Psyllid ID: psy13319

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
Protein Sequence
MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHccccccccEEEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccHccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEcccccccc
Coil and Loop (DISEMBL)
mlainkglqrfspltgdllassilpantmngsgwCIFVynlapeteESVLWQLfgpfgavqSVKVIRDLqtnkckgfgfvtmtNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS
Flexible Loop (DISEMBL)
mlainkglqrfsplTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALgnrilqvsfktnkgkts
Low Complexity Region (SEG)
MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS
Disordered region (IsUnstruct)
**********FSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF********
Disordered Region (DISOPRED)
***********************************IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ***********
Disordered Region (DISEMBL)
MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF********
Disordered Region (DISPRO)
*LAINKGLQRFSPLTGDLLAS*********GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS
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	117	2.2.26 [Sep-21-2011]
A4QNI8	400	ELAV-like protein 4 OS=Xe	yes	N/A	0.982	0.287	0.666	1e-41
Q7SZT7	400	ELAV-like protein 4 OS=Xe	N/A	N/A	0.982	0.287	0.666	1e-41
P26378	380	ELAV-like protein 4 OS=Ho	yes	N/A	0.905	0.278	0.702	7e-41
O09032	373	ELAV-like protein 4 OS=Ra	yes	N/A	0.905	0.284	0.702	8e-41
Q61701	385	ELAV-like protein 4 OS=Mu	yes	N/A	0.905	0.275	0.702	9e-41
Q5R9Z6	359	ELAV-like protein 2 OS=Po	no	N/A	0.948	0.309	0.672	2e-40
Q12926	359	ELAV-like protein 2 OS=Ho	no	N/A	0.948	0.309	0.672	2e-40
Q8CH84	359	ELAV-like protein 2 OS=Ra	no	N/A	0.948	0.309	0.672	2e-40
P16914	483	Protein elav OS=Drosophil	no	N/A	0.948	0.229	0.604	1e-39
P23241	519	Protein elav OS=Drosophil	N/A	N/A	0.948	0.213	0.604	1e-39

>sp|A4QNI8|ELAV4_XENTR ELAV-like protein 4 OS=Xenopus tropicalis GN=elavl4 PE=2 SV=1

 Score =  167 bits (424), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 80/120 (66%), Positives = 98/120 (81%), Gaps = 5/120 (4%)

Query: 1   MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
           +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct: 283 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 340

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct: 341 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKTHKS 400

Binds to AU-rich sequences (AREs) of target mRNAs. May play a role in neuron-specific RNA processing.
Xenopus tropicalis (taxid: 8364)

>sp|Q7SZT7|ELAV4_XENLA ELAV-like protein 4 OS=Xenopus laevis GN=elavl4 PE=2 SV=1

 Score =  167 bits (424), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 80/120 (66%), Positives = 98/120 (81%), Gaps = 5/120 (4%)

Query: 1   MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
           +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct: 283 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 340

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct: 341 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKTHKS 400

Binds to AU-rich sequences (AREs) of target mRNAs. May play a role in neuron-specific RNA processing.

Xenopus laevis (taxid: 8355)

>sp|P26378|ELAV4_HUMAN ELAV-like protein 4 OS=Homo sapiens GN=ELAVL4 PE=1 SV=2

 Score =  165 bits (418), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 78/111 (70%), Positives = 92/111 (82%), Gaps = 5/111 (4%)

Query: 10  RFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
           RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPFGAV +VKVI
Sbjct: 272 RFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVI 329

Query: 67  RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           RD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct: 330 RDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 380

May play a role in neuron-specific RNA processing. Protects CDKN1A mRNA from decay by binding to its 3'-UTR (By similarity). Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF and FOS mRNA.

Homo sapiens (taxid: 9606)

>sp|O09032|ELAV4_RAT ELAV-like protein 4 OS=Rattus norvegicus GN=Elavl4 PE=1 SV=1

 Score =  165 bits (417), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 78/111 (70%), Positives = 92/111 (82%), Gaps = 5/111 (4%)

Query: 10  RFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
           RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPFGAV +VKVI
Sbjct: 265 RFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVI 322

Query: 67  RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           RD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct: 323 RDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 373

Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF and FOS mRNA (By similarity). May play a role in neuron-specific RNA processing. Protects CDKN1A mRNA from decay by binding to its 3'-UTR.

Rattus norvegicus (taxid: 10116)

>sp|Q61701|ELAV4_MOUSE ELAV-like protein 4 OS=Mus musculus GN=Elavl4 PE=1 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 78/111 (70%), Positives = 92/111 (82%), Gaps = 5/111 (4%)

Query: 10  RFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
           RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPFGAV +VKVI
Sbjct: 277 RFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVI 334

Query: 67  RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           RD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct: 335 RDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 385

May play a role in neuron-specific RNA processing. Protects CDKN1A mRNA from decay by binding to its 3'-UTR. Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF and FOS mRNA.

Mus musculus (taxid: 10090)

>sp|Q5R9Z6|ELAV2_PONAB ELAV-like protein 2 OS=Pongo abelii GN=ELAVL2 PE=2 SV=1

 Score =  163 bits (413), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 78/116 (67%), Positives = 94/116 (81%), Gaps = 5/116 (4%)

Query: 1   MLAINKGLQRFSPLTGD---LLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
           +L +  G++RFSP+T D    LA   +P +   G+GWCIFVYNLAP+ +ES+LWQ+FGPF
Sbjct: 242 LLNMAYGVKRFSPMTIDGMTSLAGINIPGHP--GTGWCIFVYNLAPDADESILWQMFGPF 299

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
           GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK
Sbjct: 300 GAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 355

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Pongo abelii (taxid: 9601)

>sp|Q12926|ELAV2_HUMAN ELAV-like protein 2 OS=Homo sapiens GN=ELAVL2 PE=1 SV=2

 Score =  163 bits (413), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 78/116 (67%), Positives = 94/116 (81%), Gaps = 5/116 (4%)

Query: 1   MLAINKGLQRFSPLTGD---LLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
           +L +  G++RFSP+T D    LA   +P +   G+GWCIFVYNLAP+ +ES+LWQ+FGPF
Sbjct: 242 LLNMAYGVKRFSPMTIDGMTSLAGINIPGHP--GTGWCIFVYNLAPDADESILWQMFGPF 299

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
           GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK
Sbjct: 300 GAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 355

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Homo sapiens (taxid: 9606)

>sp|Q8CH84|ELAV2_RAT ELAV-like protein 2 OS=Rattus norvegicus GN=Elavl2 PE=2 SV=1

 Score =  163 bits (413), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 78/116 (67%), Positives = 94/116 (81%), Gaps = 5/116 (4%)

Query: 1   MLAINKGLQRFSPLTGD---LLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
           +L +  G++RFSP+T D    LA   +P +   G+GWCIFVYNLAP+ +ES+LWQ+FGPF
Sbjct: 242 LLNMAYGVKRFSPMTIDGMTSLAGINIPGHP--GTGWCIFVYNLAPDADESILWQMFGPF 299

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
           GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK
Sbjct: 300 GAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 355

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Rattus norvegicus (taxid: 10116)

>sp|P16914|ELAV_DROME Protein elav OS=Drosophila melanogaster GN=elav PE=2 SV=1

 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/124 (60%), Positives = 94/124 (75%), Gaps = 13/124 (10%)

Query: 4   INKGLQRFSPLTGDLLASSILP------------ANTMNGSGWCIFVYNLAPETEESVLW 51
           +NKGL RFSP+ GD+L   +LP              +  G  + IF+YNLAPETEE+ LW
Sbjct: 361 VNKGLARFSPMAGDML-DVMLPNGLGAAAAAATTLASGPGGAYPIFIYNLAPETEEAALW 419

Query: 52  QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT 111
           QLFGPFGAVQSVK+++D  TN+CKG+GFV+MTNYDEA +AI++LNGY +GNR+LQVSFKT
Sbjct: 420 QLFGPFGAVQSVKIVKDPTTNQCKGYGFVSMTNYDEAAMAIRALNGYTMGNRVLQVSFKT 479

Query: 112 NKGK 115
           NK K
Sbjct: 480 NKAK 483

Required for the proper development and maintenance of neurons presumably by affecting RNA metabolism.

Drosophila melanogaster (taxid: 7227)

>sp|P23241|ELAV_DROVI Protein elav OS=Drosophila virilis GN=elav PE=3 SV=1

 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/124 (60%), Positives = 94/124 (75%), Gaps = 13/124 (10%)

Query: 4   INKGLQRFSPLTGDLLASSILP------------ANTMNGSGWCIFVYNLAPETEESVLW 51
           +NKGL RFSP+ GD+L   +LP              +  G  + IF+YNLAPETEE+ LW
Sbjct: 397 VNKGLARFSPMAGDML-DVMLPNGLGAAAAAATTLASGPGGAYPIFIYNLAPETEEAALW 455

Query: 52  QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT 111
           QLFGPFGAVQSVK+++D  TN+CKG+GFV+MTNYDEA +AI++LNGY +GNR+LQVSFKT
Sbjct: 456 QLFGPFGAVQSVKIVKDPTTNQCKGYGFVSMTNYDEAAMAIRALNGYTMGNRVLQVSFKT 515

Query: 112 NKGK 115
           NK K
Sbjct: 516 NKAK 519

Probably involved in the RNA metabolism of neurons.

