531      11    99999999999999999999999999998  


Q ss_pred             ---EEEEeccCCCC
Q 033648          100 ---MIIQFGRNPAA  110 (114)
Q Consensus       100 ---l~v~~a~~~~~  110 (114)
                         +.|..+.+...
T Consensus        83 ~~~i~v~~~~~~~~   96 (115)
T 3beg_B           83 TAYIRVKVDGPRSP   96 (115)
T ss_dssp             CCBCEEEECC----
T ss_pred             eEEEEeccCCCCCC
Confidence               88887776543

>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=3.9e-18  Score=105.63  Aligned_cols=81  Identities=25%  Similarity=0.308  Sum_probs=71.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+++++++|+.+|++ ||.|..+.    +....++.++|||||+|.+.++|.+|+..|||..+.|+.|.|.+
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~-~G~i~~v~----i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~   75 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQV-GGPIANIK----IMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINW   75 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGG-GSCEEEEE----EECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHh-cCCeEEEE----EEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEE
Confidence            47999999999999999999999 99998875    22334577899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 033648          105 GRNPAA  110 (114)
Q Consensus       105 a~~~~~  110 (114)
                      +.+...
T Consensus        76 ~~~~~~   81 (166)
T 3md3_A           76 AFQSQQ   81 (166)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            986653

>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=99.77  E-value=1.8e-19  Score=110.05  Aligned_cols=83  Identities=16%  Similarity=0.197  Sum_probs=71.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+++|++ || +..+.+   +.+. .|+++|||||+|.+.++|++|+ .+|+..++|+.|
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~-~G-i~~v~i---~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i  115 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSP-LN-PVRVHI---EIGP-DGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYI  115 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCS-CC-CSEEEC---CCSS-SSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cC-CeEEEE---EECC-CCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEE
Confidence            355678999999999999999999999 99 556653   3343 4889999999999999999999 899999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|..+.....
T Consensus       116 ~V~~a~~~~~  125 (139)
T 2hgn_A          116 ELFLNSTTGA  125 (139)
T ss_dssp             CCEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999887654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.77  E-value=1.9e-18  Score=103.31  Aligned_cols=79  Identities=10%  Similarity=0.120  Sum_probs=70.4

Q ss_pred             CeEEecCC----CCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCC----HHH----HHHHHH--Hh
Q 033648           25 SVLYIKNL----AKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS----VEL----AHRALN--LV   90 (114)
Q Consensus        25 ~~l~v~nl----p~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~----~~~----a~~a~~--~l   90 (114)
                      +.|||+||    |+.+++.+|+.+|+. ||.|.+++   .+.++.||.++|||||+|.+    .++    |.+|+.  .+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~-fGeV~~~~---li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~l   78 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKK-YGEISHFE---AFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHES   78 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHT-TSCCSEEE---EEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHh-cCCeEEEE---EEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhh
Confidence            57999999    999999999999999 99999997   68899999999999999996    333    788888  78


Q ss_pred             CCcccCCceEEEEeccC
Q 033648           91 NGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        91 ~g~~~~g~~l~v~~a~~  107 (114)
                      ||..++|+.|+|.+.+.
T Consensus        79 ng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           79 SGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             TCEEETTEEEEEEECCT
T ss_pred             cCCeecCcEEEEEECcc
Confidence            99999999999998664

>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=99.77  E-value=2.5e-18  Score=107.73  Aligned_cols=80  Identities=25%  Similarity=0.356  Sum_probs=72.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+.+++++|+.+|++ ||.|..      +  ..++..+|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~-~g~v~~------~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  166 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFED-ALEIRL------V--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV  166 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTT-CSEEEE------E--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHh-cCeEEE------e--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            345689999999999999999999999 998742      2  5678899999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|++|++++
T Consensus       167 ~v~~a~~k~  175 (175)
T 1fje_B          167 SLYYTGEKG  175 (175)
T ss_dssp             EEEECSSCC
T ss_pred             EEEecCCCC
Confidence            999998763

>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=99.76  E-value=7e-18  Score=104.53  Aligned_cols=80  Identities=24%  Similarity=0.390  Sum_probs=72.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce--
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP--   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~--   99 (114)
                      .+.++|||+|||..+++++|+.+|++ ||.+..++   .+.+..+|.++|+|||+|.+.++|.+|+..|||..++|+.  
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~  161 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQ-YGRIITSR---ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEP  161 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHh-cCCEeEEE---EEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccc
Confidence            45688999999999999999999999 99998876   3556668899999999999999999999999999999975  


Q ss_pred             EEEEec
Q 033648          100 MIIQFG  105 (114)
Q Consensus       100 l~v~~a  105 (114)
                      |.|.||
T Consensus       162 i~v~~A  167 (167)
T 1fxl_A          162 ITVKFA  167 (167)
T ss_dssp             CEEEEC
T ss_pred             eEEEeC
Confidence            888886

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.76  E-value=8.5e-18  Score=100.69  Aligned_cols=79  Identities=24%  Similarity=0.277  Sum_probs=67.4

Q ss_pred             CCCCCe--EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeE-EEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           21 GNPASV--LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQ-AFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        21 ~~~~~~--l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .+|+.+  |||+||++.+++++|+.+|++ ||.|..+.+    .. .    .|| |||+|.+.++|..|+..|||..+.|
T Consensus        20 ~~ps~vl~l~V~NL~~~vt~~~L~~~Fs~-yG~V~~v~i----~~-~----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g   89 (124)
T 2e5i_A           20 SGGNKVLLLSIQNPLYPITVDVLYTVCNP-VGKVQRIVI----FK-R----NGIQAMVEFESVLCAQKAKAALNGADIYA   89 (124)
T ss_dssp             CCCCSEEEEEEESCCSCCCHHHHHHHHTT-TSCEEEEEE----EE-S----SSEEEEEEESSHHHHHHHHHHHTTCCCBT
T ss_pred             CCCCcEEEEEEcCcCCCCCHHHHHHHHHh-cCCEEEEEE----Ee-C----CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            345554  679999999999999999999 999988752    22 1    275 9999999999999999999999987


Q ss_pred             --ceEEEEeccCCC
Q 033648           98 --KPMIIQFGRNPA  109 (114)
Q Consensus        98 --~~l~v~~a~~~~  109 (114)
                        +.|.|++|++..
T Consensus        90 ~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           90 GCCTLKIEYARPTR  103 (124)
T ss_dssp             TBSEEEEECCSCSC
T ss_pred             CCeEEEEEEecCCc
Confidence              689999999775

>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=99.76  E-value=8.2e-19  Score=105.44  Aligned_cols=82  Identities=18%  Similarity=0.245  Sum_probs=69.1

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCce--ecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSID--AAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~--~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ...+.++|||+|||+.+++++|+++|++ | .+.  .+++   +.+.. |+++|||||+|.+.++|++|+. +++..++|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~-~-~i~~~~v~i---~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~g  110 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSG-L-EIVPNGITL---PVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGH  110 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTT-S-CEEEEEEEC---CCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhc-C-CceeeEEEE---EECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECC
Confidence            3456789999999999999999999999 9 455  6653   33444 8999999999999999999997 47899999


Q ss_pred             ceEEEEeccCC
Q 033648           98 KPMIIQFGRNP  108 (114)
Q Consensus        98 ~~l~v~~a~~~  108 (114)
                      |.|.|..+..+
T Consensus       111 R~I~V~~a~~~  121 (126)
T 2hgm_A          111 RYIEVFKSSQE  121 (126)
T ss_dssp             BCCCCEEECHH
T ss_pred             EEEEEEECCHH
Confidence            99999988644

>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=99.76  E-value=3.1e-18  Score=97.17  Aligned_cols=78  Identities=19%  Similarity=0.277  Sum_probs=61.1

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcc--cCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYV--FKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~--~~g   97 (114)
                      ..++.++|||+|||+++++++|+.+|++ ||.|.+++++.        .++|||||+|.+.++|++    ++|..  +.|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~-~G~i~~v~i~~--------~srGfaFV~F~~~~~A~~----~~~~~~~~~g   73 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQ-YGEVVDVFIPK--------PFRAFAFVTFADDKVAQS----LCGEDLIIKG   73 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTT-TSCEEEEECCS--------SCCSEEEEEESCHHHHHH----HTTCEEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhc-cCCEEEEEEee--------CCCCEEEEEECCHHHHHH----HcCCCcccCC
Confidence            3567889999999999999999999999 99998876432        278999999999999883    56665  569


Q ss_pred             ceEEEEeccCCCC
Q 033648           98 KPMIIQFGRNPAA  110 (114)
Q Consensus        98 ~~l~v~~a~~~~~  110 (114)
                      +.|.|.+|.++..
T Consensus        74 ~~v~v~~a~~k~~   86 (89)
T 3d2w_A           74 ISVHISNAEPKHN   86 (89)
T ss_dssp             EEEEEEECC----
T ss_pred             EEEEEEEcCCCCc
Confidence            9999999997764

>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=99.76  E-value=9.6e-18  Score=104.72  Aligned_cols=80  Identities=28%  Similarity=0.480  Sum_probs=70.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC---Cc
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK---GK   98 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---g~   98 (114)
                      .+.++|||+|||+.+++++|+++|++ ||.|..+.+   + ...+|.++|||||+|.+.++|.+|+..|||..+.   |+
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~-~G~i~~v~~---~-~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~  167 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSS-FGQIEECRI---L-RGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS  167 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGG-GSCEEEEEE---E-ECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSS
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHh-CCCEEEEEE---E-ECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCC
Confidence            35689999999999999999999999 999988752   3 3356889999999999999999999999998876   49


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      +|.|.||.
T Consensus       168 ~l~V~~ad  175 (175)
T 3nmr_A          168 PMVVKFAD  175 (175)
T ss_dssp             CCEEEECC
T ss_pred             CeEEEecC
Confidence            99999984

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.76  E-value=1.1e-17  Score=97.68  Aligned_cols=83  Identities=19%  Similarity=0.251  Sum_probs=70.2

Q ss_pred             CCCCCeEEecCCCC-----CCCHhHHHHHHhhhcCCceecccceeEEecc-CCCceeEEEEEeCCHHHHHHHHHHhCCcc
Q 033648           21 GNPASVLYIKNLAK-----DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHRALNLVNGYV   94 (114)
Q Consensus        21 ~~~~~~l~v~nlp~-----~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   94 (114)
                      ..++.+|+|.|+..     +-++++|++.|++ ||.|.++.   .+.++. ++.++|++||+|.+.++|.+|+..|||..
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~-~G~V~~v~---i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~   80 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEK-YGKVGKCV---IFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRY   80 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGG-GSCEEEEE---EEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHh-cCCEEEEE---EecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCE
Confidence            36788999999963     2367899999999 99999886   333433 36789999999999999999999999999


Q ss_pred             cCCceEEEEeccC
Q 033648           95 FKGKPMIIQFGRN  107 (114)
Q Consensus        95 ~~g~~l~v~~a~~  107 (114)
                      ++||.|.|.++..
T Consensus        81 ~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           81 FGGRVVKACFYNL   93 (105)
T ss_dssp             ETTEECEEEECCH
T ss_pred             ECCcEEEEEEcCH
Confidence            9999999999974

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.75  E-value=4.4e-18  Score=109.63  Aligned_cols=83  Identities=22%  Similarity=0.284  Sum_probs=72.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +.++|||+|||+++++++|+.+|++ ||.|..++   .+.+..+|..+|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~-~G~i~~v~---i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v  102 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAP-FGPIKSID---MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV  102 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---ECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEE
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHh-CCCEEEEE---EeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEE
Confidence            3579999999999999999999999 99998886   3445568889999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      .++....
T Consensus       103 ~~~~~~~  109 (216)
T 2qfj_A          103 GRPSNIG  109 (216)
T ss_dssp             ECCSCCG
T ss_pred             ecCCCcc
Confidence            9887654

>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=99.75  E-value=1.3e-17  Score=111.66  Aligned_cols=83  Identities=35%  Similarity=0.585  Sum_probs=74.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHH----HHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFF----FVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~----~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      .+++++|||+|||+++++++|+    .+|++ ||.|..+++      ..+++.+|||||+|.+.++|.+|+..|||..+.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~-~G~i~~v~~------~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   78 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQ-FGQILDILV------SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY   78 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhc-cCCeEEEEE------cCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC
Confidence            4778999999999999999976    89999 999987652      237889999999999999999999999999999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |+.|.|.+++.+..
T Consensus        79 g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           79 DKPMRIQYAKTDSD   92 (282)
T ss_pred             CcEEEEEEeccCcc
Confidence            99999999987653

>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=99.75  E-value=3.5e-18  Score=96.12  Aligned_cols=73  Identities=23%  Similarity=0.418  Sum_probs=63.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhc----C-------CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLF----G-------SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~----G-------~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ..+.++|||+|||+++++++|+.+|++ |    |       .+..+++         ...+|||||+|.+.++|.+|+ .
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~~~~~g~~~~~~~~v~~~~~---------~~~kg~afV~f~~~~~a~~A~-~   71 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQI---------NQDKNFAFLEFRSVDETTQAM-A   71 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHH-HHHHTTCCSSSSCSEEEEEE---------CSSSSEEEEEESSHHHHHHHG-G
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-HhhhcccccCCCCcceEEEe---------cCCCcEEEEEcCCHHHHHHHH-h
Confidence            356789999999999999999999999 9    7       6665542         134899999999999999999 9


Q ss_pred             hCCcccCCceEEEEe
Q 033648           90 VNGYVFKGKPMIIQF  104 (114)
Q Consensus        90 l~g~~~~g~~l~v~~  104 (114)
                      |||..++|+.|.|+.
T Consensus        72 l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           72 FDGIIFQGQSLKIRR   86 (87)
T ss_dssp             GTTCEETTEECEEEC
T ss_pred             cCCCEECCeEEEEeC
Confidence            999999999999974

>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=99.75  E-value=1.8e-17  Score=103.44  Aligned_cols=83  Identities=16%  Similarity=0.285  Sum_probs=72.6

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCC--CceeEEEEEeCCHHHHHHHHHHhCCcccC---C
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEG--RMRGQAFVTFPSVELAHRALNLVNGYVFK---G   97 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---g   97 (114)
                      +.++|||+|||+++++++|+++|++ ||.|..++   .+.+..++  .++|||||+|.+.++|.+|+..|||..+.   +
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~   77 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQ-YGAVYEIN---VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH   77 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---EEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEE---EEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCc
Confidence            4678999999999999999999999 99999886   45566665  88999999999999999999999998875   6


Q ss_pred             ceEEEEeccCCC
Q 033648           98 KPMIIQFGRNPA  109 (114)
Q Consensus        98 ~~l~v~~a~~~~  109 (114)
                      +.+.+.++....
T Consensus        78 ~~~~~~~~~~~~   89 (175)
T 3nmr_A           78 HPIQMKPADSEK   89 (175)
T ss_dssp             SCCEEEECGGGC
T ss_pred             cceEEccccccc
Confidence            788888887554

>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=99.74  E-value=2.1e-18  Score=108.06  Aligned_cols=86  Identities=17%  Similarity=0.218  Sum_probs=74.6

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ....+.++|||+|||+++++++|+.+|.. ||.+..+    .+.+..+|.++|||||+|.+.++|.+|+ .|||..+.|+
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~g~~~~~----~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~   81 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISE-LFAKNDL----AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGN   81 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHH-HHHHHTC----CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHH-hCCcceE----EEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCe
Confidence            34567899999999999999999999999 9987652    2445567889999999999999999999 5999999999


Q ss_pred             eEEEEeccCCCC
Q 033648           99 PMIIQFGRNPAA  110 (114)
Q Consensus        99 ~l~v~~a~~~~~  110 (114)
                      +|.|.++++...
T Consensus        82 ~l~v~~~~~~~~   93 (175)
T 1fje_B           82 EIKLEKPKGRDS   93 (175)
T ss_dssp             EEEEECCCCSSC
T ss_pred             EEEEecCCCccc
Confidence            999999987543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=8.5e-18  Score=99.29  Aligned_cols=76  Identities=16%  Similarity=0.227  Sum_probs=60.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccC---CCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ..+.++|||+|||+++++++|+++|++ ||.|. +.   .+.+..+   |.++|||||+|.+.++|++|+..|++  ++|
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~-~G~i~-~~---~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G   77 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRR-FGPLV-VD---WPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDG   77 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTT-TCCCC-EE---CTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHh-cCCEE-EE---EeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCC
Confidence            356789999999999999999999999 99997 54   2334444   78899999999999999999999832  444


Q ss_pred             ceEEEE
Q 033648           98 KPMIIQ  103 (114)
Q Consensus        98 ~~l~v~  103 (114)
                      +.+.+.
T Consensus        78 ~~~~~~   83 (114)
T 2dnl_A           78 KLYLCV   83 (114)
T ss_dssp             EEEEEE
T ss_pred             cEEEec
Confidence            444443

>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=99.73  E-value=3.8e-17  Score=109.45  Aligned_cols=84  Identities=17%  Similarity=0.269  Sum_probs=75.5

Q ss_pred             CCCCeEEecCCCCCC-CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLAKDV-VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~-~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+.++|||+|||+.+ ++++|+.+|++ ||.|..++    +....+|.++|+|||+|.+.++|.+|+..|||..++|++|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~-~G~i~~v~----i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  256 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSA-VHSPTFCQ----LACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL  256 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCS-SSCCSEEE----EEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhC-CCCeEEEE----EEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEE
Confidence            567899999999995 99999999999 99998875    3334578899999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|.+++++..
T Consensus       257 ~v~~a~~~~~  266 (284)
T 3smz_A          257 RVSFCAPGPP  266 (284)
T ss_dssp             EEEECCSSSC
T ss_pred             EEEEecCCCc
Confidence            9999998754

>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=99.73  E-value=1.7e-17  Score=108.44  Aligned_cols=81  Identities=30%  Similarity=0.493  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           19 TAGNPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      .+.+++++|||+|||+ .+++++|+++|++ ||.|..+++.   .+     .+|||||+|.+.++|.+|+..|||..+.|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~-~G~i~~v~i~---~~-----~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   99 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGV-YGDVQRVKIL---FN-----KKENALVQMADGNQAQLAMSHLNGHKLHG   99 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHH-HTCEEEEEEC---CT-----TSCCEEEEESCHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHh-CCCeEEEEEE---EC-----CCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            3356789999999999 9999999999999 9999877532   11     27899999999999999999999999999


Q ss_pred             ceEEEEeccCC
Q 033648           98 KPMIIQFGRNP  108 (114)
Q Consensus        98 ~~l~v~~a~~~  108 (114)
                      +.|.|.+++..
T Consensus       100 ~~l~v~~a~~~  110 (229)
T 2adc_A          100 KPIRITLSKHQ  110 (229)
T ss_dssp             SBCEEECCSCC
T ss_pred             eEEEEEEecCc
Confidence            99999999865

>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=99.73  E-value=3.3e-17  Score=109.66  Aligned_cols=79  Identities=23%  Similarity=0.415  Sum_probs=69.6

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-C
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-G   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g   97 (114)
                      ....++++|||+|||..+++++|+++|++ ||.|..+++   +.    + .+|||||+|.+.++|.+|+..|||..+. |
T Consensus       202 ~~~~~~~~l~v~nl~~~~~~~~l~~~F~~-~G~i~~v~~---~~----~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~g  272 (282)
T 3pgw_A          202 SENPPNHILFLTNLPEETNELMLSMLFNQ-FPGFKEVRL---VP----G-RHDIAFVEFDNEVQAGAARDALQGFKITQN  272 (282)
T ss_pred             cCCCCCCEEEEeCCCCcCCHHHHHHHHHh-cCCeEEEEE---ec----C-CCcEEEEEeCCHHHHHHHHHHcCCcEeCCC
Confidence            34456789999999999999999999999 999988753   21    1 2589999999999999999999999999 9


Q ss_pred             ceEEEEecc
Q 033648           98 KPMIIQFGR  106 (114)
Q Consensus        98 ~~l~v~~a~  106 (114)
                      +.|+|+||+
T Consensus       273 ~~l~v~~ak  281 (282)
T 3pgw_A          273 NAMKISFAK  281 (282)
T ss_pred             CEEEEEEec
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=99.73  E-value=5.1e-17  Score=108.83  Aligned_cols=85  Identities=18%  Similarity=0.297  Sum_probs=77.8

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~i~~~~---i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRP-FGSLERCF---LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHh-cCCeeEEE---EEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            456789999999999999999999999 99998886   45667789999999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|.++.+..
T Consensus       168 ~v~~a~~~~  176 (284)
T 3smz_A          168 YVHWTDAGQ  176 (284)
T ss_dssp             EEEECCGGG
T ss_pred             EEEECCCCC
Confidence            999998654

>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=99.73  E-value=1.4e-17  Score=112.03  Aligned_cols=83  Identities=19%  Similarity=0.248  Sum_probs=72.7

Q ss_pred             CCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEecc-CCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           21 GNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQ-EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      ..+.++|||+|||+. +++++|+.+|++ ||.|..+++.   .+.. +|.++|||||+|.+.++|.+|+ .|||..++|+
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~-~G~v~~v~i~---~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~  281 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEG-FGSIEKINIP---AGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNR  281 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGG-GSCEEEEECC---SCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhc-cCCeeEEEEE---ecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCc
Confidence            456789999999999 999999999999 9999887632   2333 4889999999999999999999 9999999999


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .|.|.+|+++
T Consensus       282 ~i~V~~a~~k  291 (292)
T 2ghp_A          282 EISVSLADKK  291 (292)
T ss_dssp             EEEEEECCCC
T ss_pred             EEEEEEecCC
Confidence            9999999876

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.72  E-value=9.4e-18  Score=110.44  Aligned_cols=79  Identities=19%  Similarity=0.380  Sum_probs=68.9

Q ss_pred             CCCCCeEEecCCCCCC---------CHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           21 GNPASVLYIKNLAKDV---------VPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~---------~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..+.++|||+||+..+         ++++|+.+|++ ||.|..+++   +      ..+|||||.|.+.++|+.|+..|+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~-fG~I~~v~v---~------~~kG~AFV~F~~~~~Ae~A~~am~  200 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSR-LGDIDRIRY---V------ESKNCGFVKFKYQANAEFAKEAMS  200 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHT-TSCEEEEEE---E------GGGTEEEEEESSHHHHHHHHHHHT
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHc-cCCEEEEEE---E------CCCCEEEEEeCCHHHHHHHHHHhC
Confidence            4567899999999988         79999999999 999988763   1      258999999999999999999999


Q ss_pred             Cccc------------CCceEEEEeccCCC
Q 033648           92 GYVF------------KGKPMIIQFGRNPA  109 (114)
Q Consensus        92 g~~~------------~g~~l~v~~a~~~~  109 (114)
                      |..+            .|+.|.|.||+.+.
T Consensus       201 g~~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          201 NQTLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TCCCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             CCEEeccccccccccCCCCEEEEEEccCCC
Confidence            9999            89999999999764

>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=99.72  E-value=8e-18  Score=95.03  Aligned_cols=77  Identities=21%  Similarity=0.309  Sum_probs=64.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc--ccCCce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY--VFKGKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~g~~   99 (114)
                      .++++|||+|||+++++++|+.+|++ ||.|..+++.        ..++|||||+|.+.++|+++    ++.  .+.|+.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i~--------~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~   69 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQ-YGDVMDVFIP--------KPFRAFAFVTFADDQIAQSL----CGEDLIIKGIS   69 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTT-TSCCCEEECC--------SSCCSCCEEECSCHHHHHHT----TTCEEEETTEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHH-cCCeeEEEEe--------cCCCCEEEEEECCHHHHHHH----hcCCceeCCEE
Confidence            46789999999999999999999999 9999877632        12689999999999999754    444  458999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|.+++++...
T Consensus        70 l~v~~a~~~~~~   81 (88)
T 1wf0_A           70 VHISNAEPKHNS   81 (88)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEecCCCCCC
Confidence            999999987654

>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=99.71  E-value=7.1e-17  Score=103.37  Aligned_cols=81  Identities=22%  Similarity=0.311  Sum_probs=69.1

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+.+++++|+.+|++ ||.|..+.+   +. ..++.++|||||+|.+.++|.+|+..++ ..++|++|.|.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~-~G~v~~v~i---~~-~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~  182 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLED-KGQVLNIQM---RR-TLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLIL  182 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTT-SCCEEEEEE---EE-CTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhc-CCCEEEEEE---EE-CCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEE
Confidence            478999999999999999999999 999988752   23 3468899999999999999999997665 58999999999


Q ss_pred             eccCCCC
Q 033648          104 FGRNPAA  110 (114)
Q Consensus       104 ~a~~~~~  110 (114)
                      +++.--+
T Consensus       183 ~~~~y~~  189 (193)
T 2voo_A          183 FKDDYFA  189 (193)
T ss_dssp             ETTTC--
T ss_pred             EhHHHHH
Confidence            9875433

>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=103.68  Aligned_cols=80  Identities=21%  Similarity=0.338  Sum_probs=70.7

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ++++|||+|||+++++++|+++|++ ||.|..+++   +.+..+|.++|||||+|.+.++|.+|+.  ++..++|+.|.|
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~-~G~i~~v~i---~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v   75 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGK-YGTVTDLKI---MKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDP   75 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTT-TCCEEEEEC---CCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHh-CCCEEEEEE---EECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccc
Confidence            5689999999999999999999999 999988863   4466789999999999999999999998  467899999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      .++.+.
T Consensus        76 ~~~~~~   81 (167)
T 2cjk_A           76 KRAIPR   81 (167)
T ss_dssp             EECCCH
T ss_pred             ccccch
Confidence            988653

>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=99.70  E-value=2.1e-16  Score=93.04  Aligned_cols=84  Identities=21%  Similarity=0.215  Sum_probs=69.9

Q ss_pred             CCCCCCeEEecCCCCCCC-----------HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHH
Q 033648           20 AGNPASVLYIKNLAKDVV-----------PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALN   88 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~-----------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~   88 (114)
                      ...++++|+|.||.....           +++|+.+|++ ||.|..+.    +.+   ...+|||||+|.+.++|.+|+.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~-~G~v~~v~----i~~---~~~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSK-FGQIRKLL----LFD---RHPDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGG-TSCCSEEE----EET---TCTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHc-cCCEeEEE----Eec---CCCCEEEEEEECCHHHHHHHHH
Confidence            456789999999954332           5789999999 99998763    222   2378999999999999999999


Q ss_pred             HhCCcccCCceEEEEeccCCCCC
Q 033648           89 LVNGYVFKGKPMIIQFGRNPAAA  111 (114)
Q Consensus        89 ~l~g~~~~g~~l~v~~a~~~~~~  111 (114)
                      .|||..++|++|.|.++.+....
T Consensus        83 ~lng~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           83 TLDGRWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             HSTTCEETTEECEEEECCSCCCS
T ss_pred             HcCCCEECCcEEEEEEeCCCCCc
Confidence            99999999999999999876543

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.69  E-value=5.8e-17  Score=104.64  Aligned_cols=78  Identities=21%  Similarity=0.338  Sum_probs=66.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCc--eecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc-
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSI--DAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK-   98 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i--~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~-   98 (114)
                      +|+.+|||+|||+.+++++|+++|++ ||.|  ..+++    .. ..+..+|+|||+|.+.++|.+|+..|||..+.|+ 
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~-~G~v~~~~v~~----~~-~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDE-LGVKRPTSVKV----FS-GKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHH-HTCCCCSEEEE----CS-CCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHh-cCCcceEEEEE----Ec-CCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            56789999999999999999999999 9998  55542    12 2245569999999999999999999999999887 


Q ss_pred             ---eEEEEec
Q 033648           99 ---PMIIQFG  105 (114)
Q Consensus        99 ---~l~v~~a  105 (114)
                         ++.|.+|
T Consensus       195 ~~~p~~vk~~  204 (205)
T 3tyt_A          195 GPYPYTLKLC  204 (205)
T ss_dssp             SSSCEECEEE
T ss_pred             CCcceEEEec
Confidence               6777775

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.69  E-value=3.4e-17  Score=104.21  Aligned_cols=85  Identities=20%  Similarity=0.305  Sum_probs=67.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccc--eeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSG--LIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~--~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ..+++|||+|||+++++++|+++|++ ||.+..+...  ..+.....+..+|||||+|.+.++|.+|+ .|||..+.|+.
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~-~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~   79 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHH-HHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHH-HHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCce
Confidence            35689999999999999999999999 9644332100  01223344667899999999999999999 89999999999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |.|.+++..
T Consensus        80 i~v~~~~~~   88 (198)
T 2yh0_A           80 LKIRRPHDY   88 (198)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999998865

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.69  E-value=1.1e-16  Score=102.05  Aligned_cols=78  Identities=23%  Similarity=0.298  Sum_probs=69.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-Cce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-GKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g~~   99 (114)
                      +++++|||+|||..+++++|+++|++ || .|..+++.    .    ..+|+|||+|.+.++|.+|+..|||..++ |++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~-~G~~v~~v~i~----~----~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~  188 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSS-NGGVVKGFKFF----Q----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHH  188 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHH-TTSCCCEEEES----S----TTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHH-cCCCceEEEEE----e----CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCe
Confidence            56889999999999999999999999 99 88776521    1    23789999999999999999999999999 999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |.|.|+++.
T Consensus       189 l~v~~a~~~  197 (198)
T 1qm9_A          189 LRVSFSKST  197 (198)
T ss_dssp             CCEEEECCC
T ss_pred             EEEEeeccc
Confidence            999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=5.7e-17  Score=103.45  Aligned_cols=76  Identities=29%  Similarity=0.537  Sum_probs=68.2

Q ss_pred             CCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           24 ASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        24 ~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +++|||+|||+ .+++++|+.+|++ ||.|..+++..        ..+|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~-~G~i~~v~i~~--------~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v   73 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGV-YGDVQRVKILF--------NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   73 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHT-TCCCSEEECST--------TCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHh-cCCEEEEEEEe--------CCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEE
Confidence            57899999999 9999999999999 99998775321        12789999999999999999999999999999999


Q ss_pred             EeccCC
Q 033648          103 QFGRNP  108 (114)
Q Consensus       103 ~~a~~~  108 (114)
                      .+++..
T Consensus        74 ~~a~~~   79 (198)
T 1qm9_A           74 TLSKHQ   79 (198)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999865

>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=99.68  E-value=1e-16  Score=99.93  Aligned_cols=86  Identities=20%  Similarity=0.314  Sum_probs=67.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccc--eeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSG--LIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~--~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      +.++|||+|||+++++++|+++|++ ||.+..+...  ..+.....+..+|||||+|.+.++|.+|+ .+||..+.|++|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~-~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHH-HHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHH-HhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            5689999999999999999999999 9433211000  01222234567899999999999999999 899999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|.+++....
T Consensus        81 ~v~~~~~~~~   90 (172)
T 2g4b_A           81 KIRRPHDYQP   90 (172)
T ss_dssp             EEECCSSCCC
T ss_pred             eecCCcccCC
Confidence            9999886543

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.68  E-value=2.2e-16  Score=103.20  Aligned_cols=78  Identities=23%  Similarity=0.311  Sum_probs=69.3

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC-Cce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK-GKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-g~~   99 (114)
                      +++++|||+|||+.+++++|+.+|++ || .|..+++.   .     ..+|+|||+|.+.++|.+|+..|||..++ |+.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~~i~~v~i~---~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  219 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSS-NGGVVKGFKFF---Q-----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHH  219 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHT-TSCCEEEEEEC---S-----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHH-cCCCeeEEEEE---E-----CCCcEEEEEECCHHHHHHHHHHHCCCccCCCCe
Confidence            56789999999999999999999999 99 88776521   1     24689999999999999999999999999 999


Q ss_pred             EEEEeccCC
Q 033648          100 MIIQFGRNP  108 (114)
Q Consensus       100 l~v~~a~~~  108 (114)
                      |.|.|+++.
T Consensus       220 l~v~~a~~~  228 (229)
T 2adc_A          220 LRVSFSKST  228 (229)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEEecCC
Confidence            999999864

>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=99.67  E-value=3.2e-16  Score=104.22  Aligned_cols=77  Identities=27%  Similarity=0.476  Sum_probs=69.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+++++++|+.+|++ ||.|..+.+         .+.+|||||.|.+.++|..|+..+||..+.|+.|.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i---------~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFER-YGEPSEVFI---------NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGG-GCCCSEEEE---------ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHh-cCCEEEEEE---------eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            55689999999999999999999999 999987752         13579999999999999999999999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |.++.+.
T Consensus        90 v~~a~~~   96 (261)
T 3sde_A           90 IRFATHG   96 (261)
T ss_dssp             EEECCCS
T ss_pred             eeecccC
Confidence            9998754

>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=99.66  E-value=9.1e-16  Score=102.02  Aligned_cols=84  Identities=25%  Similarity=0.360  Sum_probs=72.8

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc-ccC---
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY-VFK---   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-~~~---   96 (114)
                      ..++++|||+|||+.+++++|+.+|++ ||.|..+.   .+.+ .+|.++|||||+|.+.++|.+|+..||+. .+.   
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~-~G~i~~v~---i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~  167 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQ-FGPVEKAV---VVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT  167 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSS
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHh-cCCeEEEE---eeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCC
Confidence            456789999999999999999999999 99998886   3444 68999999999999999999999999554 444   


Q ss_pred             CceEEEEeccCCC
Q 033648           97 GKPMIIQFGRNPA  109 (114)
Q Consensus        97 g~~l~v~~a~~~~  109 (114)
                      +++|.|.++.+..
T Consensus       168 ~r~i~v~~~~~~~  180 (261)
T 3sde_A          168 PRPVIVEPMEQFD  180 (261)
T ss_dssp             CCBCEEEECCCEE
T ss_pred             CceEEEeeccccC
Confidence            9999999998653

>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=99.66  E-value=3.4e-16  Score=91.27  Aligned_cols=83  Identities=19%  Similarity=0.352  Sum_probs=68.0

Q ss_pred             CCCCCeEEecCC--CCCCC--------HhHHHHHHhhhcCCceecccceeEEeccC--CCceeEEEEEeCCHHHHHHHHH
Q 033648           21 GNPASVLYIKNL--AKDVV--------PDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAHRALN   88 (114)
Q Consensus        21 ~~~~~~l~v~nl--p~~~~--------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~   88 (114)
                      +.|+.+|.+.|+  |....        .++|++.|++ ||.|.++.++   .+..+  +.++|++||+|.+.++|.+|+.
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k-~G~V~~v~i~---~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~   77 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSK-YGLVKSIEIP---RPVDGVEVPGCGKIFVEFTSVFDCQKAMQ   77 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHT-TSCEEEEECC---CCBTTBCCTTTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHc-cCCEEEEEEe---ccCCCCCcCCcEEEEEEECCHHHHHHHHH
Confidence            357889999998  33333        3689999999 9999988642   23322  3678999999999999999999


Q ss_pred             HhCCcccCCceEEEEeccC
Q 033648           89 LVNGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        89 ~l~g~~~~g~~l~v~~a~~  107 (114)
                      .|||..++||.|.|.++..
T Consensus        78 ~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           78 GLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHTTCEETTEECEEEEECH
T ss_pred             HhCCCEeCCCEEEEEEeCH
Confidence            9999999999999999863

>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=99.66  E-value=4.1e-16  Score=104.79  Aligned_cols=84  Identities=13%  Similarity=0.169  Sum_probs=69.5

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcC-CceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFG-SIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G-~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+.++|||+|||+.+++++|+.+|.+ || .|..+.+.   .+ ..|.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~~i~~v~i~---~~-~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  189 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQD-INVVALSIRLP---SL-RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL  189 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHH-TTCCCCEEECC-----------CCEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHH-hCCCeEEEEEE---eC-CCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            35789999999999999999999999 99 99887632   22 337789999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 033648          101 IIQFGRNPAA  110 (114)
Q Consensus       101 ~v~~a~~~~~  110 (114)
                      .|.++.+...
T Consensus       190 ~v~~a~~~~~  199 (292)
T 2ghp_A          190 VTKVSNPLEK  199 (292)
T ss_dssp             EEEECCCC--
T ss_pred             EEEECCCCcc
Confidence            9999987653

>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=99.65  E-value=1.5e-15  Score=90.25  Aligned_cols=82  Identities=20%  Similarity=0.402  Sum_probs=68.8

Q ss_pred             CCCCeEEecCCCC--CC---CHhHHHHHHhhhcCCceecccceeEEecc----CCCceeEEEEEeCCHHHHHHHHHHhCC
Q 033648           22 NPASVLYIKNLAK--DV---VPDDFFFVFGSLFGSIDAAKSGLIVKLMQ----EGRMRGQAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        22 ~~~~~l~v~nlp~--~~---~~~~l~~~f~~~~G~i~~~~~~~~~~~~~----~~~~~g~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      +|+.+|++.|+-.  .+   .+++|++.|++ ||.|.++.+   +.+..    ++.++|++||+|.+.++|.+|+..|||
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k-~G~V~~v~I---~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnG   93 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGK-FGAVNRVII---YQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG   93 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTT-TSCEEEEEE---EEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhc-cCCEeEEEE---eecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCC
Confidence            5788999999842  22   35789999999 999998863   33433    457789999999999999999999999


Q ss_pred             cccCCceEEEEeccC
Q 033648           93 YVFKGKPMIIQFGRN  107 (114)
Q Consensus        93 ~~~~g~~l~v~~a~~  107 (114)
                      ..++||.|.|.++..
T Consensus        94 r~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           94 RWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEECCcEEEEEEcCh
Confidence            999999999999863

>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=99.63  E-value=1.6e-16  Score=92.58  Aligned_cols=72  Identities=18%  Similarity=0.281  Sum_probs=59.0

Q ss_pred             ecCCCCCCCHhHHHHHH------------hhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           29 IKNLAKDVVPDDFFFVF------------GSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        29 v~nlp~~~~~~~l~~~f------------~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      +.+||+.+++++|++.|            ++ ||.|..+.+    ....++.++|||||.|.+.++|.+|+..|||..++
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~-~G~V~~v~i----~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~   94 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEK-YGEVEEMNV----CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN   94 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCCEEEEEE----CCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhcc-CCceEEEEE----EeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            45566666666666555            99 999998863    23345788999999999999999999999999999


Q ss_pred             CceEEEEec
Q 033648           97 GKPMIIQFG  105 (114)
Q Consensus        97 g~~l~v~~a  105 (114)
                      ||+|.|+++
T Consensus        95 Gr~i~v~~s  103 (104)
T 1jmt_A           95 GQPIHAELS  103 (104)
T ss_dssp             TEECCEEEC
T ss_pred             CEEEEEEEc
Confidence            999999987

>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=99.58  E-value=6.6e-15  Score=101.36  Aligned_cols=77  Identities=21%  Similarity=0.307  Sum_probs=65.4

Q ss_pred             CCCCCCeEEecC--CCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc--
Q 033648           20 AGNPASVLYIKN--LAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF--   95 (114)
Q Consensus        20 ~~~~~~~l~v~n--lp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~--   95 (114)
                      ..+|+.+|||+|  |+..+++++|+++|++ ||.|..+.+     .    ..+|||||+|.+.++|++|++.|||..+  
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~-~G~V~~v~~-----~----~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEK-CGLVDALLM-----P----PNKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHT-TSCEEEEEC-----C----TTCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHh-cCCeEEEEE-----e----CCCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            368889999999  5789999999999999 999976542     1    1579999999999999999999999987  


Q ss_pred             -CCc--eEEEEecc
Q 033648           96 -KGK--PMIIQFGR  106 (114)
Q Consensus        96 -~g~--~l~v~~a~  106 (114)
                       .|+  .|.|.|+.
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence             345  68888875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=3.9e-14  Score=81.83  Aligned_cols=67  Identities=18%  Similarity=0.257  Sum_probs=57.0

Q ss_pred             CCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEeccCCCCC
Q 033648           34 KDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAA  111 (114)
Q Consensus        34 ~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~  111 (114)
                      ..+++++|+.+|++ ||.|..+.+    .    +..+|||||+|.+.++|+.|+..+++  +.|++|+|+|+++....
T Consensus        27 ~~~te~~L~~~F~~-~G~V~~v~i----~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQK-YGEVLNLVL----S----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHT-TSCEEEEEE----E----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHh-cCCEEEEEE----c----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            45899999999999 999988752    1    46789999999999999999988554  67999999999977544

>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=99.52  E-value=1.3e-13  Score=81.43  Aligned_cols=78  Identities=19%  Similarity=0.250  Sum_probs=63.6

Q ss_pred             CCCCCeEEecCCCCCCC----------HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh
Q 033648           21 GNPASVLYIKNLAKDVV----------PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV   90 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~----------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   90 (114)
                      ..|+.+|.+.|+=..-.          +++|++.|++ ||.|.++.+     ...  ..+|++||+|.+.++|.+|+..|
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~k-fG~V~~v~i-----~~~--~~~G~~fV~f~~~e~A~~Ai~~l   75 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNK-HGGVIHIYV-----DKN--SAQGNVYVKCPSIAAAIAAVNAL   75 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTT-TTCCSEEEE-----CTT--CTTCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhc-cCCEEEEEE-----ecC--CCcEEEEEEECCHHHHHHHHHHh
Confidence            45678899999843221          3578999999 999987642     111  25899999999999999999999


Q ss_pred             CCcccCCceEEEEecc
Q 033648           91 NGYVFKGKPMIIQFGR  106 (114)
Q Consensus        91 ~g~~~~g~~l~v~~a~  106 (114)
                      ||..++||.|.|.++.
T Consensus        76 nG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           76 HGRWFAGKMITAAYVP   91 (114)
T ss_dssp             TTCEETTEECEEEEEC
T ss_pred             CCCEECCEEEEEEEEc
Confidence            9999999999999986

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.5e-12  Score=73.25  Aligned_cols=77  Identities=19%  Similarity=0.325  Sum_probs=62.2