Drosophila virilis (taxid: 7244)

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	117
328700227	383	PREDICTED: ELAV-like protein 4-like isof	0.974	0.297	0.921	1e-58
328700229	392	PREDICTED: ELAV-like protein 4-like isof	0.974	0.290	0.921	2e-58
383865034	502	PREDICTED: ELAV-like protein 2-like [Meg	0.991	0.231	0.897	8e-58
307194503	349	ELAV-like protein 2 [Harpegnathos saltat	0.991	0.332	0.897	9e-58
340709266	533	PREDICTED: ELAV-like protein 2-like [Bom	0.974	0.213	0.913	1e-57
350425139	371	PREDICTED: ELAV-like protein 2-like [Bom	0.991	0.312	0.897	2e-57
328792242	378	PREDICTED: ELAV-like protein 2-like [Api	0.991	0.306	0.897	2e-57
380027075	362	PREDICTED: ELAV-like protein 2-like [Api	0.991	0.320	0.897	2e-57
332029758	359	ELAV-like protein 2 [Acromyrmex echinati	0.991	0.323	0.888	3e-57
345493619	383	PREDICTED: ELAV-like protein 3-like isof	0.991	0.302	0.888	6e-57

>gi|328700227|ref|XP_001951393.2| PREDICTED: ELAV-like protein 4-like isoform 1 [Acyrthosiphon pisum]

 Score =  229 bits (584), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 106/115 (92%), Positives = 112/115 (97%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N+MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 252 MLAINKGLQRYSPLAGDLLANSMLPGNSMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 311

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNKGK
Sbjct: 312 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKGK 366

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328700229|ref|XP_003241188.1| PREDICTED: ELAV-like protein 4-like isoform 2 [Acyrthosiphon pisum]

 Score =  229 bits (584), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 106/115 (92%), Positives = 112/115 (97%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N+MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 261 MLAINKGLQRYSPLAGDLLANSMLPGNSMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 320

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNKGK
Sbjct: 321 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKGK 375

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865034|ref|XP_003707981.1| PREDICTED: ELAV-like protein 2-like [Megachile rotundata]

 Score =  227 bits (578), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 105/117 (89%), Positives = 111/117 (94%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 256 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 315

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 316 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAA 372

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307194503|gb|EFN76795.1| ELAV-like protein 2 [Harpegnathos saltator]

 Score =  226 bits (577), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 105/117 (89%), Positives = 113/117 (96%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP NTMNG+GWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 233 MLAINKGLQRYSPLAGDLLANSMLPGNTMNGAGWCIFVYNLAPETEENVLWQLFGPFGAV 292

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNY+EAVVAIQSLNGY LGNR+LQVSFKTNK KT+
Sbjct: 293 QSVKVIRDLQTNKCKGFGFVTMTNYEEAVVAIQSLNGYTLGNRVLQVSFKTNKSKTA 349

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709266|ref|XP_003393232.1| PREDICTED: ELAV-like protein 2-like [Bombus terrestris]

 Score =  226 bits (576), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 105/115 (91%), Positives = 110/115 (95%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 255 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 314

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK K
Sbjct: 315 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKSK 369

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350425139|ref|XP_003494024.1| PREDICTED: ELAV-like protein 2-like [Bombus impatiens]

 Score =  225 bits (574), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 105/117 (89%), Positives = 111/117 (94%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 255 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 314

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 315 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAT 371

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792242|ref|XP_394166.4| PREDICTED: ELAV-like protein 2-like [Apis mellifera]

 Score =  225 bits (574), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 105/117 (89%), Positives = 111/117 (94%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 262 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 321

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 322 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAA 378

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027075|ref|XP_003697261.1| PREDICTED: ELAV-like protein 2-like [Apis florea]

 Score =  225 bits (574), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 105/117 (89%), Positives = 111/117 (94%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 246 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 305

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 306 QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAA 362

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332029758|gb|EGI69627.1| ELAV-like protein 2 [Acromyrmex echinatior]

 Score =  225 bits (573), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 104/117 (88%), Positives = 112/117 (95%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP NTMNG+GWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 243 MLAINKGLQRYSPLAGDLLANSMLPGNTMNGAGWCIFVYNLAPETEENVLWQLFGPFGAV 302

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNY+EAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 303 QSVKVIRDLQTNKCKGFGFVTMTNYEEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAA 359

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493619|ref|XP_003427110.1| PREDICTED: ELAV-like protein 3-like isoform 2 [Nasonia vitripennis]

 Score =  224 bits (570), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 104/117 (88%), Positives = 111/117 (94%)

Query: 1   MLAINKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV 60
           MLAINKGLQR+SPL GDLLA+S+LP N MNGSGWCIFVYNLAPETEE+VLWQLFGPFGAV
Sbjct: 267 MLAINKGLQRYSPLAGDLLANSMLPGNAMNGSGWCIFVYNLAPETEENVLWQLFGPFGAV 326

Query: 61  QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           QSVKVIRDLQTNKCKGFGFVTMTNY+EAVVAIQSLNGY LGNR+LQVSFKTNK K +
Sbjct: 327 QSVKVIRDLQTNKCKGFGFVTMTNYEEAVVAIQSLNGYTLGNRVLQVSFKTNKSKAA 383

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	117
FB|FBgn0086675	356	fne "found in neurons" [Drosop	0.948	0.311	0.873	4.1e-49
FB|FBgn0010263	444	Rbp9 "RNA-binding protein 9" [	0.923	0.243	0.787	1.5e-44
UNIPROTKB|A2VDK5	366	ELAVL4 "Uncharacterized protei	0.982	0.314	0.666	6.1e-39
UNIPROTKB|F1P856	382	ELAVL4 "Uncharacterized protei	0.982	0.301	0.666	6.1e-39
UNIPROTKB|J9PAL3	366	ELAVL4 "Uncharacterized protei	0.982	0.314	0.666	6.1e-39
UNIPROTKB|B1APY9	371	ELAVL4 "cDNA FLJ50619, highly	0.982	0.309	0.666	6.1e-39
ZFIN|ZDB-GENE-990415-246	408	elavl4 "ELAV (embryonic lethal	0.948	0.272	0.681	6.1e-39
UNIPROTKB|F1NLH0	371	ELAVL4 "Uncharacterized protei	0.948	0.299	0.681	9.9e-39
ZFIN|ZDB-GENE-040704-9	388	elavl2 "ELAV (embryonic lethal	0.948	0.286	0.698	1.6e-38
UNIPROTKB|B1APY8	385	ELAVL4 "ELAV-like protein 4" [	0.905	0.275	0.702	5.5e-38

FB|FBgn0086675 fne "found in neurons" [Drosophila melanogaster (taxid:7227)]

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 97/111 (87%), Positives = 103/111 (92%)

Query:     7 GLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
             G  R+SPL GDLLA+SILP N M GSGWCIFVYNLAPETEE+VLWQLFGPFGAVQSVKVI
Sbjct:   246 GRIRYSPLAGDLLANSILPGNAMTGSGWCIFVYNLAPETEENVLWQLFGPFGAVQSVKVI 305

Query:    67 RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             RDLQT+KCKGFGFVTMTNYDEAVVAIQSLNGY LGNR+LQVSFKTNK KT+
Sbjct:   306 RDLQTSKCKGFGFVTMTNYDEAVVAIQSLNGYTLGNRVLQVSFKTNKTKTT 356

GO:0003729 "mRNA binding" evidence=ISS;NAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0051252 "regulation of RNA metabolic process" evidence=IMP

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008049 "male courtship behavior" evidence=IMP

FB|FBgn0010263 Rbp9 "RNA-binding protein 9" [Drosophila melanogaster (taxid:7227)]

 Score = 469 (170.2 bits), Expect = 1.5e-44, P = 1.5e-44
 Identities = 85/108 (78%), Positives = 98/108 (90%)

Query:     8 LQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIR 67
             + R+SPLT DL+ + ++  NT+  SGWCIFVYNLAP+TEE+VLWQLFGPFGAVQSVKVIR
Sbjct:   335 ISRYSPLTSDLITNGMIQGNTIASSGWCIFVYNLAPDTEENVLWQLFGPFGAVQSVKVIR 394

Query:    68 DLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
             DLQ+NKCKGFGFVTMTNY+EAV+AIQSLNGY LGNR+LQVSFKTNK K
Sbjct:   395 DLQSNKCKGFGFVTMTNYEEAVLAIQSLNGYTLGNRVLQVSFKTNKNK 442