Q ss_pred             CCCCCCeEEecCCCC----CCCH----hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           20 AGNPASVLYIKNLAK----DVVP----DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~----~~~~----~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      .++|..|+.|...+.    .+-.    .+|...|.+ ||.+..+++.       .    ..+||+|.+.++|.+|+. ||
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~-~G~Vi~vr~~-------~----d~~fVtF~d~~sAlaAi~-mn   69 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFAS-FGEVILIRFV-------E----DKMWVTFLEGSSALNVLS-LN   69 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHT-TCCEEEEEEC-------S----SSEEEEESSHHHHHHGGG-GT
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHh-CCCeEEEEEe-------c----CCEEEEECChHHHHHHHh-cC
Confidence            468889999988772    2322    578999999 9988766531       1    228999999999999997 99


Q ss_pred             CcccCCceEEEEeccCCC
Q 033648           92 GYVFKGKPMIIQFGRNPA  109 (114)
Q Consensus        92 g~~~~g~~l~v~~a~~~~  109 (114)
                      |..++||.|+|+++.++=
T Consensus        70 G~~v~Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           70 GKELLNRTITIALKSPSG   87 (91)
T ss_dssp             TCEETTEEEEEEECCCSS
T ss_pred             CeEeCCeEEEEEeCCCCc
Confidence            999999999999998763

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.29  E-value=1.9e-11  Score=72.55  Aligned_cols=77  Identities=14%  Similarity=0.184  Sum_probs=64.5

Q ss_pred             CCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCC-HHHHHHHHHHhC--CcccC
Q 033648           21 GNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS-VELAHRALNLVN--GYVFK   96 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~-~~~a~~a~~~l~--g~~~~   96 (114)
                      -++++.|||+||++. +++++|+.+|++ ||.|.++.+.       .|  ...|||.|.+ .++|..|+..+|  |..+.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~-~G~V~~Vd~~-------~g--~~tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSN-HGEIKWIDFV-------RG--AKEGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCS-SCCEEEEECC-------TT--CSEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHh-cCCEEEEEEe-------cC--CCEEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            367899999999999 999999999999 9999877531       12  2259999999 899999999995  67799


Q ss_pred             CceEEEEeccC
Q 033648           97 GKPMIIQFGRN  107 (114)
Q Consensus        97 g~~l~v~~a~~  107 (114)
                      |..++++....
T Consensus        85 g~~~~~evL~G   95 (121)
T 1owx_A           85 NKEVTWEVLEG   95 (121)
T ss_dssp             SSSEEEEECCH
T ss_pred             CcEEEEEECCC
Confidence            99999887653

>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=99.24  E-value=5e-11  Score=77.32  Aligned_cols=67  Identities=18%  Similarity=0.328  Sum_probs=57.5

Q ss_pred             CCHhHHHHHHhhhcCCceecccceeEEec----cCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEecc
Q 033648           36 VVPDDFFFVFGSLFGSIDAAKSGLIVKLM----QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        36 ~~~~~l~~~f~~~~G~i~~~~~~~~~~~~----~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~  106 (114)
                      -.++++++.|++ ||.|.++.+   +.+.    .++.++|++||+|.+.++|.+|+..|||..++||+|.+.++.
T Consensus       141 e~~~dl~~e~~~-~G~v~~~~v---~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGK-FGAVNRVII---YQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTT-TSCEEEEEE---EEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHc-cCCeEEEEE---ecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            345789999999 999998863   3232    345889999999999999999999999999999999999975

>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=99.18  E-value=9.4e-11  Score=66.26  Aligned_cols=75  Identities=21%  Similarity=0.291  Sum_probs=60.2

Q ss_pred             CCCCCCCeEEecCCCCC------CCH---hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           19 TAGNPASVLYIKNLAKD------VVP---DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~------~~~---~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ..++|..|+.|..++..      ..+   .+|.+.|.. ||.+..+++   +.+        -+||+|.+.++|.+|+. 
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~-~G~Vilvr~---v~d--------~~fVtF~d~~sAl~AI~-   76 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGS-YGTIVLVRI---NQG--------QMLVTFADSHSALSVLD-   76 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHH-HSCCSEEEE---ETT--------EEEEECSCSHHHHHHHH-
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHH-CCCEEEEEE---ecC--------cEEEEEcChHHHHHHHh-
Confidence            45789999999988743      332   568899999 998876652   111        19999999999999998 


Q ss_pred             hCCcccCCceEEEEecc
Q 033648           90 VNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        90 l~g~~~~g~~l~v~~a~  106 (114)
                      |||..++||.|+|++..
T Consensus        77 ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           77 VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             GGGSEETTEEEEEECCC
T ss_pred             cCCeeeCCeEEEEeccC
Confidence            99999999999999754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.60  E-value=4.6e-07  Score=52.41  Aligned_cols=73  Identities=18%  Similarity=0.207  Sum_probs=61.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhc-----CCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLF-----GSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~-----G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      +...++-+.|||..++...++.+..+ +     |.+..+.     ..+    .-+-|+|+|.+...|-+|.-+|+|.+|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~-~~~i~~g~i~KI~-----L~p----DH~GAivef~d~~~AgKasLaL~G~ef~   88 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQE-EIHINEKDIRKIL-----LVS----DFNGAIIIFRDSKFAAKMLMILNGSQFQ   88 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHH-HTCCCTTTCSEEE-----EET----TTTEEEEECSCHHHHHHHHHHHSSEEET
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhh-hhccCccceeEEE-----Eec----CCCceEEEEccchhhHHHHhhcCCeeec
Confidence            44678999999999999999999999 9     7665432     222    3467999999999999999999999999


Q ss_pred             CceEEEEe
Q 033648           97 GKPMIIQF  104 (114)
Q Consensus        97 g~~l~v~~  104 (114)
                      |+.|++.-
T Consensus        89 gr~Lr~gT   96 (117)
T 2l9w_A           89 GKVIRSGT   96 (117)
T ss_dssp             TEEEEEEC
T ss_pred             CeEEEecC
Confidence            99999863

>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=98.00  E-value=7.8e-05  Score=41.84  Aligned_cols=80  Identities=19%  Similarity=0.258  Sum_probs=58.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccC--CCceeEEEEEeCCHHHHHHHHHHhCCcccCCc----
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAHRALNLVNGYVFKGK----   98 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~----   98 (114)
                      +.|-|++||+..+++++.+.+++ ...++...   .+..+.+  ....+.|+|.|.+.+++..-...++|+.+.+.    
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~-~~~~d~~~---fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~   77 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQP-MPEHDYFE---FFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQE   77 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCS-CCCEEEEE---EEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcC-cccceEEE---EeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCE
Confidence            46889999999999999999988 77654322   1222222  12348899999999999999999999886432    


Q ss_pred             -eEEEEeccCC
Q 033648           99 -PMIIQFGRNP  108 (114)
Q Consensus        99 -~l~v~~a~~~  108 (114)
                       +-.|++|--+
T Consensus        78 ~~a~VE~AP~q   88 (91)
T 1uw4_A           78 YPAIVEFAPFQ   88 (91)
T ss_dssp             EECEEEECSSC
T ss_pred             eeeEEEEcCCC
Confidence             3467777543

>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=97.88  E-value=3.7e-05  Score=44.07  Aligned_cols=75  Identities=19%  Similarity=0.133  Sum_probs=57.3

Q ss_pred             CCeEEecCCCCCC-CH----hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           24 ASVLYIKNLAKDV-VP----DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        24 ~~~l~v~nlp~~~-~~----~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      .++|+|.|++..+ ..    +.++.+|.. |+.+....    ..     ++-.-.-|.|.+.++|.+|-..||+..++|+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~-~~~~~tF~----~l-----kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~   74 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRT-YDKDTTFQ----YF-----KSFKRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHT-TCSSCEEE----EE-----TTTTEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHh-hCcCccee----ec-----CcceEEEEEeCChHHHHHHHHHhccceecCc
Confidence            4679999998754 32    456888888 88765321    11     1223457899999999999999999999999


Q ss_pred             eEEEEeccCC
Q 033648           99 PMIIQFGRNP  108 (114)
Q Consensus        99 ~l~v~~a~~~  108 (114)
                      .++|-|+.+.
T Consensus        75 ~~r~YFgq~~   84 (104)
T 1wey_A           75 EMKLYFAQTL   84 (104)
T ss_dssp             ECEEECCCCS
T ss_pred             eeEEEecCCC
Confidence            9999999754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.53  E-value=0.0013  Score=37.58  Aligned_cols=72  Identities=14%  Similarity=0.136  Sum_probs=53.7

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhh----cCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSL----FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~----~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      -..+|.|.|||+.+.++.|.-.|++.    -|.+..++      .     ..+-|+|+|.+...|++.++. ..+.+++-
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~------~-----~~~~AvItF~d~~va~rVL~k-~~H~L~~~   74 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ------R-----LGCGGVLTFREPADAERVLAQ-ADHELHGA   74 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEE------E-----ETTEEEEEESSHHHHHHHHTC-SCCBSSSS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEE------E-----cCCcEEEEEcChHHHHHHhcC-CcceecCe
Confidence            45789999999999999999999872    23444332      1     116789999999999998852 35678888


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      +|.|.-.-
T Consensus        75 ~LsV~P~~   82 (104)
T 2dhx_A           75 QLSLRPAP   82 (104)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEcCC
Confidence            88886544

>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=97.49  E-value=0.00071  Score=38.27  Aligned_cols=54  Identities=26%  Similarity=0.460  Sum_probs=42.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..+++ ++|+.+...+|..+|++ ||.+. ++   |+-       -..|||.|.+.+.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~-fggv~-I~---Wid-------DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSA-FGNIQ-IS---WID-------DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTT-TCSCC-CE---EEE-------TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhc-cCCEE-EE---EEc-------CCeEEEEecCHHHHHHHHHhcc
Confidence            44555 99999999999999999 98542 22   322       3469999999999999998663

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.29  E-value=0.0009  Score=37.85  Aligned_cols=79  Identities=13%  Similarity=0.265  Sum_probs=55.1

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccC--CCceeEEEEEeCCHHHHHHHHHHhCCcccCCc---
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE--GRMRGQAFVTFPSVELAHRALNLVNGYVFKGK---   98 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~---   98 (114)
                      +-.|-|++||+..|++++.+.+++ .-.++...   -+....+  ....+.|||.|.+.++...-...++|..+.+.   
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~-~~~~d~~~---fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~   84 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRP-LPAHDYFE---FFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGL   84 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSC-CSSEEECC---CCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCC-cCccceEE---EeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCC
Confidence            456889999999999998887776 44433221   0111111  12347899999999999999999999886432   


Q ss_pred             --eEEEEecc
Q 033648           99 --PMIIQFGR  106 (114)
Q Consensus        99 --~l~v~~a~  106 (114)
                        +-.|++|.
T Consensus        85 ~~~a~VE~AP   94 (97)
T 2l08_A           85 EYPAVVEFAP   94 (97)
T ss_dssp             EEEEEEEECC
T ss_pred             EeeeEEEecC
Confidence              45677765

>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=97.10  E-value=0.00027  Score=42.70  Aligned_cols=41  Identities=10%  Similarity=0.100  Sum_probs=37.4

Q ss_pred             CCCceeEEEEEeCCHHHHHHHHHHh-CCcccCCceEEEEeccC
Q 033648           66 EGRMRGQAFVTFPSVELAHRALNLV-NGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        66 ~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~g~~l~v~~a~~  107 (114)
                      ....+|+++++|.+.++|++|+..+ ||..++| .+.+.++..
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            3467899999999999999999999 9999999 999998875

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.90  E-value=0.00085  Score=38.05  Aligned_cols=54  Identities=26%  Similarity=0.435  Sum_probs=42.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..+++ ++|+.+...+|..+|++ ||.+. ++   |+       .-..|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~-fggv~-I~---Wi-------dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSA-FGNIQ-IS---WI-------DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTT-SEEEE-EE---EE-------ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhc-cCCEE-EE---EE-------cCCeEEEEecCHHHHHHHHHhcc
Confidence            34666 99999999999999999 98442 22   22       23469999999999999998764

>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=96.64  E-value=0.0096  Score=34.87  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=52.5

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC-ceEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG-KPMII  102 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g-~~l~v  102 (114)
                      .+.|.|-+.|+.. .+.+...|.+ ||.|.+..      .   .....+-.|.|.+..+|++|+ ..||..++| -.|-|
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~-~G~Iv~~~------~---~~~~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQ-YGNILKHV------M---SNTGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGV   91 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHT-TSCEEEEE------E---CSSSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEE
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHh-hCcEEEec------c---CCCCCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEE
Confidence            5678899999874 5677788999 99986432      1   123478999999999999999 569999985 44555


Q ss_pred             Eec
Q 033648          103 QFG  105 (114)
Q Consensus       103 ~~a  105 (114)
                      ...
T Consensus        92 ~p~   94 (119)
T 1wwh_A           92 KPC   94 (119)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.59  E-value=0.0083  Score=35.71  Aligned_cols=81  Identities=19%  Similarity=0.136  Sum_probs=53.0

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceec-cccee-----EE----eccCC-CceeEEEEEeCCHHHHHHHHHHhC
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAA-KSGLI-----VK----LMQEG-RMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~-~~~~~-----~~----~~~~~-~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ..+.+.|-+.|+. ....+...|++ ||.|.+- .....     ..    ....+ ....|..|.|.+..+|.+|+ ..|
T Consensus         6 ~e~~VtVFGFp~~-~~~~VI~~Fs~-~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~N   82 (132)
T 3p3d_A            6 GELAILVFGYPET-MANQVIAYFQE-FGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LEN   82 (132)
T ss_dssp             --CEEEEECCCGG-GHHHHHHHHGG-GSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTT
T ss_pred             CceEEEEEecCHH-HHHHHHHHHHh-hceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhC
Confidence            3456778888765 44566777999 9998641 11000     00    00001 12468899999999999999 679


Q ss_pred             CcccCCceEEEEecc
Q 033648           92 GYVFKGKPMIIQFGR  106 (114)
Q Consensus        92 g~~~~g~~l~v~~a~  106 (114)
                      |..++|.-|-|....
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            999999877776654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.57  E-value=0.0031  Score=38.19  Aligned_cols=27  Identities=7%  Similarity=0.100  Sum_probs=24.3

Q ss_pred             CceeEEEEEeCCHHHHHHHHHHhCCcc
Q 033648           68 RMRGQAFVTFPSVELAHRALNLVNGYV   94 (114)
Q Consensus        68 ~~~g~~fv~f~~~~~a~~a~~~l~g~~   94 (114)
                      .++||+||+|.+.++|++|+..+++..
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccC
Confidence            589999999999999999999988644

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.14  E-value=0.008  Score=43.03  Aligned_cols=53  Identities=17%  Similarity=0.164  Sum_probs=37.8

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHH
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL   87 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~   87 (114)
                      +.|+|. .|..+++.+|.+.|+. ||.|..+     +++...   ..|+.|+|.+.+++..++
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~-~g~i~~~-----~~~~~~---g~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQ-FGPINNH-----FFYESF---GLYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGG-GSCCCCE-----EEECSS---SEEEEEECC---CCHHHH
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHh-cCCcceE-----EEEccC---CeEEEEEeCCHHHHHHHH
Confidence            589997 7999999999999999 9999764     334332   379999999999888665

>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=88.13  E-value=2  Score=31.12  Aligned_cols=55  Identities=25%  Similarity=0.371  Sum_probs=42.9

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCC
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNG   92 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   92 (114)
                      ..++|+ +|..+...+|...|+. ||.+. +.   |       -....|||.|.+.+.|..++..+..
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~-fg~v~-V~---w-------iddt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSA-FGNIQ-IS---W-------IDDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGG-GCCCE-EE---E-------CSSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHh-cCCEE-EE---E-------EcCCeEEEEECCHHHHHHHHHHHHh
Confidence            456666 8888899999999999 99652 21   1       2345699999999999999998853

---

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	114
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-17
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-09
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-07
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:) 6e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	9e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	9e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.002

>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 = 69.0 bits (168), Expect = 2e-17
 Identities = 46/101 (45%), Positives = 60/101 (59%), Gaps = 4/101 (3%)

Query: 7   EEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE 66
           EEI  +PMF +Y  G P  VLY+KNL+  V   D   +F              I   M  
Sbjct: 1   EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP----IQFRMMT 56

Query: 67  GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           GRMRGQAF+TFP+ E+A +AL+LVNGY   GK ++I+FG+N
Sbjct: 57  GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 1e-12
 Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P   +YI NL + +  D+      ++F           + + +  +MRGQAFV F  V  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSS 58

Query: 83  AHRALNLVNGYVFKGKPMIIQFGRNPAAA 111
           A  AL  + G+ F  KPM IQ+ +  +  
Sbjct: 59  ATNALRSMQGFPFYDKPMRIQYAKTDSDI 87

>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 = 55.4 bits (133), Expect = 8e-12
 Identities = 21/110 (19%), Positives = 44/110 (40%), Gaps = 22/110 (20%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           +LPPE                  +LYI+NL   +  ++ + +FG  +G I   +      
Sbjct: 1   RLPPE---------------VNRILYIRNLPYKITAEEMYDIFGK-YGPIRQIRV----- 39

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
                  RG A+V +  +  A  A + ++G+    + +++ +     A +
Sbjct: 40  -GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 54.3 bits (130), Expect = 8e-12
 Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+IKNL      +    VF    G+I +                G  FV +   E A +A
Sbjct: 1   LFIKNLNFSTTEETLKGVFSK-VGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           L  + G+   G  + ++        KP+
Sbjct: 60  LKQLQGHTVDGHKLEVRISERA--TKPA 85

>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 = 52.6 bits (126), Expect = 3e-11
 Identities = 28/81 (34%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 24  ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           AS LY+ +L  DV     +  F    G I    S  + + M   R  G A+V F     A
Sbjct: 1   AS-LYVGDLHPDVTEAMLYEKFSP-AGPIL---SIRVCRDMITRRSLGYAYVNFQQPADA 55

Query: 84  HRALNLVNGYVFKGKPMIIQF 104
            RAL+ +N  V KGKP+ I +
Sbjct: 56  ERALDTMNFDVIKGKPVRIMW 76

>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 = 52.4 bits (125), Expect = 6e-11
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 7/89 (7%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           AGN    +Y+ NL  D+   D        +G+I        + L         AFV F  
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIED-VFYKYGAI------RDIDLKNRRGGPPFAFVEFED 62

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGRNP 108
              A  A+   +GY + G  + ++F R+ 
Sbjct: 63  PRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 52.2 bits (125), Expect = 7e-11
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
              S + ++N+       +   +F + FG +   +  L  K+   G  RG  FV F + +
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFST-FGELKTVR--LPKKMTGTGAHRGFGFVDFITKQ 62

Query: 82  LAHRALN-LVNGYVFKGKPMIIQF 104
            A +A N L +     G+ +++++
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEW 86

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 2e-10
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           G   + L+I +L ++    D       +F       S  +    Q    +   FV++ + 
Sbjct: 15  GPEGANLFIYHLPQEFGDQDLL----QMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
             A  A+  +NG+    K + +Q  R+   +K
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 49.6 bits (118), Expect = 7e-10
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 10/83 (12%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           +LY++NL      +     F ++              + +  ++R  AFV F + E A  
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIK----------PGAVERVKKIRDYAFVHFSNREDAVE 59

Query: 86  ALNLVNGYVFKGKPMIIQFGRNP 108
           A+  +NG V  G P+ +   +  
Sbjct: 60  AMKALNGKVLDGSPIEVTLAKPV 82

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 1e-09
 Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 11/92 (11%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +  S ++I NL   VV         S +G I                 +G AFV + +  
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS-----------VHKGFAFVQYVNER 61

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
            A  A+   +G +  G+ + I     P   + 
Sbjct: 62  NARAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 48.9 bits (116), Expect = 1e-09
 Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 6/91 (6%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
                LY+ NL++DV       +F  +              + +        FV F    
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKS------CKMITEHTSNDPYCFVEFYEHR 59

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAK 112
            A  AL  +NG    GK + + +   P++ K
Sbjct: 60  DAAAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 48.4 bits (115), Expect = 2e-09
 Identities = 23/78 (29%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L + NL   V   D   +F        A      V   + GR  G A V F     A +A
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKA-----AVHYDRSGRSLGTADVHFERKADALKA 57

Query: 87  LNLVNGYVFKGKPMIIQF 104
           +   NG    G+PM IQ 
Sbjct: 58  MKQYNGVPLDGRPMNIQL 75

>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 = 48.0 bits (114), Expect = 3e-09
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 4/82 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL+     +  +     LF      K  ++     +    G  FV + S   A  A
Sbjct: 10  LYVGNLSFYTTEEQIY----ELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  +NG     + +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>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 = 47.8 bits (113), Expect = 3e-09
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 10/88 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  L +++  ++F     SLFGSI   +S  +V+    G+  G  FV +   + A +A
Sbjct: 5   LIVNYLPQNMTQEEFR----SLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           +N +NG   + K + + +      A+PS
Sbjct: 61  INTLNGLRLQTKTIKVSY------ARPS 82

>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 = 47.8 bits (113), Expect = 3e-09
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++I NL  ++     +  F + FG I   ++  I++    G  +G AF+ F S + +  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSA-FGVIL--QTPKIMRDPDTGNSKGYAFINFASFDASDAA 57

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG     +P+ + +  
Sbjct: 58  IEAMNGQYLCNRPITVSYAF 77

>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 = 47.3 bits (112), Expect = 5e-09
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L +  L +D+   + + +F +  G I+   +  I++  + G   G AFV F S   + RA
Sbjct: 5   LIVNYLPQDMTDRELYALFRA-IGPIN---TCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           + ++NG   + K + + + R
Sbjct: 61  IKVLNGITVRNKRLKVSYAR 80

>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 = 47.3 bits (112), Expect = 5e-09
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 10/86 (11%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           S L++ NL  D+  ++   +F   +G             +   + +G  F+   +  LA 
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEK-YGKA---------GEVFIHKDKGFGFIRLETRTLAE 58

Query: 85  RALNLVNGYVFKGKPMIIQFGRNPAA 110
            A   ++    +GK + ++F  + A+
Sbjct: 59  IAKVELDNMPLRGKQLRVRFACHSAS 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 = 46.9 bits (111), Expect = 7e-09
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 24  ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           A  L+I  L   +  D        L  S    K+  +VK    G  +G AF  +  + + 
Sbjct: 1   AHKLFIGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 56

Query: 84  HRALNLVNGYVFKGKPMIIQF 104
            +A+  +NG     K +++Q 
Sbjct: 57  DQAIAGLNGMQLGDKKLLVQR 77

>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 = 46.7 bits (110), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 40/95 (42%), Gaps = 10/95 (10%)

Query: 16  KNYTAGNPAS-VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAF 74
           KN+    P S  L++ N+   V  +D   +F S          G++       + R  A 
Sbjct: 1   KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG--------GVVKGFKFFQKDRKMAL 52

Query: 75  VTFPSVELAHRALNLVNGY-VFKGKPMIIQFGRNP 108
           +   SVE A +AL  ++ + + +   + + F ++ 
Sbjct: 53  IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 87

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 1e-08
 Identities = 17/88 (19%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 19  TAGNPAS-VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTF 77
           ++G P   ++ ++N+   V  D+        F         + +K  ++G   G+A V F
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILD----FFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 58

Query: 78  PSVELAHRALNLVNGYVFKGKPMIIQFG 105
            S + A  A+  +N      + + +  G
Sbjct: 59  ESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 46.6 bits (110), Expect = 1e-08
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
            A  L  KNL+ ++  D+   VF                   Q+G+ +G A++ F S   
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLV---------SQDGKSKGIAYIEFKSEAD 65

Query: 83  AHRALNLVNGYVFKGKPMIIQFGR 106
           A + L    G    G+ + + +  
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 46.2 bits (109), Expect = 1e-08
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 10/93 (10%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +  + + + NL++D    D       LF    +     + K    G+ +G AF++F   E
Sbjct: 6   DDNATIRVTNLSEDTRETDLQ----ELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A RA+  V+G+ +    + +++      AKPS
Sbjct: 62  DAARAIAGVSGFGYDHLILNVEW------AKPS 88

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 2e-08
 Identities = 17/105 (16%), Positives = 39/105 (37%), Gaps = 17/105 (16%)

Query: 3   KLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVK 62
           +L  E++++        +      +Y   +A  +        F      ++       ++
Sbjct: 4   QLRFEDVVN-------QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIME-------IR 49

Query: 63  LMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
           +      +G +FV F + E A  A+  VNG   +G  +   +G+ 
Sbjct: 50  VF---PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE 91

>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 = 44.9 bits (106), Expect = 4e-08
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+ NL + +  D    +FG  +GSI       I++    GR RG AFV +   E A  A
Sbjct: 9   LYVTNLPRTITDDQLDTIFGK-YGSI---VQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 87  LNLVNGYVFKG--KPMIIQF 104
           ++ +N  + +G  +P+ ++ 
Sbjct: 65  ISALNNVIPEGGSQPLSVRL 84

>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 = 44.6 bits (105), Expect = 5e-08
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  L+ +   +       S F         ++++     R RG  FVT+ +VE    A
Sbjct: 9   LFIGGLSFETTDESLR----SHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 87  LNLVNGYVFKGKPM 100
           +N    +   G+ +
Sbjct: 65  MNA-RPHKVDGRVV 77

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 6e-08
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++  L+ D        VF       +      +VK  +  R RG  FVTF +++ A  A
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVV----VVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 87  LNLVNGYVFKGKPMIIQF 104
           +  +NG    G+ + +  
Sbjct: 64  MMAMNGKSVDGRQIRVDQ 81

>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 = 44.8 bits (105), Expect = 7e-08
 Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 10/94 (10%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           GN  SVL + NL  + V         SLF           VK++     +  A V     
Sbjct: 1   GN--SVLLVSNLNPERVTPQ------SLFILFGVYGDVQRVKILF--NKKENALVQMADG 50

Query: 81  ELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
             A  A++ +NG+   GKP+ I   ++     P 
Sbjct: 51  NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR 84

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 9e-08
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           N  + +Y+  L + V     +     LF       +  + K    G+ +G  FV F S E
Sbjct: 7   NQDATVYVGGLDEKVSEPLLW----ELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 82  LAHRALNLVNGYVFKGKPMIIQF 104
            A  A+ +++     GKP+ +  
Sbjct: 63  DADYAIKIMDMIKLYGKPIRVNK 85

>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 = 44.3 bits (104), Expect = 1e-07
 Identities = 14/98 (14%), Positives = 36/98 (36%), Gaps = 5/98 (5%)

Query: 7   EEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQE 66
           + + ++P+ +          L+I  L+ +   +       + +         ++++    
Sbjct: 3   KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLR----NYYEQWGKLTDCVVMRDPAS 58

Query: 67  GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
            R RG  FVTF S+     A+     +   G+ +  + 
Sbjct: 59  KRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR 95

>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 = 43.9 bits (103), Expect = 1e-07
 Identities = 18/77 (23%), Positives = 26/77 (33%), Gaps = 4/77 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LY+  L K +   +       LF       +  I+     G  RG  F+ F     A  A
Sbjct: 9   LYVSGLPKTMTQKELE----QLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 87  LNLVNGYVFKGKPMIIQ 103
           +  +NG    G    I 
Sbjct: 65  IKGLNGQKPSGATEPIT 81

>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 = 43.9 bits (103), Expect = 1e-07
 Identities = 21/81 (25%), Positives = 30/81 (37%), Gaps = 4/81 (4%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +P   L +  L+      D       +F          IV   Q  R RG AFV F +V+
Sbjct: 7   DPNCCLGVFGLSLYTTERDLR----EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

Query: 82  LAHRALNLVNGYVFKGKPMII 102
            A  A    NG    G+ + +
Sbjct: 63  DAKEAKERANGMELDGRRIRV 83

>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 = 43.4 bits (102), Expect = 1e-07
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++I  L+     +         FG     K  L+++     R RG  FVTF       + 
Sbjct: 3   MFIGGLSWQTTQEGLR----EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 87  LNLVNGYVFKGKPM 100
           L   + +    K +
Sbjct: 59  LAQ-SRHELDSKTI 71

>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 = 43.1 bits (101), Expect = 2e-07
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 26  VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
           VLY+  LA++V        F   FG I       I    +  + RG AFV F   E A  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIP-FGDI---TDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 86  ALNLVNGYVFKGKPMIIQFGR 106
           A++ +N     G+ + +   +
Sbjct: 63  AIDNMNESELFGRTIRVNLAK 83

>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 = 43.0 bits (101), Expect = 4e-07
 Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 8/92 (8%)

Query: 21  GNPASVLYIKNL--AKDVVPDDFFFVF----GSLFGSIDAAKSGLIVKLMQEGRM--RGQ 72
           G+P  VL + N+   ++++ D+ +                 KS  I + +    +   G+
Sbjct: 1   GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60

Query: 73  AFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
            FV F SV    +A+  + G  F  + ++ ++
Sbjct: 61  IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 92

>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 = 42.0 bits (98), Expect = 6e-07
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 24  ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAK--SGLIVKLMQEGRMRGQAFVTFPSVE 81
           A  LY+ N+   +  +     F +    +       G  V  +Q  + +  AF+ F SV+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 82  LAHRALNLVNGYVFKGKPMII 102
              +A+   +G +F+G+ + I
Sbjct: 60  ETTQAMAF-DGIIFQGQSLKI 79

>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 = 42.3 bits (99), Expect = 6e-07
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           S + ++    +   + F  +    +G ++       V       + G  +V F   E A 
Sbjct: 28  SDVEMQEHYDEFFEEVFTEME-EKYGEVEEMN----VCDNLGDHLVGNVYVKFRREEDAE 82

Query: 85  RALNLVNGYVFKGKPMIIQF 104
           +A+  +N   F G+P+  + 
Sbjct: 83  KAVIDLNNRWFNGQPIHAEL 102

>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 = 42.1 bits (98), Expect = 7e-07
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLM-----QEGRMRGQAFVT 76
           +  S +Y++ L   V  DD    F    G +   K      +      + G+ +G A V+
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQ-CGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 77  FPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
           +     A  A+   +G  F+G  + +   R
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 94

>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 = 41.8 bits (98), Expect = 9e-07
 Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 5/83 (6%)

Query: 26  VLYIKNL--AKDVVPDDFFF--VFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           V+ IKN+    D   D      +   L            + L  +    G A V+F   E
Sbjct: 10  VVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-DRHPDGVASVSFRDPE 68

Query: 82  LAHRALNLVNGYVFKGKPMIIQF 104
            A   +  ++G  F G+ +  Q 
Sbjct: 69  EADYCIQTLDGRWFGGRQITAQA 91

>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 = 41.7 bits (97), Expect = 9e-07
 Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 11/90 (12%)

Query: 24  ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           +S + +KNL +D             +           +K     R +  AFVT  + E A
Sbjct: 5   SSGILVKNLPQDS-NCQEVHDLLKDYD----------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 84  HRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
             A+ + + Y F+GK +I+Q     A    
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCS 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 = 41.7 bits (97), Expect = 1e-06
 Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 7/93 (7%)

Query: 23  PASVLYIKNLAKDVV-PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
            +S L       DV    +    F SLF + D           Q  +   +  + F +  
Sbjct: 4   GSSGLIACVANDDVFSESETRAKFESLFRTYDK------DTTFQYFKSFKRVRINFSNPL 57

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            A  A   ++   F GK M + F +        
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ N+       D   +FG     +D      +  +  E   +G  FVTF +   A RA
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILD------VEIIFNERGSKGFGFVTFENSADADRA 67

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
              ++G V +G+ + +    
Sbjct: 68  REKLHGTVVEGRKIEVNNAT 87

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 4/88 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+++NL+     +D       LF +                + +G AFVTF   E A +A
Sbjct: 11  LFVRNLSYTSSEEDLE----KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
              V+G VF+G+ + +        A  S
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 40.5 bits (94), Expect = 2e-06
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
              +L++ ++ ++   D+        F      K+  +    + G  +G A V + + + 
Sbjct: 6   EGWILFVTSIHEEAQEDEIQ----EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 83  AHRALNLVNGYVFKGKPMIIQF 104
           A  A   +NG    G+ + + +
Sbjct: 62  ALAAKEALNGAEIMGQTIQVDW 83

>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 = 40.6 bits (94), Expect = 2e-06
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 10/85 (11%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
           P  +L++ NL ++        +F    G           ++         AFV F +   
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPG---------FKEVRLVPNRHDIAFVEFTTELQ 57

Query: 83  AHRALNLVNGYVF-KGKPMIIQFGR 106
           ++ A   + G+       M I F +
Sbjct: 58  SNAAKEALQGFKITPTHAMKITFAK 82

>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 = 40.8 bits (95), Expect = 2e-06
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++   LA  + P D        F ++   +   I+      R +G A+V F  ++    A
Sbjct: 21  VFCMQLAARIRPRDLE----DFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 76

Query: 87  LNLVNGYVFKGKPMIIQF 104
           + L  G    G P+I+Q 
Sbjct: 77  IGL-TGQRLLGVPIIVQA 93

>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 = 4e-06
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 12/87 (13%)

Query: 21  GNPASV-LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           G+  S  +++     D+  D+    F S +G +        + +      R  AFVTF  
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELRE-FFSQYGDV--------MDVFIPKPFRAFAFVTFAD 51

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGR 106
            ++A          + KG  + I    
Sbjct: 52  DQIAQSLCG--EDLIIKGISVHISNAE 76

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 4e-06
 Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++  L+ +   +D        F         +++      R RG  FVTF S ++  + 
Sbjct: 2   IFVGGLSVNTTVEDVK----HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 87  LNLVNGYVFKGKPMIIQF 104
             + + +    K +  + 
Sbjct: 58  CEI-HFHEINNKMVECKK 74

>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 = 40.0 bits (93), Expect = 5e-06
 Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 10/91 (10%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
              +P   + ++NL   V  D    +F   FG++       +  +      + QA + + 
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSK-FGTV-------LKIITFTKNNQFQALLQYA 53

Query: 79  SVELAHRALNLVNGYVF--KGKPMIIQFGRN 107
               A  A   ++G         + I F + 
Sbjct: 54  DPVSAQHAKLSLDGQNIYNACCTLRIDFSKL 84

>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 = 39.6 bits (92), Expect = 5e-06
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++IKNL K +     +  F +    +          +  E   +G  FV F + E A RA
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILS------CKVVCDENGSKGYGFVHFETQEAAERA 64

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG +   + + +   +
Sbjct: 65  IEKMNGMLLNDRKVFVGRFK 84

>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 = 39.6 bits (92), Expect = 5e-06
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 6/82 (7%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           S L +  L       D        F +        + K ++ G  +G  FV F   E   
Sbjct: 9   SDLIVLGLPWKTTEQDLK----EYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 85  RALNLVNGYVFKGKPMIIQFGR 106
           + ++    ++  G+    +   
Sbjct: 65  KVMS--QRHMIDGRWCDCKLPN 84

>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 = 38.6 bits (89), Expect = 8e-06
 Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 4/72 (5%)

Query: 27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
          LYI+ L       D       L        S   +      + +G  FV F S   A +A
Sbjct: 1  LYIRGLQPGTTDQDLV----KLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 56

Query: 87 LNLVNGYVFKGK 98
          +  +     + +
Sbjct: 57 VTALKASGVQAQ 68

>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 = 39.4 bits (91), Expect = 8e-06
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++ N+  +   +    +F  +   +       +V   + G+ +G  F  +   E A  A
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFR----LVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 87  LNLVNGYVFKGKPMIIQFGRNP 108
           +  +NG  F G+ + +    + 
Sbjct: 67  MRNLNGREFSGRALRVDNAASE 88

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.9 bits (92), Expect = 8e-06
 Identities = 21/114 (18%), Positives = 40/114 (35%), Gaps = 5/114 (4%)

Query: 1   MGKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLI 60
           + +L  ++   +P  +     +    L +  +   V           LF      +S  I
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR----QLFERYGPIESVKI 74

Query: 61  VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
           V   +  + RG  FV F S   A +A+  +NG+    K + +         +P 
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA-SGHQRPG 127

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 9e-06
 Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 12/89 (13%)

Query: 21  GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV 80
           G P+ VL+I+ L  +V   +   +        +          +   + + QAF+   + 
Sbjct: 5   GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTN----------ILMLKGKNQAFLELATE 54

Query: 81  ELAHRALNLV--NGYVFKGKPMIIQFGRN 107
           E A   +N         + +P+ IQ+  +
Sbjct: 55  EAAITMVNYYSAVTPHLRNQPIYIQYSNH 83

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.4 bits (91), Expect = 9e-06
 Identities = 12/94 (12%), Positives = 28/94 (29%), Gaps = 12/94 (12%)

Query: 23  PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
            + V++++ L + VV  D                       +     + QA V F +++ 
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICY----------VMMMPFKRQALVEFENIDS 63

Query: 83  AHRALNLV--NGYVFKGKPMIIQFGRNPAAAKPS 114
           A   +           G+     +  +    +P 
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-05
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
           +P    ++ NL  DV  +         F  ++ +   L  +     R++G  +  F  ++
Sbjct: 13  SPPYTAFLGNLPYDVTEESIK----EFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLD 68

Query: 82  LAHRALNLVNGYVFKGKPMIIQFGRNP 108
               AL+L N      K + +      
Sbjct: 69  SLLSALSL-NEESLGNKRIRVDVADQA 94

>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 = 38.2 bits (88), Expect = 2e-05
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + I+NL+ +++ ++        FGSI+        K  +       AF+ F + + A RA
Sbjct: 7   IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK--EHSFNNCCAFMVFENKDSAERA 64

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
           L + N  +   + + +      A  KP
Sbjct: 65  LQM-NRSLLGNREISVSL----ADKKP 86

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 2e-05
 Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 12/97 (12%)

Query: 18  YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTF 77
           Y   NP + L++  L  +         F                  +   +    A++ +
Sbjct: 11  YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRT----------IDHVKGDSFAYIQY 60

Query: 78  PSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKPS 114
            S++ A  A   + G+   G    ++   + A + PS
Sbjct: 61  ESLDAAQAACAKMRGFPLGGPDRRLRV--DFAKSGPS 95

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (89), Expect = 2e-05
 Identities = 13/95 (13%), Positives = 26/95 (27%), Gaps = 10/95 (10%)

Query: 19  TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFP 78
           ++G   +V+  KNL    +  +    F                  +        A V F 
Sbjct: 5   SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGR----------VLLPEGGITAIVEFL 54

Query: 79  SVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
               A +A   +    F   P+ +++         
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAA 89

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (87), Expect = 2e-05
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 11/83 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + I+ L  DV   +   +                       + +G AFVT  + E A  A
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-----------CFVDKYKGTAFVTLLNGEQAEAA 49

Query: 87  LNLVNGYVFKGKPMIIQFGRNPA 109
           +N  +    + + + +Q     A
Sbjct: 50  INTFHQSRLRERELSVQLQPTDA 72

>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 = 37.5 bits (86), Expect = 3e-05
 Identities = 10/80 (12%), Positives = 27/80 (33%), Gaps = 4/80 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L++ N        +   +       +      + +  ++    R  A++   S E A   
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQD-INVV---ALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 59

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +  +NG   +G  ++ +   
Sbjct: 60  VEKLNGLKIEGYTLVTKVSN 79

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 3e-05
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 12/87 (13%)

Query: 20  AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPS 79
           A    + LY+     D+ P      F      ID          +     R  AFVT+  
Sbjct: 1   APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIID----------LSMDPPRNCAFVTYEK 48

Query: 80  VELAHRALNLVNGYVFKGKPMIIQFGR 106
           +E A +A+  +NG   +   + +   R
Sbjct: 49  MESADQAVAELNGTQVESVQLKVNIAR 75

>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 = 37.7 bits (87), Expect = 3e-05
 Identities = 14/89 (15%), Positives = 29/89 (32%), Gaps = 10/89 (11%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  + K    ++       +   +             + + RG AFV + S   A  A
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIV--YASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 87  LNLVNGYVFK--GKPMIIQFGRNPAAAKP 113
              +     +  G  + + +      A+P
Sbjct: 62  RRKLMPGRIQLWGHQIAVDW------AEP 84

>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 = 36.9 bits (85), Expect = 4e-05
 Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 5/74 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           ++I  L+ D    D        F          +      GR RG  FV F   E   + 
Sbjct: 2   MFIGGLSWDTTKKDLK----DYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57

Query: 87  LNLVNGYVFKGKPM 100
           ++    +   GK +
Sbjct: 58  MDQ-KEHKLNGKVI 70

>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 = 37.0 bits (85), Expect = 6e-05
 Identities = 15/87 (17%), Positives = 26/87 (29%), Gaps = 5/87 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++  L                F      +  +++   Q G+ RG  FVT      A RA
Sbjct: 13  IFVGGLPYHTTDASLR----KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 87  LNLVNGYVFKGKPMIIQFGRNPAAAKP 113
               N     G+   +      A  + 
Sbjct: 69  CKDPNPI-IDGRKANVNLAYLGAKPRS 94

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 7e-05
 Identities = 16/80 (20%), Positives = 22/80 (27%), Gaps = 5/80 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           LYI NL   +   +   +       I        +     G  RG  F    S E     
Sbjct: 21  LYISNLPLSMDEQELENMLKPFGQVIST-----RILRDSSGTSRGVGFARMESTEKCEAV 75

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           +   NG   K  P +     
Sbjct: 76  IGHFNGKFIKTPPGVSAPTE 95

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 1e-04
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 26  VLYIKNLAKDVVPDDF--FFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELA 83
           ++++  L++ +   +      +   FG I                    A+VT+   E A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 84  HRALNLVNGYVFKGKPM 100
            RA+  VN  V  G+ +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>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 = 35.8 bits (82), Expect = 1e-04
 Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 11/83 (13%)

Query: 25  SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAH 84
           + LYI NL+  V  DD   +FG             +    Q     G AFV +P    A 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGD-RK---------LPLAGQVLLKSGYAFVDYPDQNWAI 51

Query: 85  RALNLVNG-YVFKGKPMIIQFGR 106
           RA+  ++G     GK M + +  
Sbjct: 52  RAIETLSGKVELHGKIMEVDYSV 74

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (83), Expect = 2e-04
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           L+I  L+ +   +     F   +G++      ++++     R RG  FVT+ +VE    A
Sbjct: 9   LFIGGLSFETTDESLRSHFEQ-WGTL---TDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 87  LNLVNGYVFKGKPM 100
           +N     V      
Sbjct: 65  MNARPHKVDGRVVE 78