GO:0003729 "mRNA binding" evidence=ISS;NAS

GO:0003730 "mRNA 3'-UTR binding" evidence=TAS

GO:0007293 "germarium-derived egg chamber formation" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0048477 "oogenesis" evidence=IMP

GO:0036093 "germ cell proliferation" evidence=IMP

GO:0060856 "establishment of blood-brain barrier" evidence=IMP

UNIPROTKB|A2VDK5 ELAVL4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 80/120 (66%), Positives = 98/120 (81%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   249 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 306

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct:   307 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 366

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P856 ELAVL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 80/120 (66%), Positives = 98/120 (81%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   265 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 322

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct:   323 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 382

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9PAL3 ELAVL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 80/120 (66%), Positives = 98/120 (81%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   249 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 306

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct:   307 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 366

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B1APY9 ELAVL4 "cDNA FLJ50619, highly similar to ELAV-like protein 4" [Homo sapiens (taxid:9606)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 80/120 (66%), Positives = 98/120 (81%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   254 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 311

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct:   312 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 371

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-990415-246 elavl4 "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)" [Danio rerio (taxid:7955)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 79/116 (68%), Positives = 97/116 (83%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   291 LLNMAYGVKRFSPITIDSMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 348

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK
Sbjct:   349 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 404

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|F1NLH0 ELAVL4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 79/116 (68%), Positives = 97/116 (83%)

Query:     1 MLAINKGLQRFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPF
Sbjct:   254 LLNMAYGVKRFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPF 311

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK
Sbjct:   312 GAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 367

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

ZFIN|ZDB-GENE-040704-9 elavl2 "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)" [Danio rerio (taxid:7955)]

 Score = 412 (150.1 bits), Expect = 1.6e-38, P = 1.6e-38
 Identities = 81/116 (69%), Positives = 95/116 (81%)

Query:     1 MLAINKGLQRFSPLTGD---LLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
             +L +  G++RFSP+T D    LA   LPA+   G+GWCIFVYNLAP+ +E+VLWQ+FGPF
Sbjct:   271 LLNMAYGVKRFSPMTIDGVTSLAGINLPAHA--GTGWCIFVYNLAPDADENVLWQMFGPF 328

Query:    58 GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             GAV +VKVIRD  TNKCKGFGFVTMTNYDEA VAI SLNGY LG+R+LQVSFKTNK
Sbjct:   329 GAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAVAIASLNGYRLGDRVLQVSFKTNK 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|B1APY8 ELAVL4 "ELAV-like protein 4" [Homo sapiens (taxid:9606)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 78/111 (70%), Positives = 92/111 (82%)

Query:    10 RFSPLTGDLLASSI---LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
             RFSP+T D + S +   +P +T  G+GWCIFVYNL+P+++ESVLWQLFGPFGAV +VKVI
Sbjct:   277 RFSPITIDGMTSLVGMNIPGHT--GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVI 334

Query:    67 RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
             RD  TNKCKGFGFVTMTNYDEA +AI SLNGY LG+R+LQVSFKTNK   S
Sbjct:   335 RDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKAHKS 385

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O09032	ELAV4_RAT	No assigned EC number	0.7027	0.9059	0.2841	yes	N/A
P26378	ELAV4_HUMAN	No assigned EC number	0.7027	0.9059	0.2789	yes	N/A
Q61701	ELAV4_MOUSE	No assigned EC number	0.7027	0.9059	0.2753	yes	N/A
A4QNI8	ELAV4_XENTR	No assigned EC number	0.6666	0.9829	0.2875	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	117
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-57
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-55
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-48
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-48
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-47
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-43
smart00360	73	smart00360, RRM, RNA recognition motif	6e-25
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-21
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-21
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-20
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-20
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	7e-20
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-19
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-18
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-17
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-16
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-16
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-16
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-16
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-16
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	9e-16
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-15
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-15
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-15
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-15
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-15
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-15
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-15
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-14
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-14
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-14
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-14
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-13
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-13
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-13
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	7e-13
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	8e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-13
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	9e-13
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-12
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-12
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-12
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-12
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	5e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-11
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-11
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-11
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-11
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-11
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-11
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-11
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-11
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-10
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-10
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-10
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	4e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-10
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-10
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-09
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-09
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-09
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-09
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-09
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-09
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-09
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-09
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	7e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-08
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-08
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-08
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-08
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-08
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-08
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-08
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	4e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-08
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	5e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-08
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	6e-08
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	6e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	6e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-08
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	1e-07
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-07
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-07
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	1e-07
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-07
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-07
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-07
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	3e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	7e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	7e-06
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	8e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-06
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	9e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	9e-06
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	1e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	1e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	1e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-05
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	3e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	4e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	5e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	5e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	7e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	9e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	1e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	1e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	1e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	2e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	2e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	2e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	2e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	3e-04
cd12628	76	cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in	3e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-04
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	4e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	4e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	4e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	4e-04
cd12256	89	cd12256, RRM2_LKAP, RNA recognition motif 2 in Lim	5e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-04
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	5e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	6e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	6e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	7e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	7e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	7e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	8e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	8e-04
cd12695	93	cd12695, RRM3_PTBP1, RNA recognition motif 3 in ve	8e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	8e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.001
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	0.001
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.001
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.001
cd12630	76	cd12630, RRM2_IGF2BP3, RNA recognition motif 2 in	0.001
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.002
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.002
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	0.002
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	0.002
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.002
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.002
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.003
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.003
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12754	87	cd12754, RRM2_RBM10, RNA recognition motif 2 in ve	0.003
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.004
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	0.004
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.004
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.004
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	0.004

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

 Score =  181 bits (460), Expect = 1e-57
 Identities = 71/110 (64%), Positives = 88/110 (80%), Gaps = 3/110 (2%)

Query: 9   QRFSPLTGDLLASSILPANTM---NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKV 65
           QR SP   D   + +     +   +G+G+CIFVYNL+P+T+E+VLWQLFGPFGAVQ+VK+
Sbjct: 242 QRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKI 301

Query: 66  IRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           IRDL TN+CKG+GFV+MTNYDEA +AI SLNGY LGNR+LQVSFKTNK  
Sbjct: 302 IRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY 351

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

 Score =  165 bits (421), Expect = 3e-55
 Identities = 61/78 (78%), Positives = 68/78 (87%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           GWCIFVYNL P+ +ES+LWQLF PFGAV +VKVIRDL TNKCKG+GFVTMTNY+EA  AI
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 93  QSLNGYALGNRILQVSFK 110
            SLNGY LG R+LQVSFK
Sbjct: 61  ASLNGYRLGGRVLQVSFK 78

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

 Score =  149 bits (378), Expect = 1e-48
 Identities = 68/84 (80%), Positives = 77/84 (91%)

Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           G+GWCIFVYNL+P+++ESVLWQLFGPFGAV +VKVIRD  TNKCKGFGFVTMTNYDEA +
Sbjct: 1   GTGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60

Query: 91  AIQSLNGYALGNRILQVSFKTNKG 114
           AI SLNGY LG+R+LQVSFKTNK 
Sbjct: 61  AIASLNGYRLGDRVLQVSFKTNKT 84

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

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

 Score =  147 bits (373), Expect = 8e-48
 Identities = 67/83 (80%), Positives = 76/83 (91%)

Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           G+GWCIFVYNLAP+ +ES+LWQ+FGPFGAV +VKVIRD  TNKCKGFGFVTMTNYDEA +
Sbjct: 1   GTGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           AI SLNGY LG+R+LQVSFKTNK
Sbjct: 61  AIASLNGYRLGDRVLQVSFKTNK 83

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

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

 Score =  146 bits (368), Expect = 4e-47
 Identities = 67/81 (82%), Positives = 74/81 (91%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           GWCIFVYNL+PE +ESVLWQLFGPFGAV +VKVIRD  TNKCKGFGFVTMTNYDEA +AI
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 93  QSLNGYALGNRILQVSFKTNK 113
            SLNGY LG+R+LQVSFKT+K
Sbjct: 61  ASLNGYRLGDRVLQVSFKTSK 81

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

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

 Score =  136 bits (343), Expect = 2e-43
 Identities = 60/81 (74%), Positives = 71/81 (87%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           GWCIF+YNL  + +E +LWQ+FGPFGAV +VKVIRD  TNKCKGFGFVTMTNY+EA +AI
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 93  QSLNGYALGNRILQVSFKTNK 113
            SLNGY LG++ILQVSFKT+K
Sbjct: 61  ASLNGYRLGDKILQVSFKTSK 81

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

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

 Score = 89.2 bits (222), Expect = 6e-25
 Identities = 33/73 (45%), Positives = 48/73 (65%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV NL P+T E  L +LF  FG V+SV+++RD +T K KGF FV   + ++A  A+++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 95  LNGYALGNRILQV 107
           LNG  L  R L+V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 81.1 bits (201), Expect = 1e-21
 Identities = 30/70 (42%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+T E  L  LF  FG ++S++++RD +T + KGF FV   + ++A  A+++L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 96  NGYALGNRIL 105
           NG  LG R L
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 78.7 bits (195), Expect = 9e-21
 Identities = 28/72 (38%), Positives = 43/72 (59%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           V NL+ + +E  L +LF PFG +  V + +D +T + +GF FVT    ++A  AI+ LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 98  YALGNRILQVSF 109
           +   N IL V +
Sbjct: 64  FGYDNLILSVEW 75