>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 = 34.6 bits (79), Expect = 3e-04
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           +++  L+ D   +     FG  FG +++ +   +    +  + RG  F+TF   E   + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGG-FGEVESIE---LPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 87  LNLVNGYVFKGKPMIIQ 103
           +     +        I+
Sbjct: 58  MEK-KYHNVGLSKCEIK 73

>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 = 34.4 bits (78), Expect = 5e-04
 Identities = 18/97 (18%), Positives = 33/97 (34%), Gaps = 12/97 (12%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
                ++I+NL+ D   +        +       K   +V        +G AF  F + E
Sbjct: 6   TEGKTVFIRNLSFDSEEEALG----EVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 82  LAHRALNLVN------GYVFKGKPMIIQF--GRNPAA 110
            A + L   +      G    G+ + +     R+ AA
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.0 bits (77), Expect = 9e-04
 Identities = 9/80 (11%), Positives = 18/80 (22%), Gaps = 11/80 (13%)

Query: 27  LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
           + +  L       D                         + +  G   V +   E    A
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVC-----------YADVQKDGMGMVEYLRKEDMEYA 66

Query: 87  LNLVNGYVFKGKPMIIQFGR 106
           L  ++   F+       + R
Sbjct: 67  LRKLDDTKFRSHEGETSYIR 86

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.7 bits (74), Expect = 0.002
 Identities = 14/93 (15%), Positives = 27/93 (29%), Gaps = 11/93 (11%)

Query: 22  NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVE 81
               V++I +  +              FG I                   +AF+   + E
Sbjct: 6   ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL---------ILNKINEAFIEMATTE 56

Query: 82  LAHRALNLV--NGYVFKGKPMIIQFGRNPAAAK 112
            A  A++       +  GKP+ +   +     K
Sbjct: 57  DAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIK 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	114
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.95
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.93
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.92
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.92
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.92
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.92
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.92
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.92
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.92
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.92
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.92
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.91
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.9
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.9
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.9
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.9
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.89
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.89
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.88
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.88
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.88
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.88
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.87
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.87
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.87
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.87
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.86
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.86
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.86
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.85
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.85
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.84
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.82
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.82
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.82
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.75
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	99.7
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.66
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.61
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.52
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.07
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.55
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.45
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.73

>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=99.95  E-value=7.7e-28  Score=138.86  Aligned_cols=100  Identities=47%  Similarity=0.807  Sum_probs=92.5

Q ss_pred             hhhhcCCCCCcCCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHH
Q 033648            7 EEILSLPMFKNYTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA   86 (114)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   86 (114)
                      ||++.+|..+++++..|+++|||+|||.++++++|+.+|+. ||.+..+.   .+.+..+|..+|||||+|.+.++|..|
T Consensus         1 ee~~~~p~~~~~~~~~ps~tl~V~nLp~~~t~~~l~~~f~~-~G~v~~~~---~~~~~~~g~~~g~~fV~f~~~~~A~~A   76 (102)
T d2cpxa1           1 EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFAR-FQEKKGPP---IQFRMMTGRMRGQAFITFPNKEIAWQA   76 (102)
T ss_dssp             SSSCCCSCCCCCCCCSCCSEEEEECCCTTCCHHHHHHHTHH-HHHSSSSC---CEEEEECSSSCSEEEEECSSHHHHHHH
T ss_pred             ChhhhCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhh-ccceeeEE---eecccccccccccceEEeccHHHHHHH
Confidence            57889999999999999999999999999999999999999 99998876   355667899999999999999999999


Q ss_pred             HHHhCCcccCCceEEEEeccCCCC
Q 033648           87 LNLVNGYVFKGKPMIIQFGRNPAA  110 (114)
Q Consensus        87 ~~~l~g~~~~g~~l~v~~a~~~~~  110 (114)
                      +..|||..++|++|.|+||+++.+
T Consensus        77 i~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          77 LHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             HHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             HHHhCCCEECCEEEEEEeCCCccc
Confidence            999999999999999999998764

>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=99.93  E-value=1.3e-25  Score=129.46  Aligned_cols=88  Identities=24%  Similarity=0.371  Sum_probs=81.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+++++|||+|||+++++++|+++|++ ||.+..++   .+.+..+|.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~~~---~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i   90 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAK---VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   90 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGG-GSCCSEEE---EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-hccccccc---eeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            467789999999999999999999999 99998886   46678899999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCC
Q 033648          101 IIQFGRNPAAAK  112 (114)
Q Consensus       101 ~v~~a~~~~~~~  112 (114)
                      +|++|+++.+.+
T Consensus        91 ~V~~a~~k~~~k  102 (102)
T d2cpza1          91 KVQLKRSKNDSK  102 (102)
T ss_dssp             EEECCCCSCCCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999987654

>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=99.92  E-value=8.3e-25  Score=124.10  Aligned_cols=86  Identities=17%  Similarity=0.234  Sum_probs=79.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .++++|||+|||+++++++|+++|++ ||.|.++.   .+.++.++.++|||||+|.+.++|..|+..|||..++|++|.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   80 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSK-SGDIKKII---MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR   80 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHH-HCCcceec---cccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            56789999999999999999999999 99999886   456778899999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |+||.+....
T Consensus        81 V~~a~~~~~g   90 (93)
T d1h2vz_          81 TDWDAGFKEG   90 (93)
T ss_dssp             EEEESCCCTT
T ss_pred             EEEcCCCCCC
Confidence            9999876544

>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=99.92  E-value=2.5e-25  Score=123.51  Aligned_cols=80  Identities=25%  Similarity=0.508  Sum_probs=74.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      +++|||+|||+++++++|+++|++ ||.|..++   .+.++.+|.++|||||+|.+.++|.+|+..|||..++|++|+|+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~-~G~v~~~~---i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRA-IGPINTCR---IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHT-TSCEEEEE---CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHH-hCCcceee---eeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            578999999999999999999999 99999887   35577889999999999999999999999999999999999999


Q ss_pred             eccC
Q 033648          104 FGRN  107 (114)
Q Consensus       104 ~a~~  107 (114)
                      +|++
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9986

>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=99.92  E-value=7.6e-25  Score=123.10  Aligned_cols=84  Identities=17%  Similarity=0.271  Sum_probs=76.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ...+++|||+|||+.+++++|+++|++ ||.|.+++   .+.++.+|.++|||||+|.+.++|++|+..|||..++|+.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~-~G~i~~v~---i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l   79 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIH---LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   79 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-cCCccccc---ccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345689999999999999999999999 99999887   45677899999999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|+||.++
T Consensus        80 ~V~~a~~k   87 (88)
T d1rk8a_          80 QVDWCFVK   87 (88)
T ss_dssp             EEEESEEC
T ss_pred             EEEEecCC
Confidence            99999865

>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=99.92  E-value=1.2e-24  Score=120.71  Aligned_cols=80  Identities=26%  Similarity=0.502  Sum_probs=74.5

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+++|++ ||.|..++   .+.+..+|..+|||||+|.+.++|+.|+..|||..++|++|+|+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~-~G~v~~v~---i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~   77 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGS-IGEIESCK---LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHH-hCCccccc---ceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            367999999999999999999999 99998886   45677889999999999999999999999999999999999999


Q ss_pred             eccC
Q 033648          104 FGRN  107 (114)
Q Consensus       104 ~a~~  107 (114)
                      +|+|
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            9986

>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=99.92  E-value=7.8e-25  Score=121.03  Aligned_cols=80  Identities=31%  Similarity=0.443  Sum_probs=74.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      +.|||+|||+.+++++|+++|++ ||.|.+++   .+.++.+|.++|||||+|.+.++|..|++.|||..++|++|+|++
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~-~G~i~~v~---i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~   76 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSP-AGPILSIR---VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   76 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHH-hCCEeEEE---EEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            36999999999999999999999 99999887   456788899999999999999999999999999999999999999


Q ss_pred             ccCC
Q 033648          105 GRNP  108 (114)
Q Consensus       105 a~~~  108 (114)
                      |+.+
T Consensus        77 a~~d   80 (80)
T d1cvja1          77 SQRD   80 (80)
T ss_dssp             CCCC
T ss_pred             eCCC
Confidence            9753

>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=99.92  E-value=6.8e-25  Score=124.47  Aligned_cols=85  Identities=22%  Similarity=0.298  Sum_probs=77.9

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .++.++|||+|||.++++++|+++|++ ||.|..+++   +.+..+|.++|||||+|.+.++|++|+..|||..++|+.|
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~-~G~v~~v~~---~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTHM---PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHH-hCCccccce---eecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345689999999999999999999999 999988863   4567789999999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      +|++|+++.
T Consensus        82 ~V~~A~~~~   90 (93)
T d1x5ua1          82 RVNKASAHN   90 (93)
T ss_dssp             EEEETTTTS
T ss_pred             EEEEcCCCC
Confidence            999999876

>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=99.92  E-value=8.3e-25  Score=123.41  Aligned_cols=84  Identities=25%  Similarity=0.422  Sum_probs=77.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||..+++++|+++|++ ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~-~G~v~~v~---i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~   81 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRP-FGSISRIY---LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   81 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTT-TCCEEEEE---EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHH-hccccccc---ccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            45678999999999999999999999 99998886   456777899999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |++|+++.
T Consensus        82 v~~akp~~   89 (90)
T d2cq0a1          82 VEWAKPST   89 (90)
T ss_dssp             EEESSCCC
T ss_pred             EEeeeCCC
Confidence            99999875

>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=99.92  E-value=3.6e-24  Score=129.46  Aligned_cols=84  Identities=23%  Similarity=0.326  Sum_probs=77.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...++|||+|||+++++++|+++|++ ||.|.+++   .+.+..+|.++|||||+|.+.++|..|+..|||..++|+.|+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~  115 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFER-YGPIESVK---IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHH-HSCEEEEE---EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHh-hccccccc---cccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34468999999999999999999999 99999887   466788999999999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |++|+...
T Consensus       116 V~~a~~~~  123 (139)
T d1u6fa1         116 VALAASGH  123 (139)
T ss_dssp             EEESSCCC
T ss_pred             EEEcCCCC
Confidence            99998654

>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=99.92  E-value=5.6e-25  Score=123.90  Aligned_cols=84  Identities=25%  Similarity=0.328  Sum_probs=77.1

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+|||+|||+++++++|+++|++ ||.|.++++   +.++.+|.++|||||+|.+.++|++|+..|||..++|++|.|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~-~G~i~~v~i---~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v   79 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   79 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTT-TSCCCCEEC---CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhh-CCeEEeccc---ccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4578999999999999999999999 999988863   456778999999999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      ++|++...
T Consensus        80 ~~a~p~~~   87 (89)
T d2cqba1          80 NLAKPMRI   87 (89)
T ss_dssp             EECCCCCC
T ss_pred             EEeCCCCC
Confidence            99998754

>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=99.92  E-value=1.4e-24  Score=123.36  Aligned_cols=88  Identities=18%  Similarity=0.366  Sum_probs=77.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEe-ccCCCceeEEEEEeCCHHHHHHHHHHh-CCcccCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKL-MQEGRMRGQAFVTFPSVELAHRALNLV-NGYVFKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~g   97 (114)
                      ...++++|||+|||+.+++++|+.+|++ ||.|..+++   +.+ ..+|.++|||||+|.+.++|.+|+..| ||..++|
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~-~G~i~~v~i---~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G   79 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFST-FGELKTVRL---PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   79 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCceEEEE---EeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECC
Confidence            3466788999999999999999999999 999988863   233 347899999999999999999999998 8999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      ++|.|+||+++...
T Consensus        80 r~l~V~~A~~~~~~   93 (94)
T d2cpha1          80 RRLVLEWADSEVTV   93 (94)
T ss_dssp             CBCEEEECCCCCCC
T ss_pred             EEEEEEEcCCCCCc
Confidence            99999999988654

>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=99.91  E-value=2e-24  Score=121.74  Aligned_cols=87  Identities=24%  Similarity=0.400  Sum_probs=78.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+|||+|||+++++++|+++|++ ||.|..+.   .+.+..+|.++|||||+|.++++|+.|+..|||..++|+.|.|
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~-~G~i~~~~---~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   79 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSK-YGQISEVV---VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   79 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHH-HSCCCEEE---ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhc-ccccccee---eccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4567999999999999999999999 99998775   3456678999999999999999999999999999999999999


Q ss_pred             EeccCCCCCCC
Q 033648          103 QFGRNPAAAKP  113 (114)
Q Consensus       103 ~~a~~~~~~~~  113 (114)
                      ++|.++.+.++
T Consensus        80 ~~a~~~~~~rs   90 (90)
T d1x5sa1          80 DQAGKSSDNRS   90 (90)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEcCCCCCCCC
Confidence            99998887653

>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=99.91  E-value=4e-24  Score=122.52  Aligned_cols=86  Identities=24%  Similarity=0.327  Sum_probs=78.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||+.+++++|+++|.+ ||.|..+++   +.+..++.++|||||+|.+.++|.+|+..|||..++|+.|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~-~g~v~~v~i---~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~   81 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSA-YGPLSELHY---PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHh-cCCceeeee---cccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            45678999999999999999999999 999988863   45677899999999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.+|+++...
T Consensus        82 V~~a~~~~~~   91 (99)
T d1whwa_          82 VLPSTIKKEA   91 (99)
T ss_dssp             EEECCCCSTT
T ss_pred             EEECCCCCcc
Confidence            9999987654

>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=99.91  E-value=1.6e-24  Score=120.04  Aligned_cols=80  Identities=13%  Similarity=0.207  Sum_probs=67.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+++|++ ||.+..+.   .+.+..+|.++|||||+|.+.++|.+|+..|||..++|++|.|+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~-~G~v~~~~---~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~   76 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQD-INVVALSI---RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK   76 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHH-TTCCCCEE---ECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHH-hCcEEeee---eecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            378999999999999999999999 99997664   34456678899999999999999999999999999999999999


Q ss_pred             eccC
Q 033648          104 FGRN  107 (114)
Q Consensus       104 ~a~~  107 (114)
                      +|+|
T Consensus        77 ~a~P   80 (81)
T d2ghpa1          77 VSNP   80 (81)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9986

>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=99.91  E-value=6.5e-24  Score=118.00  Aligned_cols=78  Identities=31%  Similarity=0.400  Sum_probs=72.0

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      +.|+++|||+|||+++++++|+++|++ ||.|.+++   .+.+..+|.++|||||+|.+.++|..|+..|||..++|++|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~-~G~i~~v~---i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   81 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVS---IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   81 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHT-TSCEEEEE---EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHH-hCCCcccc---ccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEe
Confidence            356789999999999999999999999 99998886   45677889999999999999999999999999999999999


Q ss_pred             EE
Q 033648          101 II  102 (114)
Q Consensus       101 ~v  102 (114)
                      +|
T Consensus        82 ~V   83 (83)
T d2cqca1          82 RV   83 (83)
T ss_dssp             EE
T ss_pred             EC
Confidence            87

>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=99.91  E-value=1.1e-23  Score=117.62  Aligned_cols=79  Identities=25%  Similarity=0.445  Sum_probs=72.2

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--ceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--KPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~~l  100 (114)
                      .+++|||+|||+.+++++|+++|++ ||.|.+++   .+.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~-~G~v~~v~---i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i   80 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQ-YGRIITSR---ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI   80 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHH-hCCccccc---cccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEE
Confidence            3578999999999999999999999 99999887   45677889999999999999999999999999999987  569


Q ss_pred             EEEec
Q 033648          101 IIQFG  105 (114)
Q Consensus       101 ~v~~a  105 (114)
                      .|.||
T Consensus        81 ~V~~A   85 (85)
T d1fxla2          81 TVKFA   85 (85)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99986

>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=99.90  E-value=1.6e-23  Score=116.87  Aligned_cols=79  Identities=30%  Similarity=0.563  Sum_probs=72.9

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC--ceE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG--KPM  100 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g--~~l  100 (114)
                      ..++|||+|||+++++++|+.+|++ ||.|..++   .++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~-~G~i~~~~---~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l   80 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGK-YGSIVQKN---ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL   80 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTS-SSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHh-hCCEeeee---eecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEE
Confidence            4567999999999999999999999 99999887   46677899999999999999999999999999999876  889


Q ss_pred             EEEec
Q 033648          101 IIQFG  105 (114)
Q Consensus       101 ~v~~a  105 (114)
                      +|+||
T Consensus        81 ~V~~A   85 (85)
T d1b7fa2          81 SVRLA   85 (85)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99987

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=4.7e-24  Score=119.11  Aligned_cols=81  Identities=25%  Similarity=0.374  Sum_probs=75.3

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .+|||+|||+++++++|+.+|++ ||.|..++   .++++.+|.++|||||+|.+.++|..|+..|||..++|++|.|++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~-~G~v~~v~---i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTS-FGPLKAFN---LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTS-SSCEEEEE---EECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHh-cCccceEE---eeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            46999999999999999999999 99999887   455778899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 033648          105 GRNPA  109 (114)
Q Consensus       105 a~~~~  109 (114)
                      |++..
T Consensus        78 A~~~~   82 (85)
T d2u2fa_          78 ASVGA   82 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98654

>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=99.90  E-value=2.9e-23  Score=116.98  Aligned_cols=84  Identities=24%  Similarity=0.357  Sum_probs=73.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+.++|||+|||.++++++|+++|+. ||.|..+++   +.+..+  .++||||+|.+.++|.+|+..|||..++|+.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~-~G~i~~v~i---~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~   79 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQ-IGPCKSCKM---ITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   79 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHH-HSCEEEEEE---ECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHh-cCCceeeee---ecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            45678999999999999999999999 999988762   333333  478999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.+|++....
T Consensus        80 v~~a~~~~~~   89 (90)
T d2cqia1          80 VNWATTPSSQ   89 (90)
T ss_dssp             EEECCCTTCC
T ss_pred             EEEcCCCCCC
Confidence            9999977644

>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=99.90  E-value=1.3e-23  Score=116.82  Aligned_cols=81  Identities=22%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEecc
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~  106 (114)
                      |||+|||+++++++|+++|++ ||.+..+.  ..+.+..+|+++|||||+|.+.++|.+|+..|||..++|++|+|++|.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~-~G~i~~~~--~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSA-FGVILQTP--KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHT-TSCBSSCC--EECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHH-hCceeeeE--EEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEec
Confidence            799999999999999999999 99986542  135567789999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 033648          107 NPAA  110 (114)
Q Consensus       107 ~~~~  110 (114)
                      ++..
T Consensus        78 ~k~~   81 (83)
T d1x5ta1          78 KKDS   81 (83)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            7764

>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=99.90  E-value=2.1e-23  Score=114.69  Aligned_cols=77  Identities=31%  Similarity=0.413  Sum_probs=70.6

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      +|||+|||+++++++|+++|++ ||.|..+++    ....+|+++|||||+|.+.++|.+|+..|||..++|++|+|++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~-~G~v~~~~i----~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAE-FGTLKKAAV----HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHH-HSCEEEEEE----SCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHH-hCCCeEEEE----EEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            5999999999999999999999 999988763    33458899999999999999999999999999999999999998


Q ss_pred             cC
Q 033648          106 RN  107 (114)
Q Consensus       106 ~~  107 (114)
                      .+
T Consensus        77 ~S   78 (78)
T d1no8a_          77 TS   78 (78)
T ss_dssp             CC
T ss_pred             eC
Confidence            64

>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=99.90  E-value=2.5e-23  Score=120.07  Aligned_cols=82  Identities=17%  Similarity=0.360  Sum_probs=75.8

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..+|||+|||+++++++|+++|++ ||.|.+++   .+.+..+|.++|||||+|.+.++|..|+..|||..++|+.|.|+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~-~G~i~~v~---i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSE-VGPVVSFR---LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHT-TSCCSEEE---EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhc-cccccccc---cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            357999999999999999999999 99998886   46677889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 033648          104 FGRNPA  109 (114)
Q Consensus       104 ~a~~~~  109 (114)
                      +|.++.
T Consensus        84 ~a~~~~   89 (104)
T d1p1ta_          84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             ECCCCC
Confidence            998654

>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=99.89  E-value=3.4e-23  Score=118.89  Aligned_cols=91  Identities=22%  Similarity=0.368  Sum_probs=77.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccc-----eeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSG-----LIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~-----~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      ....++|||+|||+.+++++|+++|.. ||.+..+.+.     ....+..+|..+|||||+|.+.++|..|+..|||..+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~-~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQ-CGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTT-TSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHH-CceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            356789999999999999999999999 9987533211     1234456789999999999999999999999999999


Q ss_pred             CCceEEEEeccCCCCCC
Q 033648           96 KGKPMIIQFGRNPAAAK  112 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~~~  112 (114)
                      +|+.|+|++|+++...+
T Consensus        84 ~gr~i~V~~a~~~~p~~  100 (101)
T d2cpea1          84 QGSKLKVSLARKKPPMN  100 (101)
T ss_dssp             TTEECEEECSSCCCCST
T ss_pred             CCEEEEEEEcCCCCCCC
Confidence            99999999999877654

>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=99.89  E-value=2.4e-23  Score=116.14  Aligned_cols=78  Identities=24%  Similarity=0.379  Sum_probs=69.2

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCC---CceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEG---RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      |||+|||+++++++|+.+|++ ||.|..+++   +.+..++   .++|||||+|.+.++|.+|+..|||..++|+.|.|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~-~G~v~~v~i---~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSK-VGAIKSCTI---SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHT-TSCEEEEEE---EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHH-hCCccccce---ecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            799999999999999999999 999998873   3444443   468999999999999999999999999999999999


Q ss_pred             eccCC
Q 033648          104 FGRNP  108 (114)
Q Consensus       104 ~a~~~  108 (114)
                      +|+..
T Consensus        77 ~a~~~   81 (85)
T d2cpfa1          77 ISERA   81 (85)
T ss_dssp             CSSCS
T ss_pred             ECCCC
Confidence            98643

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=9.8e-23  Score=114.76  Aligned_cols=83  Identities=18%  Similarity=0.277  Sum_probs=74.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ...++|||+|||+++++++|+.+|++ ||.|..++   .++++.+|.++|||||.|.+.++|++|++.  +..++|+.|.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~   79 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFST-FGEVLMVQ---VKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCD   79 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGG-GSCEEEEE---EEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHh-hcccceee---eccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeE
Confidence            45678999999999999999999999 99999887   466788999999999999999999999984  4579999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |.+|.++..
T Consensus        80 v~~a~~k~~   88 (90)
T d2cqga1          80 CKLPNSKQS   88 (90)
T ss_dssp             EECCCTTCC
T ss_pred             EEeCCCCCC
Confidence            999988764

>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=99.89  E-value=8.3e-23  Score=116.59  Aligned_cols=86  Identities=21%  Similarity=0.371  Sum_probs=75.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC------Cccc
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN------GYVF   95 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------g~~~   95 (114)
                      ..+++|||+|||+++++++|+++|.+ ||.+..+.   .+.+..++.++|||||+|.+.++|.+|+..+|      |..+
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~-~G~v~~~~---~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQ-FGDLKYVR---VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHT-TSCEEEEE---CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhc-cccceeee---eccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            45678999999999999999999999 99988775   34466688899999999999999999999987      6678


Q ss_pred             CCceEEEEeccCCCCC
Q 033648           96 KGKPMIIQFGRNPAAA  111 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~~  111 (114)
                      +|+.|.|++|+++.++
T Consensus        82 ~gr~l~v~~a~~k~~a   97 (98)
T d1x4ha1          82 DGRQLKVDLAVTRDEA   97 (98)
T ss_dssp             SSCEEEEECCCCCCCC
T ss_pred             CCEEEEEEECCCCCcC
Confidence            9999999999987654

>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=99.89  E-value=1.3e-22  Score=115.36  Aligned_cols=83  Identities=29%  Similarity=0.399  Sum_probs=73.5

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ..+++++|||+|||+++++++|+++|+. ||.+..+.      ....+..++||||+|.+.++|..|+..|||..+.|++
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~~~------~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~   82 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYK-YGAIRDID------LKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR   82 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE------ECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhc-CCceEEEE------ecccccccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4577789999999999999999999999 99987543      3345567899999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |+|++|++..
T Consensus        83 l~V~~a~~~r   92 (95)
T d1x4aa1          83 LRVEFPRSGR   92 (95)
T ss_dssp             CEEECCCCCC
T ss_pred             EEEEeccCCC
Confidence            9999998754

>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=99.89  E-value=1.2e-23  Score=115.41  Aligned_cols=76  Identities=20%  Similarity=0.294  Sum_probs=70.5

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      |+|||+|||+++++++|+++|++ ||.|..++   .+.++.+|.++|||||+|.+.++|++|+. +|+..++|+.|.|+.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQ-FGEVKECL---VMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTT-TSCCCCEE---EECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHH-hCCcceee---eecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEE
Confidence            67999999999999999999999 99998886   45678889999999999999999999996 799999999999987


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      |
T Consensus        76 A   76 (77)
T d1uawa_          76 A   76 (77)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.89  E-value=1.2e-23  Score=121.28  Aligned_cols=83  Identities=17%  Similarity=0.248  Sum_probs=75.1

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+.+|++ ||.|..+.   ...+..++.++|||||+|.+.++|.+|+ .++|..++|+.|.|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~-~G~i~~~~---i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~~l~G~~i~V~   94 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQ-WGKLTDCV---VMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPK   94 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTS-SCCCSEEE---EECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHh-hCccccee---ecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEE
Confidence            478999999999999999999999 99998886   3557778899999999999999999998 579999999999999


Q ss_pred             eccCCCCC
Q 033648          104 FGRNPAAA  111 (114)
Q Consensus       104 ~a~~~~~~  111 (114)
                      +|+++...
T Consensus        95 ~a~~ke~~  102 (103)
T d1x4ba1          95 RAVAREES  102 (103)
T ss_dssp             CCSSCCCC
T ss_pred             ECcccCCC
Confidence            99987653

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=7.4e-23  Score=117.95  Aligned_cols=82  Identities=23%  Similarity=0.341  Sum_probs=73.3

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ..++|||+|||+.+++++|+++|++ ||.|.+++   .+.+..+|.++|||||+|.+.++|++|++.+|+ .++|+.|.|
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~-~G~i~~v~---i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEG-FGDIEEAV---VITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHT-TSCEEEEE---ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhh-ccccccee---ccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            3467999999999999999999999 99999886   345677899999999999999999999998886 799999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      ++|....
T Consensus        84 ~~a~~~~   90 (103)
T d2cqda1          84 NLAYLGA   90 (103)
T ss_dssp             EESTTTC
T ss_pred             EEcCCCC
Confidence            9998653

>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=99.88  E-value=1.8e-22  Score=112.37  Aligned_cols=79  Identities=20%  Similarity=0.308  Sum_probs=72.4

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..+|||+|||+++++++|+++|++ ||.|..++   .+++..+|.++|||||+|.+.++|++|++ ++|..++|+.|.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~-~G~i~~v~---i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~   80 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQ-WGTLTDCV---VMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPK   80 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHh-hcccccee---ecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            368999999999999999999999 99999887   46678899999999999999999999996 69999999999999


Q ss_pred             eccC
Q 033648          104 FGRN  107 (114)
Q Consensus       104 ~a~~  107 (114)
                      .|.+
T Consensus        81 ~A~s   84 (84)
T d1l3ka1          81 RAVS   84 (84)
T ss_dssp             ECCC
T ss_pred             eeeC
Confidence            8863

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=3.4e-22  Score=113.13  Aligned_cols=85  Identities=24%  Similarity=0.314  Sum_probs=73.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      .....++|||+|||+.+++++|+++|++ ||.|..+++   +.+  .+..+|||||+|.+.++|.+|+..|||..++|+.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~-~G~v~~v~~---~~~--~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQ-FGKILDVEI---IFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGG-TSCEEEEEE---ECC--TTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhh-cceeeeccc---ccc--ccCCcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3455678999999999999999999999 999988763   223  2346899999999999999999999999999999


Q ss_pred             EEEEeccCCCC
Q 033648          100 MIIQFGRNPAA  110 (114)
Q Consensus       100 l~v~~a~~~~~  110 (114)
                      |+|++|+++..
T Consensus        81 l~V~~A~~r~~   91 (93)
T d2cq3a1          81 IEVNNATARVM   91 (93)
T ss_dssp             CEEEECCSSCC
T ss_pred             EEEEecCcCCC
Confidence            99999998653

>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=99.88  E-value=4.4e-23  Score=115.33  Aligned_cols=82  Identities=20%  Similarity=0.304  Sum_probs=68.9

Q ss_pred             CCCeEEecCCCCCCC-HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           23 PASVLYIKNLAKDVV-PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~-~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .+++|||+|||++++ +++|+++|++ ||.|..+++.  ..+..++.++|||||+|.+.++|.+|++ |||..++|+.|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~-~G~i~~v~i~--~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~   78 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEG-FGSIEKINIP--AGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREIS   78 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGG-GSCEEEEECC--SCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHh-hhhccceeee--cccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            467899999999876 5669999999 9999888642  2234678899999999999999999995 999999999999


Q ss_pred             EEeccCC
Q 033648          102 IQFGRNP  108 (114)
Q Consensus       102 v~~a~~~  108 (114)
                      |++|+++
T Consensus        79 V~~a~~k   85 (86)
T d2ghpa3          79 VSLADKK   85 (86)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999875

>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=99.88  E-value=2e-23  Score=117.88  Aligned_cols=82  Identities=17%  Similarity=0.218  Sum_probs=73.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .....+|||+|||+++++++|+.+|++ ||.+..+.+    .+..+|+++|||||+|.+.++|++|++ |||..++|++|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~-~G~i~~~~v----~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i   83 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISE-LFAKNDLAV----VDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEI   83 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHH-HHHHHTCCC----CEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhc-CCcEEEeee----eecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEE
Confidence            345568999999999999999999999 999987753    355688999999999999999999995 99999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|++|+++
T Consensus        84 ~V~~ak~k   91 (91)
T d1fjeb1          84 KLEKPKGR   91 (91)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99999864

>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=99.88  E-value=2.4e-22  Score=117.59  Aligned_cols=81  Identities=20%  Similarity=0.460  Sum_probs=72.5

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      +..+++|||+|||..+++++|+.+|++ ||.|..++      ...++.++|||||+|.+.++|..|+..|||..+.|+.|
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~-~G~v~~i~------~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   76 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGK-YGPIRQIR------VGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYL   76 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHT-TSCEEEEE------EECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhh-cCCeEeec------ccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            456789999999999999999999999 99998764      23466788999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      .|.+++..
T Consensus        77 ~V~~a~~~   84 (114)
T d2f9da1          77 VVLYYNAN   84 (114)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99998743

>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=99.88  E-value=9.1e-23  Score=115.13  Aligned_cols=82  Identities=35%  Similarity=0.602  Sum_probs=72.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHH----HHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           22 NPASVLYIKNLAKDVVPDDFFF----VFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~----~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      +|+++|||+|||+.+++++|++    +|++ ||.|.+++      ...++.++|||||+|.+.++|..|+..+||..++|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~-~G~i~~i~------~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g   73 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSR-FGQILDIL------VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   73 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGG-GSCEEEEE------CCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcc-cccccceE------EeeeccCCCceEEEECCHHHHHHHHHHhCCCEECC
Confidence            4688999999999999998864    5788 99987654      33467789999999999999999999999999999


Q ss_pred             ceEEEEeccCCCC
Q 033648           98 KPMIIQFGRNPAA  110 (114)
Q Consensus        98 ~~l~v~~a~~~~~  110 (114)
                      ++|.|++|+++++
T Consensus        74 ~~l~v~~ak~~~~   86 (91)
T d1nu4a_          74 KPMRIQYAKTDSD   86 (91)
T ss_dssp             EECEEEECSSCCT
T ss_pred             EEEEEEEeCCCch
Confidence            9999999998764

>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=99.88  E-value=8.6e-23  Score=114.80  Aligned_cols=81  Identities=26%  Similarity=0.416  Sum_probs=71.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      ..+|||+|||+++++++|+++|++ ||.|..+++.   .+  .+.++|||||+|.+.++|.+|+..|||..++|+.|.|+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~~~i~---~~--~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~   81 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSA-FGNILSCKVV---CD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   81 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHT-TSCEEEEEEC---CB--TTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHh-cCCceEEEEE---ee--cCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            457999999999999999999999 9999887632   22  34468999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 033648          104 FGRNPAA  110 (114)
Q Consensus       104 ~a~~~~~  110 (114)
                      +|+++.+
T Consensus        82 ~a~~~~~   88 (89)
T d1cvja2          82 RFKSRKE   88 (89)
T ss_dssp             ECCCTTT
T ss_pred             ECCCCCC
Confidence            9998764

>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=99.88  E-value=1.9e-22  Score=115.81  Aligned_cols=82  Identities=21%  Similarity=0.303  Sum_probs=72.7

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ....++|||+|||+++++++|+++|++ ||.|..+.    +....++.++|||||+|.+.++|.+|+..|||..+.|+++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~i~~~~----~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKP-FGQVISTR----ILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTT-TSCEEEEE----EEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhh-ccccccee----eecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            445688999999999999999999999 99997764    3344688899999999999999999999999999999999


Q ss_pred             EEEeccC
Q 033648          101 IIQFGRN  107 (114)
Q Consensus       101 ~v~~a~~  107 (114)
                      .|..++|
T Consensus        90 ~v~~~~P   96 (101)
T d1x5oa1          90 VSAPTEP   96 (101)
T ss_dssp             SCCCSSC
T ss_pred             ccCCCCC
Confidence            8877765

>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=99.88  E-value=2.7e-22  Score=112.48  Aligned_cols=79  Identities=22%  Similarity=0.285  Sum_probs=69.4

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc-CCceE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF-KGKPM  100 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-~g~~l  100 (114)
                      +|+++|||+|||+++++++|+++|++ ||.+..+.+       ..++.+++|||+|.+.++|.+|+..|||..+ +|++|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~-~G~v~~~~~-------~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l   79 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSS-NGGVVKGFK-------FFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL   79 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHT-TSCCEEEEE-------ECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhc-cCCEEEEEE-------eeecccceeEEEECCHHHHHHHHHhccCCEecCCCEE
Confidence            67889999999999999999999999 998865431       2345678999999999999999999999998 58999


Q ss_pred             EEEeccCC
Q 033648          101 IIQFGRNP  108 (114)
Q Consensus       101 ~v~~a~~~  108 (114)
                      +|+|+++.
T Consensus        80 ~v~~sk~~   87 (88)
T d2adca2          80 RVSFSKST   87 (88)
T ss_dssp             EEEECSSC
T ss_pred             EEEeCCCC
Confidence            99999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.6e-22  Score=109.40  Aligned_cols=76  Identities=18%  Similarity=0.335  Sum_probs=70.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      .+|||+|||+++++++|+++|++ ||.+..++   ...+..++.++|||||+|.+.+++.+|+ .+||..++|++|.|+.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~-~G~i~~~~---~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQ-YGKIEVIE---IMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRK   77 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTT-TSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHH-hccccccc---cccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEE
Confidence            57999999999999999999999 99998886   4567778999999999999999999998 5899999999999987


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.87  E-value=6.6e-22  Score=110.42  Aligned_cols=80  Identities=20%  Similarity=0.291  Sum_probs=71.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      +..++|||+|||+++++++|+++|.. +|.+....   .+....++.++|+|||+|.+.++|.+|+..|||..++|++|+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~-~~~~~~~~---~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYG-YQVIPGSV---CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTT-SCCCTTTC---EEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhh-cccceeEE---EEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            44567999999999999999999999 99886543   455667899999999999999999999999999999999999


Q ss_pred             EEec
Q 033648          102 IQFG  105 (114)
Q Consensus       102 v~~a  105 (114)
                      |++|
T Consensus        83 v~l~   86 (86)
T d2cqpa1          83 LVLG   86 (86)
T ss_dssp             EEES
T ss_pred             EEEC
Confidence            9986

>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=99.87  E-value=1e-22  Score=116.96  Aligned_cols=80  Identities=24%  Similarity=0.403  Sum_probs=72.9

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||+++++++|+.+|+. ||.|..++   .+.+..+|.++|||||+|.+.++|.+|+ .|||..++|+.|.|+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~-~G~V~~v~---i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~   92 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSA-VGKVRDVR---IISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   92 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTT-TSCEEEEE---ECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcC-CCeEEEEE---eeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEE
Confidence            468999999999999999999999 99998886   3556778999999999999999999999 599999999999999


Q ss_pred             eccCC
Q 033648          104 FGRNP  108 (114)
Q Consensus       104 ~a~~~  108 (114)
                      +|++.
T Consensus        93 ~a~~~   97 (101)
T d2cq4a1          93 ASQAE   97 (101)
T ss_dssp             EHHHH
T ss_pred             ECCCC
Confidence            98643

>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=99.87  E-value=3.5e-22  Score=113.70  Aligned_cols=82  Identities=23%  Similarity=0.339  Sum_probs=73.2

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+.++|||+|||+++++++|+.+|.+ ||.+..+        ..++..++||||+|.+.++|.+|+..|||..++|++|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~-~g~v~~~--------~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFED-ALEIRLV--------SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCS-EEEECCE--------EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHh-cccceee--------eecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            355689999999999999999999999 9987533        2467889999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|.||+++...
T Consensus        84 ~V~~a~~k~~~   94 (96)
T d1fjca_          84 SLYYTGEKGGT   94 (96)
T ss_dssp             EEEECSSSCCC
T ss_pred             EEEEeCCCCCC
Confidence            99999987653

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.5e-22  Score=110.42  Aligned_cols=75  Identities=23%  Similarity=0.290  Sum_probs=68.5

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      .|||+|||+++++++|+++|++ ||.|..+++   +.++.+++++|||||+|.+.++|++|+. +++..++|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~-~G~i~~~~i---~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSK-FGEVVDCTL---KLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHT-TSCEEEEEC---CCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHh-hcccccccc---ccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            4899999999999999999999 999998873   4577889999999999999999999996 7999999999999754

>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=99.87  E-value=3.8e-22  Score=113.56  Aligned_cols=79  Identities=23%  Similarity=0.345  Sum_probs=70.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ++.++|||+|||..+++++|+.+|++ ||.|.++++.         ..+|||||+|.+.++|..|+..|||..++|+.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~-fG~i~~v~i~---------~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~   85 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSP-FGQIMEIRVF---------PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   85 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHH-HSCEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHH-hCCceEEEEE---------ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            45678999999999999999999999 9999887631         2378999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |+||+++..
T Consensus        86 v~~ak~~p~   94 (96)
T d1x4ga1          86 CYWGKESPD   94 (96)
T ss_dssp             EECCCCCCS
T ss_pred             EEEcCCCCC
Confidence            999987653

>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=99.87  E-value=6.5e-22  Score=109.81  Aligned_cols=78  Identities=19%  Similarity=0.345  Sum_probs=68.8

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc-CCc
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF-KGK   98 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-~g~   98 (114)
                      ..+|+++|||+|||.++++++|+.+|+. ||.+..+++.        ...+|||||+|.+.++|..|+..|||..+ +|+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~-~G~i~~v~~~--------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   74 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQ-FPGFKEVRLV--------PNRHDIAFVEFTTELQSNAAKEALQGFKITPTH   74 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTT-STTEEEEEEC--------TTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhcc-CccEEEeeee--------cccceeEEEecCCHHHHHHHHHHhCCcEeCCCc
Confidence            4577899999999999999999999999 9999877531        12468999999999999999999999998 578


Q ss_pred             eEEEEecc
Q 033648           99 PMIIQFGR  106 (114)
Q Consensus        99 ~l~v~~a~  106 (114)
                      +|+|+||+
T Consensus        75 ~i~v~~ak   82 (83)
T d2b0ga1          75 AMKITFAK   82 (83)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEec
Confidence            99999997

>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=99.87  E-value=2.4e-22  Score=109.47  Aligned_cols=75  Identities=21%  Similarity=0.335  Sum_probs=68.7

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      +|||+|||+++++++|+++|+. ||.+..+.   .+.++.++..++||||+|.+.++|.+|++ +||..++|++|.|+.|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~-~G~i~~~~---~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQ-FGKVDDAM---LMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHT-TSCCSEEC---CBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHH-hCCcceee---eeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            4899999999999999999999 99998876   34567788999999999999999999996 9999999999999986

>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=99.87  E-value=4.2e-22  Score=114.84  Aligned_cols=87  Identities=17%  Similarity=0.272  Sum_probs=72.7

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      +..|.++|||+|||+++++++|+++|++ || +..+.+  ......++..+|||||+|.+.++|++|+ .|||..++|+.
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~-~g-~~~~~~--~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~   85 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRG-LN-ISAVRL--PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR   85 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTT-SC-EEEEEC--CBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHH-hc-ccccee--eeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEE
Confidence            3456789999999999999999999999 99 544442  2223457888999999999999998776 69999999999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |+|.+|+++...
T Consensus        86 l~V~~a~~~~~~   97 (104)
T d1wi8a_          86 IRVDVADQAQDK   97 (104)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999977654

>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=99.86  E-value=7.2e-22  Score=114.95  Aligned_cols=79  Identities=20%  Similarity=0.251  Sum_probs=70.7

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .+..++|||+|||+.+++++|+++|++ ||.|..+.+         ...++||||+|.+.++|.+|+..|||..+.|++|
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~-fG~I~~v~l---------~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l   76 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSR-FGSLGRVLL---------PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPL   76 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHT-TSCEEEEEC---------CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhc-cCCccEEEe---------eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeE
Confidence            345679999999999999999999999 999987653         2467999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 033648          101 IIQFGRNPA  109 (114)
Q Consensus       101 ~v~~a~~~~  109 (114)
                      .|++|....
T Consensus        77 ~v~~a~~~~   85 (111)
T d1whxa_          77 YLEWAPIGV   85 (111)
T ss_dssp             EEEEEETTT
T ss_pred             EEEECCCCc
Confidence            999998654

>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=99.86  E-value=8.3e-22  Score=110.02  Aligned_cols=77  Identities=23%  Similarity=0.383  Sum_probs=68.5

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+|||+|||+.+++++|+.+|++ ||.+..+.         .+..+|||||+|.+.++|..|+..|||..++|+.|.|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~-~g~i~~~~---------~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V   76 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNN-IKPGAVER---------VKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   76 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHT-TSTTCEEE---------EEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcc-cceeeeEE---------EccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3468999999999999999999999 99886443         1346789999999999999999999999999999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      +||+|..
T Consensus        77 ~~akP~~   83 (86)
T d2cpda1          77 TLAKPVD   83 (86)
T ss_dssp             ECCCCCC
T ss_pred             EeccCCC
Confidence            9999764