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

 Score = 77.0 bits (190), Expect = 4e-20
 Identities = 32/73 (43%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+T E  L +LF  FG ++SV+++RD +  K KGF FV   + ++A  A+++L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 96  NGYALGNRILQVS 108
           NG  L  R L+VS
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 76.9 bits (190), Expect = 6e-20
 Identities = 33/74 (44%), Positives = 42/74 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E  L  LFG FG V S +VI D +T + +GFGFV M   +EA  AI+ L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 96  NGYALGNRILQVSF 109
           NG   G R L V+ 
Sbjct: 62  NGTDFGGRTLTVNE 75

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|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 76.5 bits (189), Expect = 7e-20
 Identities = 31/73 (42%), Positives = 46/73 (63%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+Y+L  E  +  L+QLF PFG V S KV  D  T + K FGFV+  N + A  AI+++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 96  NGYALGNRILQVS 108
           NG+ +G + L+V 
Sbjct: 61  NGFQVGGKRLKVQ 73

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

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

 Score = 75.5 bits (186), Expect = 2e-19
 Identities = 33/77 (42%), Positives = 48/77 (62%), Gaps = 4/77 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV +L+PE +   L   F PFG +   +V++D+QT K KG+GFV+    ++A  AIQS+
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 96  NGYALGNRILQVSFKTN 112
           NG  LG R    + +TN
Sbjct: 62  NGQWLGGR----AIRTN 74

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

 Score = 78.1 bits (191), Expect = 2e-18
 Identities = 30/87 (34%), Positives = 44/87 (50%)

Query: 30  NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
                 +FV NL  +  E  L +LF  FG V+ V+++RD +T K +GF FV   + + A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 90  VAIQSLNGYALGNRILQVSFKTNKGKT 116
            AI+ LNG  L  R L+V       + 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQP 198

Length = 306

>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 = 72.6 bits (179), Expect = 2e-18
 Identities = 29/72 (40%), Positives = 45/72 (62%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+  T E  L  LF  FG V+ V +++D +T + +GFGFVT  + ++A  AI+ L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 96  NGYALGNRILQV 107
           NG  L  R+++V
Sbjct: 64  NGKELEGRVIKV 75

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

 Score = 70.8 bits (174), Expect = 1e-17
 Identities = 29/78 (37%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           G  +F+ NL PE +E +L+  F  FG  +Q+ K++RD  T   KGF F++  +++ +  A
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 92  IQSLNGYALGNRILQVSF 109
           I+++NG  L NR + VS+
Sbjct: 61  IEAMNGQYLCNRPITVSY 78

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

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

 Score = 67.6 bits (166), Expect = 2e-16
 Identities = 24/75 (32%), Positives = 45/75 (60%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G ++ V+V+ D +T + +GFGFV   + ++A  A + 
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60

Query: 95  LNGYALGNRILQVSF 109
           LNG  +  R ++V +
Sbjct: 61  LNGMEIDGRRIRVDY 75

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

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

 Score = 66.9 bits (164), Expect = 4e-16
 Identities = 25/73 (34%), Positives = 44/73 (60%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E  L  +F PFG ++ V++ RD +T + KG+GF+   + ++A  A++ L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 96  NGYALGNRILQVS 108
           NG+ L  R ++V 
Sbjct: 61  NGFELAGRPIKVG 73

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

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

 Score = 66.8 bits (164), Expect = 5e-16
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  + EE  L + F   G V++V+++RD +T   KGFG+V     D   +A++ L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-L 60

Query: 96  NGYALGNRILQVS 108
           NG  L  R ++V 
Sbjct: 61  NGIKLKGRKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 66.5 bits (163), Expect = 7e-16
 Identities = 23/74 (31%), Positives = 39/74 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +T +  L + F   G ++   V++D  + KC+GFG+VT    ++A  A++  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 96  NGYALGNRILQVSF 109
                G R + V F
Sbjct: 62  KKTKFGGRKIHVEF 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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 66.4 bits (162), Expect = 9e-16
 Identities = 26/72 (36%), Positives = 46/72 (63%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ +T E  L Q+F  +G +  V V++D +T + +GFGFVT  N D+A  A+ ++
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 96  NGYALGNRILQV 107
           NG ++  R ++V
Sbjct: 63  NGKSVDGRQIRV 74

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

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

 Score = 66.1 bits (162), Expect = 9e-16
 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL  + ++  L +LFG +G + S KV++D    K KGFGFV   N++ A  A++ L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 96  NGYALGNRILQV 107
           NG  +  + L V
Sbjct: 63  NGKEVNGKKLYV 74

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

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

 Score = 65.6 bits (160), Expect = 2e-15
 Identities = 33/75 (44%), Positives = 47/75 (62%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  ++ L Q+F PFG V S KV  D  TN+ K FGFV+  N   A  AI
Sbjct: 4   GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63

Query: 93  QSLNGYALGNRILQV 107
           Q++NG+ +G + L+V
Sbjct: 64  QAMNGFQIGMKRLKV 78

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

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

 Score = 65.3 bits (160), Expect = 2e-15
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E  L + F PFGA++ V+V +D      KG+ FV    ++ A  AI ++
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 96  NGYALGNRILQVS 108
           NG ++  + ++ S
Sbjct: 57  NGTSINGQTVKCS 69

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

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

 Score = 65.4 bits (159), Expect = 2e-15
 Identities = 35/75 (46%), Positives = 47/75 (62%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  ++ L Q F PFG V S KV  D QTN  K FGFV+  N D A  AI
Sbjct: 4   GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63

Query: 93  QSLNGYALGNRILQV 107
           Q++NG+ +G + L+V
Sbjct: 64  QAMNGFQIGTKRLKV 78

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

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

 Score = 65.1 bits (158), Expect = 3e-15
 Identities = 36/81 (44%), Positives = 49/81 (60%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  +  L Q+F PFG V S KV  D QTN  K FGFV+  N   A  AI
Sbjct: 7   GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66

Query: 93  QSLNGYALGNRILQVSFKTNK 113
           Q++NG+ +G + L+V  K +K
Sbjct: 67  QAMNGFQIGMKRLKVQLKRSK 87

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

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

 Score = 64.2 bits (157), Expect = 4e-15
 Identities = 25/73 (34%), Positives = 42/73 (57%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  LA E +E VL   F PFG ++ +++  D +T K +GF FV     ++A  AI ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 96  NGYALGNRILQVS 108
           N   L  R ++V+
Sbjct: 61  NESELFGRTIRVN 73

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

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

 Score = 63.8 bits (156), Expect = 7e-15
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL   T E  L +LF  +G V+ VK I+D        + FV     D+AV A++ +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 96  NGYALGNRILQVSF 109
           NG  L    ++VS 
Sbjct: 56  NGKELEGSPIEVSL 69

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|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 63.4 bits (155), Expect = 9e-15
 Identities = 27/74 (36%), Positives = 41/74 (55%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+  +  E  L ++F   G V S +++ D  T K KG+GF    + + A  AI++L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 96  NGYALGNRILQVSF 109
           NGY    R L+V F
Sbjct: 61  NGYEFNGRALRVDF 74

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

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

 Score = 63.3 bits (154), Expect = 1e-14
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 36  IFVYNLAPETEESVLWQLF-GPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           IFV +L+PE  ES L  LF   F + +S K++ D  T   +G+GFV  ++ ++   A+  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 95  LNGYALGNRILQVSFKT 111
           + G   G R +++S  T
Sbjct: 64  MQGVYCGGRPMRISTAT 80

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

 Score = 63.1 bits (154), Expect = 1e-14
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 40  NLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY 98
           N  P+   +  L  LF   G ++S K++RD  T +  G+GFV   + ++A  AI +LNG+
Sbjct: 6   NYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65

Query: 99  ALGNRILQVSF 109
            + N+ L+VS+
Sbjct: 66  EIRNKRLKVSY 76

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

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

 Score = 63.4 bits (155), Expect = 1e-14
 Identities = 26/73 (35%), Positives = 47/73 (64%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV +L  E  + VL + F  + + Q  KV+RD +T K KG+GFV+ ++ ++ + A++ +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 96  NGYALGNRILQVS 108
           NG  +GNR +++ 
Sbjct: 69  NGKYVGNRPIKLR 81

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

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

 Score = 61.0 bits (148), Expect = 8e-14
 Identities = 23/74 (31%), Positives = 46/74 (62%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV +L+PE  ++ L+  F  F +    +V+ D+++ + +G+GFV+  +  +A  AI  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 96  NGYALGNRILQVSF 109
           NG  LG+R ++ ++
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 60.1 bits (146), Expect = 2e-13
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL    +E  L +LF  FG +  V V  D ++ K KGF +V   + ++AV A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 96  NGYALGNRILQV 107
           +G     R++ +
Sbjct: 65  DGKVFQGRLIHI 76

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

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

 Score = 59.6 bits (145), Expect = 4e-13
 Identities = 21/72 (29%), Positives = 34/72 (47%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+  L     E  + +L   FG +++  +++D  T   KG+ F    +      AI  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 96  NGYALGNRILQV 107
           NG  LG++ L V
Sbjct: 63  NGMQLGDKKLTV 74

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

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

 Score = 58.8 bits (143), Expect = 6e-13
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 41  LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL 100
           L P T +  L +L  PFG + S K I D +TNKCKG+GFV   + + A+ AI+ LNG   
Sbjct: 8   LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRG- 66

Query: 101 GNRILQVSF 109
               +Q  F
Sbjct: 67  ----VQAQF 71

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

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

 Score = 58.6 bits (142), Expect = 7e-13
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V    P+T ES + ++F P+GAV+ VK+I          F FV   + + A+ A  S+
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53

Query: 96  NGYALGNRILQVSF 109
           +G  L N  L V++
Sbjct: 54  HGKVLNNNPLYVTY 67

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

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

 Score = 58.6 bits (141), Expect = 8e-13
 Identities = 28/76 (36%), Positives = 45/76 (59%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L+PE     +   F PFG +   +V++D+ T K KG+GFV+  N  +A  AIQ +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 96  NGYALGNRILQVSFKT 111
            G  LG R ++ ++ T
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

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

 Score = 62.6 bits (152), Expect = 9e-13
 Identities = 27/74 (36%), Positives = 46/74 (62%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E  L Q+F PFG ++ V++ RD +T + KGFGF+   + +EA  A++ +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 96  NGYALGNRILQVSF 109
           NG+ L  R ++V +
Sbjct: 249 NGFELAGRPIKVGY 262

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 58.4 bits (142), Expect = 9e-13
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 36  IFVYNLAPETEESVLWQLF-GPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           IFV +LAP+  + +L + F   + +V+  KV+ D  T + KG+GFV   + DE   A+  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 95  LNGYALGNRILQVSFKT 111
           +NG    +R ++VS  T
Sbjct: 64  MNGVYCSSRPMRVSPAT 80

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

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 58.1 bits (141), Expect = 1e-12
 Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +  E    +LF  +G V  V +      NK KGFGF+ +     A  A   L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAEL 57

Query: 96  NGYALGNRILQVSF 109
           +G     R L+V F
Sbjct: 58  DGIMRKGRQLRVRF 71

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 58.1 bits (141), Expect = 1e-12
 Identities = 27/72 (37%), Positives = 37/72 (51%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL   T E  L +LF  FG +  V +  D +T + KGF FV+    + AV A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 96  NGYALGNRILQV 107
           +G     R+L V
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 57.7 bits (140), Expect = 2e-12
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+P+  +  L + F   G +  V +I+  + N    F F+       A  A++S 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIK--RANHTNAFAFIKFEREQAAARAVESE 63

Query: 96  NGYALGNRILQVSFK 110
           N   L N+ + V +K
Sbjct: 64  NHSMLKNKTMHVQYK 78

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

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L +LF   G + S KV+ D +    +GFGFV  +N +EA  A+  +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 96  NGYALGNRILQVSFKTNK 113
           +G  LG + L V+    K
Sbjct: 347 HGRMLGGKPLYVALAQRK 364

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 21/46 (45%), Positives = 31/46 (67%)

Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
          C+FV NL  E  E  LW++FG  G ++ V+++RD +TN  KGF +V
Sbjct: 1  CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYV 46

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 57.8 bits (140), Expect = 2e-12
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 40  NLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY 98
           N  P+T  +     LF   G V++ K++RD +T    GFGFV   + ++A  AI++LNG 
Sbjct: 6   NYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGL 65

Query: 99  ALGNRILQVSF 109
            L N+ ++V++
Sbjct: 66  QLQNKRIKVAY 76

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

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

 Score = 57.3 bits (139), Expect = 2e-12
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL  +  E+ L +LF PFG V  V + R     K KGF FV  T+  +A  AI+ +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 96  NGYALGNRILQVSF 109
           NG  +  R + V +
Sbjct: 61  NGKKIKGRPVAVDW 74

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

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

 Score = 60.6 bits (147), Expect = 5e-12
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL P   E  L +LF  FG + S  V++D  + + +GF FV    +++A  A++ +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 96  NGYALG 101
           NG  +G
Sbjct: 240 NGKKIG 245

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

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

 Score = 56.6 bits (136), Expect = 5e-12
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L+PE     +   F PFG +   +V++D+ T K KG+GFV+  N  +A  AI  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 96  NGYALGNRILQVSFKT 111
            G  LG R ++ ++ T
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

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

 Score = 56.5 bits (137), Expect = 6e-12
 Identities = 25/77 (32%), Positives = 38/77 (49%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V NL  E  +    +L  PFGAV+   ++    T + KG+GFV   +   A+ A   
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 95  LNGYALGNRILQVSFKT 111
           L+G  +G R LQV +  
Sbjct: 61  LDGKQIGGRKLQVDWAD 77

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

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

 Score = 55.6 bits (135), Expect = 1e-11
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL P   E  L + F P+G V+ V+++R+   ++ +GF FV   + ++A  A++ L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 96  NGYALGNR 103
           NG  L  R
Sbjct: 59  NGLVLDGR 66

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

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

 Score = 55.6 bits (135), Expect = 1e-11
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 37 FVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN 96
          FV  L     E  +  LF  +G ++ V +IRD  T + KG  FV  ++ +EA  AI++L+
Sbjct: 3  FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 97 G 97
          G
Sbjct: 63 G 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 55.2 bits (133), Expect = 1e-11
 Identities = 27/74 (36%), Positives = 42/74 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+  E  E  L  +F   G V S +++ D +T K KG+GF    + + A+ A+++L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 96  NGYALGNRILQVSF 109
           NGY L  R L+V  
Sbjct: 61  NGYELNGRQLRVDN 74

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

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

 Score = 55.3 bits (134), Expect = 1e-11
 Identities = 23/73 (31%), Positives = 42/73 (57%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL  +  E +LW+LF   G V +V + +D  T   +G+GFV   + ++A  AI+ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 96  NGYALGNRILQVS 108
           N   L  + ++V+
Sbjct: 61  NMIKLYGKPIRVN 73

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

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

 Score = 55.3 bits (134), Expect = 1e-11
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL    ++  L + F PFG + S KV+ D +  + KGFGFV  ++ +EA  A+  +
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 96  NGYALGNRILQVSF 109
           NG  +G + L V+ 
Sbjct: 63  NGRIIGGKPLYVAL 76

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

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 25/83 (30%), Positives = 40/83 (48%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           GW IFV  +  E +E  +   F  FG ++++ +  D +T   KG+  +      EA  AI
Sbjct: 6   GWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAI 65

Query: 93  QSLNGYALGNRILQVSFKTNKGK 115
           + LNG  L  + + V +   KG 
Sbjct: 66  EGLNGKELLGQTISVDWAFVKGP 88

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

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

 Score = 55.2 bits (133), Expect = 2e-11
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NLA    +  L   F     ++   V+ D +T + +G+GFVT    ++A  A+  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 96  NGYALGNRILQVSFKT 111
               L  RIL++    
Sbjct: 62  KNKKLHGRILRLDIAE 77

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

 Score = 55.0 bits (133), Expect = 2e-11
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V ++ P+  E  +  +F  FG ++S  +  D +T K KG+GF+   N   A  AI S+
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 96  NGYALGNRILQVS 108
           N + LG + L+V 
Sbjct: 63  NLFDLGGQQLRVG 75

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

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

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
          +FV  L  +  E  L + F  +G V+SV+++ D +T K +GF FVT  +YD
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYD 52

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

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

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV---IRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           I+V NL  + +E  L  +F  FG V+S+++     + Q     GF FVT  +   A  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 93  QSLNGYALGNRILQVS 108
           Q LNG  LG R + VS
Sbjct: 63  Q-LNGTELGGRKISVS 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 54.2 bits (131), Expect = 3e-11
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E +L +LF   G ++S K+IR+   +    + FV   ++  A  A+Q++
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57

Query: 96  NGYALGNRILQV 107
           NG  +  + ++V
Sbjct: 58  NGRLILGQEIKV 69

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

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

 Score = 54.3 bits (131), Expect = 4e-11
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+ + +E  +++ FG +G + SV++  D  + + KGFG+V  ++ + A  A+ +L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 96  NGYALGNR 103
            G  L  R
Sbjct: 61  GGTDLLGR 68

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

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

 Score = 54.5 bits (131), Expect = 4e-11
 Identities = 27/67 (40%), Positives = 36/67 (53%), Gaps = 4/67 (5%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA----VVA 91
          +FV  L  +  E  L + F  FG V+  +VI D QT K +GFGFV   N+D A    VV 
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 92 IQSLNGY 98
             +NG+
Sbjct: 62 FHPINGH 68