>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=99.86  E-value=5.6e-22  Score=111.20  Aligned_cols=78  Identities=26%  Similarity=0.358  Sum_probs=67.8

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      .+++|||+|||+++++++|+++|.+ ||.. .+         ..+..++||||+|.+.++|++|+..|||..++|++|.|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~-~G~~-~~---------~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V   72 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKD-YDLK-YC---------YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV   72 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCS-SCCC-CE---------EEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHh-cCce-ee---------eeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4578999999999999999999999 9932 11         12457899999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 033648          103 QFGRNPAAA  111 (114)
Q Consensus       103 ~~a~~~~~~  111 (114)
                      ++++++...
T Consensus        73 ~~a~~~~~~   81 (88)
T d1wg1a_          73 QLQPTDALL   81 (88)
T ss_dssp             EECCCCCCC
T ss_pred             EEcCCCCCC
Confidence            999877544

>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=99.86  E-value=5.4e-22  Score=109.41  Aligned_cols=76  Identities=30%  Similarity=0.402  Sum_probs=67.4

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCc-ccCCceEEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGY-VFKGKPMIIQ  103 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-~~~g~~l~v~  103 (114)
                      ++|||+|||+++++++|+.+|++ ||.+....+         ...+|||||+|.+.++|.+|++.|||. .++|++|.|+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~-~G~i~~~~~---------~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~   71 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGD-RKLPLAGQV---------LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   71 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHH-TTCCCSSCE---------EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHH-hCcEEEeEE---------ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEE
Confidence            46999999999999999999999 999876542         135789999999999999999999996 5999999999


Q ss_pred             eccCCCC
Q 033648          104 FGRNPAA  110 (114)
Q Consensus       104 ~a~~~~~  110 (114)
                      +|.++..
T Consensus        72 ~a~~k~~   78 (80)
T d2cqha1          72 YSVSKKL   78 (80)
T ss_dssp             ECCCCCC
T ss_pred             EcCCcCc
Confidence            9998664

>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=99.86  E-value=8.1e-22  Score=110.09  Aligned_cols=78  Identities=21%  Similarity=0.386  Sum_probs=70.3

Q ss_pred             CCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           23 PASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +.++|||+|||+++++++|+.+|++ ||.|.++++    .     +.++||||+|.+.++|..|+..|||..++|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~-~G~i~~i~~----~-----~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V   76 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEK-YGKAGEVFI----H-----KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   76 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTST-TCCCSEEEE----E-----TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHH-hCCceEeee----e-----cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4568999999999999999999999 999987752    1     24689999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 033648          103 QFGRNPAA  110 (114)
Q Consensus       103 ~~a~~~~~  110 (114)
                      ++|.++..
T Consensus        77 ~~A~~~~~   84 (86)
T d2cpja1          77 RFACHSAS   84 (86)
T ss_dssp             EESSCCSC
T ss_pred             EECCCcCC
Confidence            99998764

>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=99.86  E-value=2.4e-22  Score=109.55  Aligned_cols=75  Identities=17%  Similarity=0.287  Sum_probs=68.1

Q ss_pred             eEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEec
Q 033648           26 VLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG  105 (114)
Q Consensus        26 ~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a  105 (114)
                      .|||+|||+++++++|+++|++ ||.|..++   .+.++.++.++|||||+|.+.++|++|++ .++..++|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGG-FGEVESIE---LPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHH-HSCEEEEE---CCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHH-hCCccccc---ccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            4899999999999999999999 99999887   35577889999999999999999999995 5778899999999875

>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=99.85  E-value=1.5e-21  Score=106.42  Aligned_cols=72  Identities=21%  Similarity=0.342  Sum_probs=64.5

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEecc
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR  106 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~  106 (114)
                      |||+|||+++++++|+++|.+ || +..+         ..++.+|+|||.|.+.++|.+|+..|||..++|++|.|++++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~-~g-~~~~---------~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSD-YE-LKYC---------FVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTT-SC-EEEE---------EEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhc-cc-ccce---------eecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            799999999999999999999 99 3222         134678999999999999999999999999999999999998


Q ss_pred             CCC
Q 033648          107 NPA  109 (114)
Q Consensus       107 ~~~  109 (114)
                      +++
T Consensus        70 ~d~   72 (75)
T d1wi6a1          70 TDA   72 (75)
T ss_dssp             STT
T ss_pred             CCC
Confidence            876

>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=99.85  E-value=2.2e-21  Score=110.73  Aligned_cols=81  Identities=23%  Similarity=0.342  Sum_probs=70.1

Q ss_pred             CCCCCCCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC
Q 033648           19 TAGNPASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g   97 (114)
                      ++....++|||+|||+ .+++++|+.+|++ ||.|..+++           .++||||+|.+.++|.+|+..|||..+.|
T Consensus        10 ~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~-~G~i~~~~i-----------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (98)
T d1wf2a_          10 DPRSMNSRVFIGNLNTLVVKKSDVEAIFSK-YGKIVGCSV-----------HKGFAFVQYVNERNARAAVAGEDGRMIAG   77 (98)
T ss_dssp             CCSSCCCCEEEEEECTTTCCHHHHHHSSTT-SSCEEEEEE-----------ETEEEEEEESSHHHHHHHHHTTTTCEETT
T ss_pred             CCCCCCcEEEEeCCCcccCCHHHHHHHHhh-cCCEEEEEE-----------eCCeEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4455667899999974 6778899999999 999987652           47999999999999999999999999999


Q ss_pred             ceEEEEeccCCCCC
Q 033648           98 KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 ~~l~v~~a~~~~~~  111 (114)
                      +.|+|++|++....
T Consensus        78 ~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          78 QVLDINLAAEPKVN   91 (98)
T ss_dssp             EECEEEETTSCCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            99999999865543

>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=99.85  E-value=2.3e-21  Score=110.27  Aligned_cols=84  Identities=14%  Similarity=0.132  Sum_probs=70.5

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCC-ceecccceeEEe-ccCCCceeEEEEEeCCHHHHHHHHHHhCCc--ccCCce
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGS-IDAAKSGLIVKL-MQEGRMRGQAFVTFPSVELAHRALNLVNGY--VFKGKP   99 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~-i~~~~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~g~~   99 (114)
                      +|+|||+|||.++++++|+++|++ ||. +..+.+   +.+ ..++.++|||||+|.++++|..|++.|++.  .++|++
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~-~g~~i~~v~~---~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~   76 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAK-VTEGVLDVIV---YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   76 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHH-HSTTEEEEEC---CSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHH-hCCcceEEEE---eeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEE
Confidence            468999999999999999999999 995 666652   223 236789999999999999999999999754  467999


Q ss_pred             EEEEeccCCCCC
Q 033648          100 MIIQFGRNPAAA  111 (114)
Q Consensus       100 l~v~~a~~~~~~  111 (114)
                      |.|.||+++.+.
T Consensus        77 i~V~~A~p~~~~   88 (96)
T d2disa1          77 IAVDWAEPEIDV   88 (96)
T ss_dssp             CEEEESCSSCST
T ss_pred             EEEEEcCCCCCC
Confidence            999999976644

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=6.2e-21  Score=106.23  Aligned_cols=77  Identities=23%  Similarity=0.379  Sum_probs=69.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ  103 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~  103 (114)
                      .++|||+|||.++++++|+++|+. ||.+..+.    +....+|.++|||||+|.+.++|.+|++ ++|..+.|+.|.|+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~-~G~v~~v~----l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~   79 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLED-KGQVLNIQ----MRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   79 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTT-SCCEEEEE----EEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHH-hcccccce----eeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            468999999999999999999999 99998875    3445688999999999999999999995 79999999999999


Q ss_pred             ecc
Q 033648          104 FGR  106 (114)
Q Consensus       104 ~a~  106 (114)
                      +++
T Consensus        80 ~~~   82 (85)
T d1zh5a2          80 FKD   82 (85)
T ss_dssp             EGG
T ss_pred             EcC
Confidence            865

>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=99.85  E-value=3.7e-21  Score=111.59  Aligned_cols=77  Identities=29%  Similarity=0.529  Sum_probs=68.0

Q ss_pred             CCeEEecCCCC-CCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           24 ASVLYIKNLAK-DVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        24 ~~~l~v~nlp~-~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      +++|||+|||+ .+++++|+++|++ ||.|..+++..        ..+|||||+|.+.++|.+|+..|||..++|+.|.|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~-fG~I~~v~i~~--------~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v   72 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGV-YGDVQRVKILF--------NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   72 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHH-HTCEEEEEECC--------TTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhh-ccccceEEEEe--------cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            57899999965 5899999999999 99999876321        13689999999999999999999999999999999


Q ss_pred             EeccCCC
Q 033648          103 QFGRNPA  109 (114)
Q Consensus       103 ~~a~~~~  109 (114)
                      ++++...
T Consensus        73 ~~s~~~~   79 (109)
T d2adca1          73 TLSKHQN   79 (109)
T ss_dssp             ECCSCCC
T ss_pred             EECCCCC
Confidence            9998654

>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=99.85  E-value=6.6e-21  Score=108.55  Aligned_cols=83  Identities=19%  Similarity=0.392  Sum_probs=72.3

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCC-
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKG-   97 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g-   97 (114)
                      ...+|+++|||+|||+++++++|+++|++ ||.|..+++         .+.++||||+|.+.++|..|+..|||..+.| 
T Consensus        12 g~~~Ps~tl~V~nLp~~~t~~~l~~~f~~-~G~i~~~~~---------~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~   81 (97)
T d1whya_          12 GKANPTTRLWVGGLGPNTSLAALAREFDR-FGSIRTIDH---------VKGDSFAYIQYESLDAAQAACAKMRGFPLGGP   81 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHT-TSCEEEEEE---------CSSSCCEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHh-hcccceEee---------eccccEEEeccCCHHHHHHHHHHhCCCEeCCC
Confidence            34578899999999999999999999999 999987652         1246899999999999999999999999976 


Q ss_pred             -ceEEEEeccCCCCC
Q 033648           98 -KPMIIQFGRNPAAA  111 (114)
Q Consensus        98 -~~l~v~~a~~~~~~  111 (114)
                       ++|+|+||++++.+
T Consensus        82 ~~~l~v~~ak~~~~s   96 (97)
T d1whya_          82 DRRLRVDFAKSGPSS   96 (97)
T ss_dssp             SCBCEEEECCCCCCC
T ss_pred             ceEEEEEeCCCCCCC
Confidence             58999999987653

>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=99.84  E-value=3.2e-21  Score=106.04  Aligned_cols=76  Identities=24%  Similarity=0.343  Sum_probs=67.8

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ..+++|||+|++  +++++|+++|++ ||.|..+++         .+.++||||+|.+.++|..|+..|||..++|+.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~-~G~I~~v~~---------~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   70 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSP-FGNIIDLSM---------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLK   70 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHST-TCCCSCEEE---------ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhc-cCccceeee---------ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEE
Confidence            456899999996  899999999999 999987752         13568999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 033648          102 IQFGRNPA  109 (114)
Q Consensus       102 v~~a~~~~  109 (114)
                      |+||++++
T Consensus        71 V~~a~~~P   78 (79)
T d2bz2a1          71 VNIARKQP   78 (79)
T ss_dssp             EEECCSSC
T ss_pred             EEEecCCC
Confidence            99998764

>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=99.84  E-value=2.5e-21  Score=108.68  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=65.9

Q ss_pred             CCCeEEecCCCCCCCHhHH---HHHHhhhcCCceecccceeEEeccCCC---ceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           23 PASVLYIKNLAKDVVPDDF---FFVFGSLFGSIDAAKSGLIVKLMQEGR---MRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        23 ~~~~l~v~nlp~~~~~~~l---~~~f~~~~G~i~~~~~~~~~~~~~~~~---~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      ..++|||+|||+.+++++|   +++|++ ||.|..+.+   +.++.++.   .+|||||+|.+.++|.+|+..|||..++
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~-~G~I~~v~i---~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~   82 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGK-FGKIHKVVI---NNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   82 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTT-TSCEEEEEE---ECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcc-cCCceEEEE---eeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC
Confidence            3467999999999999999   678999 999998863   33444433   4599999999999999999999999999


Q ss_pred             CceEEEE
Q 033648           97 GKPMIIQ  103 (114)
Q Consensus        97 g~~l~v~  103 (114)
                      |++|+|+
T Consensus        83 gr~lkvS   89 (89)
T d2cpia1          83 GRTLKAS   89 (89)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEC
Confidence            9999985

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.3e-21  Score=105.85  Aligned_cols=71  Identities=21%  Similarity=0.336  Sum_probs=65.2

Q ss_pred             EEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           27 LYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        27 l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      |||+|||+++++++|+++|++ ||.+..++   .+.+..++..+|+|||+|.+.++|.+|+..|||..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~-~G~v~~~~---~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQP-YGKIVSTK---AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTT-TSCEEEEE---EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhh-hccccccc---cccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999 99998876   455677899999999999999999999999999999998763

>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=99.83  E-value=4.2e-21  Score=107.55  Aligned_cols=79  Identities=19%  Similarity=0.296  Sum_probs=69.0

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      .++++|||+|||+.+++++|+++|++ ||.+..+++        ....++||||+|.+.++|++|+.  ++..++|++|.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~-~G~v~~v~~--------~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~   71 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQ-YGDVMDVFI--------PKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVH   71 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTT-TSCCCEEEC--------CSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHH-cCCceEEEE--------eeccCceEEEEECCHHHHHHHHh--CCCEECCEEeE
Confidence            45789999999999999999999999 999876642        34568999999999999999984  88899999999


Q ss_pred             EEeccCCCCC
Q 033648          102 IQFGRNPAAA  111 (114)
Q Consensus       102 v~~a~~~~~~  111 (114)
                      |.+|+++...
T Consensus        72 v~~a~~k~~~   81 (88)
T d1wf0a_          72 ISNAEPKHNS   81 (88)
T ss_dssp             EECCCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876654

>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=99.83  E-value=2e-20  Score=104.71  Aligned_cols=81  Identities=22%  Similarity=0.347  Sum_probs=70.5

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh--CCcccCC
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV--NGYVFKG   97 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~g   97 (114)
                      ..+|+++|||+|||+++++++|+++|++ ||.|..+++    .     +.+++|||+|.+.++|.+|+..+  ++..++|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~-~G~i~~v~~----~-----~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g   73 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLP-FGKVTNILM----L-----KGKNQAFLELATEEAAITMVNYYSAVTPHLRN   73 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTT-TSCEEEEEE----E-----TTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhc-ccccccccc----c-----ccceEEEEEeCCHHHHHHHHHHHccCCCccCC
Confidence            3678999999999999999999999999 999987642    1     34689999999999999999876  4678999


Q ss_pred             ceEEEEeccCCCC
Q 033648           98 KPMIIQFGRNPAA  110 (114)
Q Consensus        98 ~~l~v~~a~~~~~  110 (114)
                      ++|.|+|++.+..
T Consensus        74 ~~l~v~~sk~~~l   86 (88)
T d2cq1a1          74 QPIYIQYSNHKEL   86 (88)
T ss_dssp             EECEEEECSCSSC
T ss_pred             CEEEEEECCCCCC
Confidence            9999999997653

>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=99.83  E-value=2.4e-20  Score=107.07  Aligned_cols=86  Identities=14%  Similarity=0.273  Sum_probs=72.7

Q ss_pred             CCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce
Q 033648           20 AGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP   99 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~   99 (114)
                      ....+.+|||+|||+++++++|+++|.. +|.+ .+.    +....++..+|||||+|.+.++|++|++ +|+..|+||.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~-~~~~-~v~----~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSP-LNPM-RVH----IEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCS-CCCS-EEE----EEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhc-cCcc-eee----eEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            3456679999999999999999999999 9854 342    3344568899999999999999999985 8999999999


Q ss_pred             EEEEeccCCCCCC
Q 033648          100 MIIQFGRNPAAAK  112 (114)
Q Consensus       100 l~v~~a~~~~~~~  112 (114)
                      |.|.+++.....+
T Consensus        84 I~V~~s~~~~~~~   96 (102)
T d1weza_          84 VELFLNSTAGTSG   96 (102)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEcCCCCCCC
Confidence            9999999776543

>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=99.83  E-value=2.1e-20  Score=107.65  Aligned_cols=87  Identities=17%  Similarity=0.240  Sum_probs=74.6

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      .....+|||+|||+++++++|+++|.. +|.+....   .+....++..+|+|||+|.+.++|++|++ +|+..|+||.|
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~-~g~v~~~v---~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i   86 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSG-LEIVPNGM---TLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYI   86 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTT-CCEEEEEE---ECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHh-cCCceEEE---EEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEE
Confidence            344567999999999999999999999 99876542   34466788999999999999999999995 99999999999


Q ss_pred             EEEeccCCCCCC
Q 033648          101 IIQFGRNPAAAK  112 (114)
Q Consensus       101 ~v~~a~~~~~~~  112 (114)
                      .|..+++....+
T Consensus        87 ~V~~~~~~~~~~   98 (104)
T d1wg5a_          87 EIFKSSRAEVRT   98 (104)
T ss_dssp             EEEEECTTTSCC
T ss_pred             EEEECCHHHhcc
Confidence            999999876543

>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=99.82  E-value=2.5e-20  Score=107.14  Aligned_cols=81  Identities=16%  Similarity=0.179  Sum_probs=71.1

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ....+|||+|||+++++++|+.+|.. ||.+..+.   .+....+|.++|+|||+|.+.++|++|+. +||..|+|+.|.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~-~g~i~~~~---~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~   80 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEG-IPVDENAV---HVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAF   80 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTT-SCCCSTTE---EECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcc-cceEEEEE---EEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEE
Confidence            44567999999999999999999999 99886542   34566789999999999999999999995 999999999999


Q ss_pred             EEeccC
Q 033648          102 IQFGRN  107 (114)
Q Consensus       102 v~~a~~  107 (114)
                      |..+..
T Consensus        81 V~~~~~   86 (103)
T d2cpya1          81 VHVVTL   86 (103)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            998763

>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=99.82  E-value=2.2e-20  Score=106.54  Aligned_cols=78  Identities=14%  Similarity=0.075  Sum_probs=69.2

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEE
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMI  101 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~  101 (114)
                      ....+|||+|||+.+++++|+++|++ ||.|..+++          ..+|||||+|.+.++|++|++.|||..+.|+.|.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~-~G~v~~~~i----------~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMRE-AGDVCYADV----------QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTT-SSCEEEEEE----------ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHh-hcccccccc----------cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            45678999999999999999999999 999987652          1358999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 033648          102 IQFGRNPAA  110 (114)
Q Consensus       102 v~~a~~~~~  110 (114)
                      |.+++.+.+
T Consensus        82 v~~~~~~~~   90 (98)
T d1wg4a_          82 TSYIRVYPE   90 (98)
T ss_dssp             EEEEEEECC
T ss_pred             EEEEecCCC
Confidence            999985543

>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=99.82  E-value=9.3e-20  Score=104.91  Aligned_cols=85  Identities=16%  Similarity=0.291  Sum_probs=72.4

Q ss_pred             CCCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC--Cccc
Q 033648           18 YTAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN--GYVF   95 (114)
Q Consensus        18 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~   95 (114)
                      ....+|+.+|||+|||+.+++++|+.+|.+ ||.|..+.+         .+.+++|||+|.+.++|..|+..|+  +..+
T Consensus         9 ~~~~~ps~~l~v~nlp~~~te~~l~~~F~~-fG~I~~~~~---------~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~   78 (104)
T d1wexa_           9 HHKVSVSPVVHVRGLCESVVEADLVEALEK-FGTICYVMM---------MPFKRQALVEFENIDSAKECVTFAADVPVYI   78 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTT-TSCEEEEEE---------ETTTTEEEEEESSHHHHHHHHHHHHHSCCBS
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHhhhh-cccceEEEE---------EecceeEEEEeCCHHHHHHHHHHHcCCCcEE
Confidence            344578899999999999999999999999 999987642         1357899999999999999999884  5668


Q ss_pred             CCceEEEEeccCCCCCC
Q 033648           96 KGKPMIIQFGRNPAAAK  112 (114)
Q Consensus        96 ~g~~l~v~~a~~~~~~~  112 (114)
                      +|++|.|+|++.+...+
T Consensus        79 ~g~~l~v~~s~~~~~~~   95 (104)
T d1wexa_          79 AGQQAFFNYSTSKRITR   95 (104)
T ss_dssp             SSSBCEEEECSSSSCCC
T ss_pred             eeEEEEEEEcCCCccCC
Confidence            99999999999766544

>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=99.82  E-value=5.7e-20  Score=106.45  Aligned_cols=80  Identities=19%  Similarity=0.235  Sum_probs=69.6

Q ss_pred             CCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc--CCce
Q 033648           22 NPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF--KGKP   99 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~--~g~~   99 (114)
                      .+..+|||+|||+.+++++|+++|++ ||.|..+.+   +..    +.+|+|||+|.+.++|+.|+..|||..+  .|+.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~-~G~i~~~~i---~~~----~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~   76 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSK-FGTVLKIIT---FTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   76 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTT-TSCEEEEEE---EEE----TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCC
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHcc-CCcEEEEEE---Eee----CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcE
Confidence            45678999999999999999999999 999988753   222    3589999999999999999999999998  5789