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

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

 Score = 54.2 bits (131), Expect = 4e-11
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          IFV  L   T +  L + F  FG ++   VI D QT K +G+GFVT  + + A  A +  
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 96 N 96
          N
Sbjct: 63 N 63

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

 Score = 54.0 bits (130), Expect = 5e-11
 Identities = 23/58 (39%), Positives = 36/58 (62%)

Query: 52  QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
            LF   G ++S K+IRD  T +  G+GFV   + ++A  AI +LNG  L N+ ++VS+
Sbjct: 20  SLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77

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

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 53.4 bits (129), Expect = 6e-11
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 9/70 (12%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL   T    L  LF  +G V    V+++        +GFV M   ++A  AI++L
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 96  NGYAL-GNRI 104
           NGY   G RI
Sbjct: 54  NGYEFMGKRI 63

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

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

 Score = 53.5 bits (129), Expect = 7e-11
 Identities = 25/74 (33%), Positives = 42/74 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+   ++  L   F  FG V   +VI D +T + +GFG+V   + ++A  AI+++
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 96  NGYALGNRILQVSF 109
           +G  L  R + V F
Sbjct: 62  DGKELDGRPINVDF 75

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

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

 Score = 53.4 bits (129), Expect = 1e-10
 Identities = 25/57 (43%), Positives = 35/57 (61%)

Query: 41 LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
          L P  +E+ ++  F   G V SVK+IR+ QT K  G+GFV    ++ A  A+QSLNG
Sbjct: 7  LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

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

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

 Score = 52.9 bits (128), Expect = 1e-10
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV  D +    KG+GFV     + AV AI+ +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 96  NGYALGNRILQV 107
           NG  L ++ + V
Sbjct: 64  NGMLLNDKKVFV 75

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

 Score = 52.9 bits (128), Expect = 1e-10
 Identities = 22/62 (35%), Positives = 39/62 (62%)

Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           ++V +L P+  E++L+++F P G V S++V RDL T +  G+ +V   N  +A  A+ +
Sbjct: 1  SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 95 LN 96
          LN
Sbjct: 61 LN 62

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

 Score = 52.9 bits (127), Expect = 1e-10
 Identities = 25/72 (34%), Positives = 41/72 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I++ +L     E  L + F  FG V++V+V R  +T   K +GF+   N + A +A +S+
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 96  NGYALGNRILQV 107
           N Y L  ++LQV
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 52.8 bits (127), Expect = 2e-10
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK--CKGFGFVTMTNYDEAVVAIQ 93
           + V N+     +  L Q+FG FG +  V++I     N+   KGFGFVT  N  +A  A +
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEII----FNERGSKGFGFVTFANSADADRARE 58

Query: 94  SLNGYALGNRILQVSFKT 111
            L+G  +  R ++V+  T
Sbjct: 59  KLHGTVVEGRKIEVNNAT 76

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

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

 Score = 51.9 bits (125), Expect = 4e-10
 Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA--VVAIQ 93
          IFV  + P+T E  L   F  FG+V+ VK+I D      KG+GFVT    ++A  ++A+ 
Sbjct: 5  IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMG 63

Query: 94 SLN 96
          +LN
Sbjct: 64 NLN 66

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

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

 Score = 51.7 bits (124), Expect = 4e-10
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +++ E  E  + Q F PFG ++S+ +  D  T K KGF FV     + A +A++ +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 96  NGYALGNRILQV 107
           NG  LG R ++V
Sbjct: 63  NGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 51.9 bits (125), Expect = 4e-10
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S + I++  L  E  E  +  +F  +G +  + ++RD +T K KGF F+   +    ++A
Sbjct: 9   SAY-IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILA 67

Query: 92  IQSLNGYALGNRILQV 107
           + +LNG  L  R ++V
Sbjct: 68  VDNLNGIKLLGRTIRV 83

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

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

 Score = 51.6 bits (124), Expect = 5e-10
 Identities = 20/59 (33%), Positives = 30/59 (50%)

Query: 45  TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
             E  L + F PFG +Q + V++D QT + KG  +V       A  A++ +NG  LG  
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

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

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

 Score = 51.1 bits (123), Expect = 6e-10
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL P   +  L   F  +G ++SV V R        GF FV   +  +A  A+++L
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 96  NGYAL-GNRI 104
           +G  + GNR+
Sbjct: 57  DGRRICGNRV 66

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

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

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+ +  E  L++ F   G V+ V++IRD  + + KG  +V   + +   +A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60

Query: 96  NGYALGNRILQV 107
            G  L  + + V
Sbjct: 61  TGQRLLGQPIMV 72

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

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

 Score = 50.4 bits (121), Expect = 1e-09
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL      + L ++F  +G V  V +++D +T K KG  F+   + ++A   +++L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 96  NGYALGNRILQVS 108
           N   L  R L+ S
Sbjct: 64  NNKELFGRTLKCS 76

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

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

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 36/72 (50%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NLA    E  L +LF  +G +  V +  D  T K KGF FVT    + AV A   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 96  NGYALGNRILQV 107
           +G     R+L +
Sbjct: 65  DGTVFQGRLLHL 76

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

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

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIR-----DLQTNKCKGFGFVTMTNYDEAV 89
            +FV NL  +T E  L + F   G V+SV + +             G+GFV   + + A 
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 90  VAIQSLNGYALGNRILQVSF 109
            A++ L G  L    L++  
Sbjct: 62  KALKRLQGTVLDGHALELKL 81

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

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

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NL  +  E  L +LF  FG V+  ++++D  T   KG  FV     + A   +++ 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 96  N-----GYALGNRILQVSF 109
           +     G +L  R L V+ 
Sbjct: 63  DNAEDSGLSLDGRRLIVTL 81

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

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

 Score = 50.8 bits (121), Expect = 1e-09
 Identities = 26/79 (32%), Positives = 42/79 (53%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 95  LNGYALGNRILQVSFKTNK 113
            NG  L  R ++V F   K
Sbjct: 71  ANGMELDGRRIRVDFSITK 89

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

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

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L P+  E+ L+ LF PFG V SV+V RD  T +  G+G+V   N  +A  A++++
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 96  NGYALGNRILQV 107
           N   LG + +++
Sbjct: 63  NFKRLGGKPIRI 74

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

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

 Score = 49.9 bits (120), Expect = 2e-09
 Identities = 20/73 (27%), Positives = 38/73 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ +L     E  L + F  FG V  +++ R  +T K KG+ FV   + + A +  +++
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 96  NGYALGNRILQVS 108
           N Y L  R+L+  
Sbjct: 62  NNYLLFERLLKCK 74

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

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

 Score = 49.7 bits (119), Expect = 2e-09
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L P+  E    + F  FG V   ++++D  T + +GFGFVT  + + AV  + S 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 96  NGYALGNRILQVSFK 110
               LG +  QV  K
Sbjct: 61  GMLELGGK--QVEVK 73

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

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

 Score = 49.6 bits (119), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV NL     E +L++LF   G ++ VK+ +D      K F FVT  +      AIQ 
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP-KSFAFVTFKHEVSVPYAIQL 61

Query: 95  LNGYALGNRILQVS 108
           LNG  L  R L++ 
Sbjct: 62  LNGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 49.6 bits (119), Expect = 2e-09
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 9/76 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVAIQ 93
           +FV N+    E+  L  LF  FG ++++          CK  GF+ ++ YD   A  A +
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTA-------CKHRGFIMVSYYDIRAARRAKR 56

Query: 94  SLNGYALGNRILQVSF 109
           +L G  LG R L + F
Sbjct: 57  ALQGTELGGRKLDIHF 72

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

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

 Score = 49.3 bits (118), Expect = 3e-09
 Identities = 24/72 (33%), Positives = 41/72 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L+  T+ + L QLF  +G V   K++ + ++   + FGFVTM + +EA   IQ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 96  NGYALGNRILQV 107
           +   L  R++ V
Sbjct: 62  HRTELHGRVISV 73

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

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

 Score = 50.8 bits (121), Expect = 3e-09
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 4/97 (4%)

Query: 21  SSILPANTMNGS----GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKG 76
           +  +P  +M GS       +F+  L+  T+++ L   F  FG V   KVI D +T + +G
Sbjct: 18  NGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRG 77

Query: 77  FGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
           FGFV   +   A  AI  ++G  L  R ++V+   ++
Sbjct: 78  FGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 48.9 bits (116), Expect = 4e-09
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 10/76 (13%)

Query: 36  IFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           ++V NL  ET E  + + FG F  G V+ VK IRD        + FV  T+ ++AV A+ 
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD--------YAFVHFTSREDAVHAMN 55

Query: 94  SLNGYALGNRILQVSF 109
           +LNG  L    ++V+ 
Sbjct: 56  NLNGTELEGSCIEVTL 71

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

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

 Score = 51.9 bits (124), Expect = 5e-09
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 53  LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           LF   G ++S K++RD  T +  G+GFV     ++A  A+ SLNG  L N+ ++VS+
Sbjct: 23  LFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSY 79

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

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

 Score = 49.1 bits (118), Expect = 5e-09
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQ--SVKVIRDLQTNKCKGFGFVTMTNYDEAVV-- 90
            + +  L   T E  + Q      +V    V++IRD  T   +GF FV   + ++A    
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 91  -AIQSLNGYALGNRILQVSFK 110
            A+ +L+ + +  R+++VS+ 
Sbjct: 64  DALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P+   +G G  IFV NL    +   L+  F  FG + S KV  D +  K +G+GFV    
Sbjct: 81  PSLRRSGVG-NIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEK 138

Query: 85  YDEAVVAIQSLNGYALGNR 103
            + A  AIQ +NG  L ++
Sbjct: 139 EESAKAAIQKVNGMLLNDK 157

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

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

 Score = 48.8 bits (116), Expect = 6e-09
 Identities = 24/79 (30%), Positives = 42/79 (53%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V V+ D +T + +GF FV     D++  A++ 
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60

Query: 95  LNGYALGNRILQVSFKTNK 113
            NG  L  R ++V +   K
Sbjct: 61  ANGMELDGRRIRVDYSITK 79

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

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

 Score = 48.5 bits (116), Expect = 6e-09
 Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L P   E  L  LFGPFG +  VK+         KG GFV   +   A  AIQ L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQQL 57

Query: 96  NGYALGNRILQVS 108
            G  +G   +++S
Sbjct: 58  QGTIIGGSRIRLS 70

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

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

 Score = 48.5 bits (116), Expect = 7e-09
 Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
          IFV  L+PET E  + + FG FG +  +++  D +TNK +GF F+T  + +E V
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS-EEPV 54

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

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

 Score = 48.4 bits (116), Expect = 8e-09
 Identities = 20/74 (27%), Positives = 36/74 (48%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L P T +  L  +F  FG ++S +VIRD +T     + F+     ++   A   +
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 96  NGYALGNRILQVSF 109
           +   + +R + V F
Sbjct: 66  DNVLIDDRRIHVDF 79

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 51.2 bits (122), Expect = 9e-09
 Identities = 25/80 (31%), Positives = 45/80 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +++ E  E  + + F PFG ++S+ +  D  T K KGF FV     + A +A++ +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 96  NGYALGNRILQVSFKTNKGK 115
           NG  LG R ++V   +N  +
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQ 189

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 48.0 bits (115), Expect = 1e-08
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVA 91
          +F+  L+ +T E  L + F  +G V    +++D  T + +GFGFVT  +    + V+A
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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

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

 Score = 48.4 bits (116), Expect = 1e-08
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 15/74 (20%)

Query: 38 VYNLAPETEESVLWQLF---------GPFGAVQSVKVIRDLQ------TNKCKGFGFVTM 82
          + NL    +E  L +LF              ++ VK++RDL+        K KG+GFV  
Sbjct: 5  IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 83 TNYDEAVVAIQSLN 96
          TN++ A+ A+++LN
Sbjct: 65 TNHEHALKALRALN 78

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

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           V  L  +T E  L   F  FG +  V+V +D +T + KGFGFV   +Y++ V  +     
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS--QR 61

Query: 98  YALGNRILQVSFKTNK 113
           + +  R   V    +K
Sbjct: 62  HMIDGRWCDVKIPNSK 77

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

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

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I++ NL     E  + +L   FG +++  +I+D+ T   KG+ F    +     VAI +L
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 96  NGYALGNRILQVSFKT 111
           NG   G+  L V    
Sbjct: 358 NGKDTGDNKLHVQRAC 373

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 47.3 bits (112), Expect = 2e-08
 Identities = 19/49 (38%), Positives = 34/49 (69%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +FV  L+P+T E  + + FG FG ++++++  D +TN+ +GF FVT T+
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50

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

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

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 15/47 (31%), Positives = 25/47 (53%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTM 82
          +FV  L+P   ES L + F  FG V  V++I+       +GF ++ +
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48

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

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

 Score = 47.3 bits (113), Expect = 2e-08
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L     +  L  LF P+G + + +++ D  T   +G GF+      EA  AI++L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 96  NGYAL--GNRILQVSF 109
           NG         + V F
Sbjct: 63  NGTIPPGATEPITVKF 78

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 47.4 bits (112), Expect = 2e-08
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 37  FVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
            + N  P+   +  L  LFG  G ++S K++RD  T +  G+GFV   +  +A  AI +L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 96  NGYALGNRILQVSF 109
           NG  L  + ++VS+
Sbjct: 67  NGLRLQTKTIKVSY 80

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

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 46.9 bits (112), Expect = 3e-08
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGP-FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +FV +L P+ ++  L++ F   + + +  KV+ D Q    +G+GFV  ++  E   A+  
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62

Query: 95  LNGY-ALGNRILQVSFKTNK 113
           + G   LG + ++VS    K
Sbjct: 63  MQGASGLGGKPIRVSLAIPK 82

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 46.7 bits (111), Expect = 3e-08
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
           +FV NL+ ET E  L   FG  G ++ V+++    + KCKGF FV     + A  A++  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 94  SLNGYALG 101
            LNG AL 
Sbjct: 61  HLNGRALR 68

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 46.8 bits (111), Expect = 3e-08
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL P   E +L Q+F   G VQ+VK+I D + NK   +GFV      +A +A+Q+L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 96  NGYALGNRILQVSF 109
           NG  + N  ++V++
Sbjct: 60  NGRQIENNEIRVNW 73

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

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

 Score = 46.7 bits (111), Expect = 4e-08
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +FV  L+ +  E+ +  +F PFG+++   V+RD Q  + +G  FVT  +   A+ AI+++
Sbjct: 4  LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKAM 62

Query: 96 N 96
          +
Sbjct: 63 H 63

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

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

 Score = 46.7 bits (110), Expect = 4e-08
 Identities = 23/60 (38%), Positives = 34/60 (56%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++  L P T +  L +L  P+G + S K I D  TNKCKG+GFV   +   A  A+ +L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 46.6 bits (111), Expect = 4e-08
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVT 81
          +F+  L+ ET +  L   F  +G +    V++D  T + +GFGFVT
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVT 47

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

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

 Score = 46.2 bits (109), Expect = 5e-08
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
          IFV  L+P+T E  + + FG FG V+S+++  D +TNK +GF F+T    +
Sbjct: 2  IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

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

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

 Score = 46.3 bits (109), Expect = 6e-08
 Identities = 22/57 (38%), Positives = 36/57 (63%)

Query: 53  LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           LFG  G ++S K++RD  T +  G+GFV   + ++A  AI +LNG  L  + ++VS+
Sbjct: 23  LFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSY 79

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

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

 Score = 46.2 bits (109), Expect = 6e-08
 Identities = 19/51 (37%), Positives = 32/51 (62%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
          +FV  +  +TEE  L   F  +G + ++++I D Q+ K +GFGFVT  ++D
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 45.6 bits (108), Expect = 6e-08
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL PE  E  +  LF  +G V    +I        K +GFV M +   A  AI++L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54

Query: 96  NGYALGNRILQV 107
           + Y L    + V
Sbjct: 55  HHYKLHGVAINV 66

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

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

 Score = 46.1 bits (110), Expect = 6e-08
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVI--RDLQTNKCKGF-GFVTMTNYDEAVVAI 92
           ++V NL P+  E VL Q FG FG + SVK++  R  +  +     GFV   N  +A  A+
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 93  QSLNGYALGNRILQVSF 109
             L+G  +    L++ +
Sbjct: 64  DELDGKDVMGYELKLGW 80

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

 Score = 46.5 bits (111), Expect = 6e-08
 Identities = 15/45 (33%), Positives = 29/45 (64%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
          +FV  L+ +T E  L ++F  +G ++ ++++RD+ T   KG+ FV
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50

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

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

 Score = 46.1 bits (110), Expect = 7e-08
 Identities = 15/45 (33%), Positives = 29/45 (64%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
          +FV  L  +T ES L + F  +G ++ ++++RD +T K +G+ F+
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFI 48

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 45.2 bits (108), Expect = 8e-08
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 50  LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           L++LF PFG V+ +K+++     K  GF FV  +  + A  A+Q LNG   G R L+V +
Sbjct: 1   LYKLFSPFGNVEKIKLLK-----KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 45.5 bits (107), Expect = 1e-07
 Identities = 23/60 (38%), Positives = 34/60 (56%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++  L P T +  L +L  P+G + S K I D  TNKCKG+GFV   +   A  A+ +L
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV NL  +     L ++F   G V    +  D +  K +G G V   +  EAV AI   
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 96  NGYALGNRILQV 107
           NG  L +R ++V
Sbjct: 60  NGQMLFDRPMRV 71