Q ss_pred             EEEEeccCCC
Q 033648          100 MIIQFGRNPA  109 (114)
Q Consensus       100 l~v~~a~~~~  109 (114)
                      |.|.++++..
T Consensus        77 l~v~~s~~~~   86 (108)
T d2adba1          77 LRIDFSKLTS   86 (108)
T ss_dssp             CEEEECSSCS
T ss_pred             EEEEecCCcc
Confidence            9999998654

>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=99.81  E-value=7.7e-21  Score=106.26  Aligned_cols=73  Identities=15%  Similarity=0.079  Sum_probs=64.7

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+.+++++|+++|++ ||.|..+++          ...|||||+|.+.++|++|+..|||..++|+.|.|.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~-~G~v~~~~i----------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMRE-AGDVCYADV----------YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGG-GSCEEEEEE----------CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CeEEEECCCCcCCHHHHHHHHhh-hcccccccc----------cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            36999999999999999999999 999987652          1238999999999999999999999999999999888


Q ss_pred             ccCC
Q 033648          105 GRNP  108 (114)
Q Consensus       105 a~~~  108 (114)
                      ++.+
T Consensus        70 ~~~~   73 (87)
T d3begb1          70 IRVK   73 (87)
T ss_dssp             CEEE
T ss_pred             EecC
Confidence            7644

>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=99.81  E-value=1.2e-19  Score=105.73  Aligned_cols=84  Identities=13%  Similarity=0.189  Sum_probs=73.6

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCc
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGK   98 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~   98 (114)
                      .+..+..+|||+|||+.+++++|+++|+. +|.+..+.   .+....+|..+|+|||+|.+.++|.+|+. +||..|+||
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~-~g~~~~~~---~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR   87 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKK-LDIVEDSI---YIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   87 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCS-SCBCTTTC---EEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhh-ccccccce---eeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCE
Confidence            34556779999999999999999999999 99886553   45677889999999999999999999995 999999999


Q ss_pred             eEEEEeccC
Q 033648           99 PMIIQFGRN  107 (114)
Q Consensus        99 ~l~v~~a~~  107 (114)
                      .|.|..+..
T Consensus        88 ~i~V~~~~~   96 (112)
T d1wela1          88 FIQVHPITK   96 (112)
T ss_dssp             CBEEEEECH
T ss_pred             EEEEEEcCh
Confidence            999988754

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.80  E-value=3.5e-19  Score=96.83  Aligned_cols=74  Identities=18%  Similarity=0.187  Sum_probs=63.9

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+.+++++|+++|+. ||.|..+++   +.++ . ..+++|||+|.+.++|.+|+ .+||..++|++|.|+.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~-~G~I~~v~~---~~~~-~-~~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDV---ADSL-K-KNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGG-GSCEEEEEE---EECT-T-SSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhc-CCceEEEEE---Eeec-c-ccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEE
Confidence            57999999999999999999999 999988752   2333 2 34579999999999999998 5899999999999986


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      +
T Consensus        74 ~   74 (75)
T d2ghpa2          74 L   74 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=2.2e-19  Score=102.46  Aligned_cols=79  Identities=19%  Similarity=0.288  Sum_probs=68.2

Q ss_pred             CCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHH--HhCCcccCC
Q 033648           21 GNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALN--LVNGYVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~--~l~g~~~~g   97 (114)
                      ..++++|||+|||.+ +++++|..+|++ ||.|..+.+    .     ..+++|||+|.+.++|.+|+.  .+++..++|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~-fG~V~~v~~----~-----~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~g   84 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEP-YGKIKNYIL----M-----RMKSQAFIEMETREDAMAMVDHCLKKALWFQG   84 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTT-TSCCSEEEE----E-----TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhcc-ccceeEEEE----e-----ecCCcEEEEecchHHHHHHHHHHhcCCceECC
Confidence            466789999999975 899999999999 999987752    1     346899999999999999997  578889999


Q ss_pred             ceEEEEeccCCC
Q 033648           98 KPMIIQFGRNPA  109 (114)
Q Consensus        98 ~~l~v~~a~~~~  109 (114)
                      +.|.|++|+...
T Consensus        85 r~l~V~~s~~~~   96 (99)
T d1x4fa1          85 RCVKVDLSEKYK   96 (99)
T ss_dssp             SCCEEEEECSCS
T ss_pred             EEEEEEEcCCcc
Confidence            999999997654

>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=99.79  E-value=3.3e-19  Score=99.91  Aligned_cols=80  Identities=16%  Similarity=0.234  Sum_probs=68.8

Q ss_pred             CCCCCeEEecCCCCC-CCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh--CCcccCC
Q 033648           21 GNPASVLYIKNLAKD-VVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV--NGYVFKG   97 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~-~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~g   97 (114)
                      ..++.+|||+|||.. +|+++|.++|++ ||.|..+.+.         ..+++|||+|.+.++|..|+..+  ++..+.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~-fG~I~~i~i~---------~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~g   74 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEP-FGVISNHLIL---------NKINEAFIEMATTEDAQAAVDYYTTTPALVFG   74 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGG-GSCEEEEEEC---------SSSSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHh-hCCeEEEEee---------ccceEEEEEEcchhhHHHHHHHHhhCCCccCC
Confidence            467889999999986 789999999999 9999877521         24579999999999999999976  6778999


Q ss_pred             ceEEEEeccCCCC
Q 033648           98 KPMIIQFGRNPAA  110 (114)
Q Consensus        98 ~~l~v~~a~~~~~  110 (114)
                      ++|.|+||+....
T Consensus        75 r~l~V~~s~~~~~   87 (89)
T d1x4da1          75 KPVRVHLSQKYKR   87 (89)
T ss_dssp             EECEEEEECCCTT
T ss_pred             ceEEEEECCCccc
Confidence            9999999987654

>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=99.77  E-value=1.5e-20  Score=105.59  Aligned_cols=81  Identities=20%  Similarity=0.334  Sum_probs=69.1

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccc--eeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEE
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSG--LIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~--~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ++|||+|||.++++++|+++|+. ||.+..+.+.  ..+.+..++.++|||||+|.+.++|++|+ .|||..+.|+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~-~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHH-HHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHh-hCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEE
Confidence            57999999999999999999999 9988665432  12455667888999999999999999998 59999999999999


Q ss_pred             EeccC
Q 033648          103 QFGRN  107 (114)
Q Consensus       103 ~~a~~  107 (114)
                      +.++.
T Consensus        80 ~r~k~   84 (90)
T d1u2fa_          80 RRPHD   84 (90)
T ss_dssp             BCTTC
T ss_pred             CCCCC
Confidence            86553

>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=99.77  E-value=7.3e-19  Score=109.73  Aligned_cols=86  Identities=16%  Similarity=0.247  Sum_probs=76.3

Q ss_pred             CCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceE
Q 033648           21 GNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM  100 (114)
Q Consensus        21 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l  100 (114)
                      ..+..+|||+|||+.+++++|+.+|+. ||.+..+.   .+.+..+|..+|||||.|.+.++|.+|+. +++..++|++|
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~-~G~v~~~~---i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i  168 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQ-YGKIEVIE---IMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNC  168 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhcc-CCceeeee---eecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEE
Confidence            355679999999999999999999999 99998876   45667789999999999999999999996 79999999999


Q ss_pred             EEEeccCCCCC
Q 033648          101 IIQFGRNPAAA  111 (114)
Q Consensus       101 ~v~~a~~~~~~  111 (114)
                      .|.+|.++.+.
T Consensus       169 ~V~~A~~k~e~  179 (183)
T d1u1qa_         169 EVRKALSKQEM  179 (183)
T ss_dssp             EEEECCCHHHH
T ss_pred             EEEecCCcccc
Confidence            99999876543

>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=99.75  E-value=4.9e-19  Score=101.82  Aligned_cols=79  Identities=18%  Similarity=0.113  Sum_probs=67.5

Q ss_pred             CCCCeEEecCCCCCC-CH----hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccC
Q 033648           22 NPASVLYIKNLAKDV-VP----DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFK   96 (114)
Q Consensus        22 ~~~~~l~v~nlp~~~-~~----~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   96 (114)
                      .+.++|||+||+.++ ++    ++|+.+|+. ||.|.++++    .     +++++|||.|.+.++|.+|+..|||..++
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~-~G~i~~~~~----~-----k~~~~afV~f~~~~~A~~Ai~~lng~~~~   72 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRT-YDKDTTFQY----F-----KSFKRVRINFSNPLSAADARLRLHKTEFL   72 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHT-TCSSCEEEE----E-----TTTTEEEEECSSTTHHHHHHHTSTTSEET
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcc-cccceEEEE----e-----cCCCEEEEEECCHHHHHHHHHHhcccccC
Confidence            457889999999875 33    568999999 999987652    1     36789999999999999999999999999


Q ss_pred             CceEEEEeccCCCC
Q 033648           97 GKPMIIQFGRNPAA  110 (114)
Q Consensus        97 g~~l~v~~a~~~~~  110 (114)
                      |++|+|.||++...
T Consensus        73 g~~l~v~~a~~~~~   86 (104)
T d1weya_          73 GKEMKLYFAQTLHI   86 (104)
T ss_dssp             TEECEEECCCCSSC
T ss_pred             CCEeEEeecccCCC
Confidence            99999999986643

>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=99.70  E-value=1.3e-18  Score=99.98  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=68.6

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      +.++|.+++..+++++|+++|++ ||.|.+++    +....+|.++|+|||+|.+.++|.+|+..|||..++|++|.|+|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k-~G~I~~v~----I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEK-YGEVEEMN----VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH-TCCEEEEE----ECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhcc-CCCEEEEE----eecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEE
Confidence            35778888888999999999999 99999886    33556899999999999999999999999999999999999998


Q ss_pred             c
Q 033648          105 G  105 (114)
Q Consensus       105 a  105 (114)
                      +
T Consensus       103 s  103 (104)
T d1jmta_         103 S  103 (104)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.66  E-value=2.1e-16  Score=90.14  Aligned_cols=66  Identities=21%  Similarity=0.282  Sum_probs=57.1

Q ss_pred             CCCCCCeEEecC--CCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCccc
Q 033648           20 AGNPASVLYIKN--LAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVF   95 (114)
Q Consensus        20 ~~~~~~~l~v~n--lp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   95 (114)
                      ...|..+++|.|  ||.++++++|+.+|++ ||.+..+.+         -..++||||+|.+.++|.+|+..|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~-~G~i~~i~~---------~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEK-CGLVDALLM---------PPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHH-HSCEEEEEC---------CTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHh-hCcccEEee---------ccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            346778899955  9999999999999999 999987642         13468999999999999999999999986

>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=99.61  E-value=1.3e-15  Score=86.48  Aligned_cols=82  Identities=23%  Similarity=0.268  Sum_probs=67.0

Q ss_pred             CCCCCeEEecCC--CCCCC---------HhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHH
Q 033648           21 GNPASVLYIKNL--AKDVV---------PDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNL   89 (114)
Q Consensus        21 ~~~~~~l~v~nl--p~~~~---------~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   89 (114)
                      ...+.+|+|.|+  |.+..         .++|++.|++ ||.|..+.+       ..+..+|++||+|.+.++|.+|+..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~-~G~V~~v~~-------~~~~~~G~~fV~f~~~e~A~~A~~~   76 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSK-FGQIRKLLL-------FDRHPDGVASVSFRDPEEADYCIQT   76 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGG-TSCCSEEEE-------ETTCTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcC-cccEEEEec-------cCCCCccEEEEEECCHHHHHHHHHH
Confidence            456789999998  54321         2578899999 999976642       2345679999999999999999999


Q ss_pred             hCCcccCCceEEEEeccCCCC
Q 033648           90 VNGYVFKGKPMIIQFGRNPAA  110 (114)
Q Consensus        90 l~g~~~~g~~l~v~~a~~~~~  110 (114)
                      |||..++||+|.|+++.+...
T Consensus        77 lng~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          77 LDGRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             STTCEETTEECEEEECCSCCC
T ss_pred             hCCcEECCEEEEEEEeCCcCC
Confidence            999999999999999987653

>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=99.60  E-value=1.9e-15  Score=87.78  Aligned_cols=74  Identities=12%  Similarity=0.122  Sum_probs=62.4

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCH-HHHHHHHHHhCCcccCCceEEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSV-ELAHRALNLVNGYVFKGKPMII  102 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~-~~a~~a~~~l~g~~~~g~~l~v  102 (114)
                      ...+||||||+.+|+++|+.+|++ ||.|.++.++         ..++||||.|.+. ++|..|+..+|+..+.++.+.|
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~-fG~V~~v~i~---------~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSN-HGEIKWIDFV---------RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCS-SCCEEEEECC---------TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHh-cCChheEEEe---------cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            445699999999999999999999 9999887642         3479999999884 7899999999999988877777


Q ss_pred             EeccC
Q 033648          103 QFGRN  107 (114)
Q Consensus       103 ~~a~~  107 (114)
                      .++..
T Consensus        81 ~~~~~   85 (113)
T d1owxa_          81 TWEVL   85 (113)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            66543

>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=99.59  E-value=6.9e-15  Score=91.36  Aligned_cols=79  Identities=20%  Similarity=0.309  Sum_probs=68.0

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEe
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF  104 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~  104 (114)
                      ++|||+|||+.+++++|+++|++ ||.|..+.   .+.+..++.++|+|||+|.+.++|.+|+. .++..++++.+.+..
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~-~G~v~~~~---~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQ-WGTLTDCV---VMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGG-GSCEEEEE---EEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHH-cCCEEEEE---eeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhh
Confidence            68999999999999999999999 99998876   45677789999999999999999999986 456667777877776


Q ss_pred             ccCC
Q 033648          105 GRNP  108 (114)
Q Consensus       105 a~~~  108 (114)
                      ....
T Consensus        82 ~~~~   85 (183)
T d1u1qa_          82 AVSR   85 (183)
T ss_dssp             CCCT
T ss_pred             hhhc
Confidence            6544

>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=99.56  E-value=2.1e-15  Score=86.35  Aligned_cols=83  Identities=20%  Similarity=0.370  Sum_probs=66.8

Q ss_pred             CCCCCeEEecCC--CCCCC--------HhHHHHHHhhhcCCceecccceeEEecc--CCCceeEEEEEeCCHHHHHHHHH
Q 033648           21 GNPASVLYIKNL--AKDVV--------PDDFFFVFGSLFGSIDAAKSGLIVKLMQ--EGRMRGQAFVTFPSVELAHRALN   88 (114)
Q Consensus        21 ~~~~~~l~v~nl--p~~~~--------~~~l~~~f~~~~G~i~~~~~~~~~~~~~--~~~~~g~~fv~f~~~~~a~~a~~   88 (114)
                      ++|+.+|.+.|+  |....        .++|++.|++ ||.|..+.+.   ++..  .....|++||+|.+.++|.+|+.
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k-~G~v~~v~I~---~~~~~~~~~~~g~vfV~f~~~e~A~~A~~   76 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSK-YGLVKSIEIP---RPVDGVEVPGCGKIFVEFTSVFDCQKAMQ   76 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTT-TSCEEEEECC---CCTTSSSCTTCCEEEEEESCHHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcc-cCceEEEEEe---ecCCCCccCCceEEEEEECCHHHHHHHHH
Confidence            468899999999  54433        2468999999 9999987632   2222  23346899999999999999999


Q ss_pred             HhCCcccCCceEEEEeccC
Q 033648           89 LVNGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        89 ~l~g~~~~g~~l~v~~a~~  107 (114)
                      .|||..++||.|.|.|+..
T Consensus        77 ~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          77 GLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HHSSCCSSSSCCEEEEECH
T ss_pred             HHCCCEECCeEEEEEEcCH
Confidence            9999999999999999863

>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=99.52  E-value=9.9e-15  Score=79.91  Aligned_cols=72  Identities=13%  Similarity=0.157  Sum_probs=58.6

Q ss_pred             CCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCce-EEE
Q 033648           24 ASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP-MII  102 (114)
Q Consensus        24 ~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~-l~v  102 (114)
                      .+.++|+++|++.+++.| +.|++ ||.|.+++         .+..++|+||+|.+.++|++|+. +||..++|+. |.|
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~-~G~I~~~~---------~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV   71 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQ-YGNILKHV---------MSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   71 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHT-TSCEEEEE---------ECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHh-hhhhheEE---------ecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEE
Confidence            356999999999886555 57999 99987654         24567999999999999999995 9999999985 567


Q ss_pred             EeccC
Q 033648          103 QFGRN  107 (114)
Q Consensus       103 ~~a~~  107 (114)
                      ..+..
T Consensus        72 ~~~~~   76 (81)
T d1wwha1          72 KPCID   76 (81)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            76643

>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=98.07  E-value=2.5e-05  Score=42.47  Aligned_cols=81  Identities=19%  Similarity=0.242  Sum_probs=60.6

Q ss_pred             CeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCC--CceeEEEEEeCCHHHHHHHHHHhCCcccCCc----
Q 033648           25 SVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEG--RMRGQAFVTFPSVELAHRALNLVNGYVFKGK----   98 (114)
Q Consensus        25 ~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~----   98 (114)
                      +.|-|++||+..+++++.+.++. .|.+....   .+..+.+.  .....|+|.|.+.++...-...++|+.+.+.    
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~-~~~~d~~~---f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~   77 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQP-MPEHDYFE---FFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQE   77 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCS-CCCEEEEE---EEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCC-cCceEEEE---EeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCE
Confidence            46889999999999999999988 88776543   12222221  2348999999999999999999999886431    


Q ss_pred             -eEEEEeccCCC
Q 033648           99 -PMIIQFGRNPA  109 (114)
Q Consensus        99 -~l~v~~a~~~~  109 (114)
                       +-.|++|--.+
T Consensus        78 ~~a~VE~AP~qk   89 (91)
T d1uw4a_          78 YPAIVEFAPFQK   89 (91)
T ss_dssp             EECEEEECSSCC
T ss_pred             eeeEEEEcCccc
Confidence             45677776543

>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=97.55  E-value=0.00057  Score=34.99  Aligned_cols=62  Identities=15%  Similarity=0.209  Sum_probs=48.5

Q ss_pred             hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhCCcccCCceEEEEeccC
Q 033648           39 DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN  107 (114)
Q Consensus        39 ~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~  107 (114)
                      +.|...|.+ +|.|..+.+    ...  ....-.|-|...+.++|..|+..|+..+++++.|.|+++..
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 QLLQEAFAR-HGKVKSVEL----SPH--TDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHH-HSCEEEEEE----CSC--CSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHh-heeEEEEEE----Eec--cCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            346677888 898876542    111  12335788999999999999999999999999999999864

>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=97.45  E-value=0.00023  Score=38.30  Aligned_cols=73  Identities=23%  Similarity=0.332  Sum_probs=52.9

Q ss_pred             CCCCCCeEEecCCCCC------CCH---hHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHh
Q 033648           20 AGNPASVLYIKNLAKD------VVP---DDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLV   90 (114)
Q Consensus        20 ~~~~~~~l~v~nlp~~------~~~---~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   90 (114)
                      .++|.-++.|.=..+.      .++   .+|.+.|.. ||.+.-+++           .....+|+|.+-++|.+|+ .+
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~-~GeViLvRF-----------v~d~mwVTF~dG~SAL~al-~l   77 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGS-YGTIVLVRI-----------NQGQMLVTFADSHSALSVL-DV   77 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHH-HSCCSEEEE-----------ETTEEEEECSCSHHHHHHH-HG
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhh-CCeEEEEEE-----------eCCeEEEEECCcHHHHHHh-cc
Confidence            4577777777544322      232   457788888 998754331           2345789999999999998 68


Q ss_pred             CCcccCCceEEEEec
Q 033648           91 NGYVFKGKPMIIQFG  105 (114)
Q Consensus        91 ~g~~~~g~~l~v~~a  105 (114)
                      +|.++.|+.|+|..-
T Consensus        78 ~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          78 DGMKVKGRAVKISGP   92 (95)
T ss_dssp             GGSEETTEEEEEECC
T ss_pred             CCeEEcceEEEEecC
Confidence            999999999999853

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.73  E-value=0.0078  Score=32.62  Aligned_cols=61  Identities=20%  Similarity=0.298  Sum_probs=48.4

Q ss_pred             CCCCCCCeEEecCCCCCCCHhHHHHHHhhhcCCceecccceeEEeccCCCceeEEEEEeCCHHHHHHHHHHhC
Q 033648           19 TAGNPASVLYIKNLAKDVVPDDFFFVFGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVN   91 (114)
Q Consensus        19 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~~G~i~~~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   91 (114)
                      ++.+....+|.-..|..+...+|.++|++ ||.|. +  . ++ +      -.-|||.....+++..++..+.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSp-fG~V~-V--s-wI-d------dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSA-FGNIQ-I--S-WI-D------DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTT-TCSCC-C--E-EE-E------TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcC-CCceE-E--E-Ee-c------CceEEEEecCHHHHHHHHHHhc
Confidence            44566778999999999999999999999 99873 1  1 22 2      2368999999999999887655