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

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

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 22/81 (27%), Positives = 39/81 (48%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V N+A  T    L +LFG +G +  V +  D  T + +GF +V   +  +A  A+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 96  NGYALGNRILQVSFKTNKGKT 116
           +      R +++ F     KT
Sbjct: 63  DRTRFLGREIEIQFAQGDRKT 83

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

 Score = 45.5 bits (107), Expect = 1e-07
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 37  FVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
            + N  P+   +  L  LF   G V+S K+IRD       G+GFV   N  +A  AI +L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 96  NGYALGNRILQVSF 109
           NG  L ++ ++VS+
Sbjct: 64  NGLRLQSKTIKVSY 77

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

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

 Score = 45.2 bits (107), Expect = 1e-07
 Identities = 27/72 (37%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV N+  +T +  L  LF  +GAV S  V+R         F FV +     A  AI+ L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 96  NGYALGNRILQV 107
           NG  L  R L V
Sbjct: 55  NGRELHGRKLVV 66

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 45.2 bits (107), Expect = 1e-07
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V N+ P T ++ L  LF  FG +   +   D      +GF FV +  +++A +AI  L
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 96  NGYALGNRILQVSFKTNK 113
            G+ +  R L+  +  ++
Sbjct: 57  QGFPVHGRPLRCGWGKDR 74

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

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

 Score = 45.5 bits (107), Expect = 1e-07
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 53  LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           LFG  G ++S K++RD  T +  G+GFV   +  +A  AI +LNG  L  + ++VS+
Sbjct: 22  LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78

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

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

 Score = 44.9 bits (106), Expect = 1e-07
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 34  WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           W IFV N++       L  LF  FG V        ++ +K K + FV M   +EA+ AI+
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV--------VECDKVKDYAFVHMEREEEALAAIE 52

Query: 94  SLNGYALGNRILQV 107
           +LNG  +  R + V
Sbjct: 53  ALNGKEVKGRRINV 66

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 45.0 bits (106), Expect = 1e-07
 Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA-VVAIQ- 93
          IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D    + IQ 
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62

Query: 94 --SLNGY 98
            ++NG+
Sbjct: 63 YHTVNGH 69

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 45.2 bits (108), Expect = 2e-07
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV------IRDLQTNKCKGFGFVTMTNYDEAV 89
           ++V NL+    E  L  +FG F  V S         IR +   + KG  FVT  + + A 
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 90  VAIQSLNGYALGNRILQVSF 109
            A+  +NGY L  + + + F
Sbjct: 62  KALNLVNGYVLKGKPMVIQF 81

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

 Score = 45.2 bits (107), Expect = 2e-07
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 50  LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           L ++FG +G V+   + R      C GF FVTM     A +A+++ NG  +  R + V +
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 110 KTNK 113
              K
Sbjct: 77  AVQK 80

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

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

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N+  E  +  L +LF PFG V+SV++ +       +GF FV      EA  A+++L
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 96  NGYALGNRIL 105
               L  R L
Sbjct: 62  KSTHLYGRHL 71

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

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

 Score = 45.2 bits (106), Expect = 2e-07
 Identities = 23/60 (38%), Positives = 34/60 (56%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++  L P T +  L +L  P+G + S K I D  TN+CKG+GFV   +   A  A+ SL
Sbjct: 7  LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +FV  L  +  E  + ++F P+G V+ + ++RD +  + +G  FV  ++ + A  AI++L
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 96 NG 97
          NG
Sbjct: 61 NG 62

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 15/62 (24%), Positives = 32/62 (51%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          + V  L     +  L ++F  +G V+ V +  D + N  +G+ +V   + ++A  AI+ +
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 96 NG 97
          +G
Sbjct: 61 DG 62

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 26/90 (28%), Positives = 48/90 (53%)

Query: 27  NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
           N  N SG  + V  L  +  +  L+ LF   G + + +++RD +T    G+ FV   +  
Sbjct: 101 NDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEA 160

Query: 87  EAVVAIQSLNGYALGNRILQVSFKTNKGKT 116
           ++  AI++LNG  + N+ L+VS+    G++
Sbjct: 161 DSQRAIKNLNGITVRNKRLKVSYARPGGES 190

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL    +E  L  +  P+G V S +++RD +    +G GF  M + ++    I   
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQS-RGVGFARMESREKCEDIISKF 61

Query: 96  NGYALGNRI--LQVSF 109
           NG  L      L V F
Sbjct: 62  NGKYLKGEGEPLLVKF 77

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 24/73 (32%), Positives = 37/73 (50%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+     +  + +L    G V S K ++D  T K K FGF    + + A+ A++ L
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 96  NGYALGNRILQVS 108
           NG  LG + L V 
Sbjct: 63  NGLELGGKKLLVK 75

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 44.5 bits (106), Expect = 3e-07
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK---CKGFGFVTMTNYDEAVVAI 92
           ++V NL+  T E  +++LF   G ++  ++I  L       C GF FV     ++A  A+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPC-GFCFVEYYTREDAENAV 57

Query: 93  QSLNGYALGNRILQVSF 109
           + LNG  L +RI++V +
Sbjct: 58  KYLNGTKLDDRIIRVDW 74

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

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

 Score = 44.3 bits (105), Expect = 3e-07
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVAIQ 93
          IFV  L+  T E  + + F  FG V+   ++ D QTN+ +GFGFVT  + D  + V  I 
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 44.2 bits (104), Expect = 3e-07
 Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 4/67 (5%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVA-- 91
          IFV  +  +TEE  L   F  +G +++++V+ D Q+ K +GF FVT  ++D  + +V   
Sbjct: 3  IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQK 62

Query: 92 IQSLNGY 98
            ++NG+
Sbjct: 63 YHTINGH 69

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 44.2 bits (104), Expect = 3e-07
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
          IFV  L PE  E  + + FG FG ++++++  D +TNK +GF F+T    ++ V  +
Sbjct: 7  IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE-EDPVKKV 62

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

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

 Score = 43.4 bits (103), Expect = 5e-07
 Identities = 23/70 (32%), Positives = 36/70 (51%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           V NL   T    L ++F  +G V  V + RD  T + +GF FV   +  +A  A+ +++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 98  YALGNRILQV 107
             L  R L+V
Sbjct: 63  KELDGRELRV 72

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

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

 Score = 43.6 bits (103), Expect = 5e-07
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L     +  L +LF   G V+SV+++ + ++ K KG  +V   N   A  A+  +
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLKM 63

Query: 96  NGYALGNRILQVS 108
           +G  +  + + V+
Sbjct: 64  DGTEIKEKTISVA 76

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

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

 Score = 43.0 bits (102), Expect = 7e-07
 Identities = 30/76 (39%), Positives = 36/76 (47%), Gaps = 9/76 (11%)

Query: 36  IFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           IFV NL      SV WQ    LF   G V    V  D    + KGFG V   + ++A  A
Sbjct: 1   IFVRNLP----FSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRA 55

Query: 92  IQSLNGYALGNRILQV 107
           I+  NGY L  R L+V
Sbjct: 56  IEMFNGYDLEGRELEV 71

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 43.1 bits (102), Expect = 7e-07
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ +L+ +  E  L  LF  +G +QS+ +I        +G  +V M    +A  A+Q L
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP------RGCAYVCMETRQDAHRALQKL 58

Query: 96  NGYALGNRILQVSFKTNKG 114
               L  + ++V++  NKG
Sbjct: 59  RNVKLAGKKIKVAWAPNKG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 35  CIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           C+FV  L     + S+L +LF   G     ++       + +GF FV     ++A  A Q
Sbjct: 4   CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQQ 62

Query: 94  SLNGYALGNRILQVSFKTNKGKT 116
           +LNG++L    ++VSF  N G+ 
Sbjct: 63  ALNGHSLQGSPIRVSF-GNPGRP 84

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

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVAI- 92
          IFV  L P   E+ L + F  FG V  V V+ D +  + +GFGF+T  + D  + VV   
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 93 -QSLNG 97
             +NG
Sbjct: 65 FHDING 70

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

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

 Score = 42.6 bits (100), Expect = 1e-06
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN---YDEAVVAI 92
          +F+  L  ET +  L + FG FG V    V+RD  T + +GFGF+T       +E +   
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 93 QSLNG 97
            L+G
Sbjct: 61 HILDG 65

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 45.0 bits (106), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 10/75 (13%)

Query: 36  IFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           ++V NL   T E ++ + F  F  G V+ VK IRD        + FV   + ++AV A+ 
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMD 287

Query: 94  SLNGYALGNRILQVS 108
            LNG  L    ++V+
Sbjct: 288 ELNGKELEGSEIEVT 302

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

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V ++ P+  E+ +  +F  FG +   ++ R       KG+GF+   N      AI S+
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 96  NGYALGNRILQV 107
           N + LG + L+V
Sbjct: 267 NLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NLA    E +L + FG FG ++ VK ++D        + F+     D AV A++ +
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 96  NGYALGNRILQVSF 109
           NG  L    +++ F
Sbjct: 56  NGKELEGENIEIVF 69

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

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

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 4/72 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++          S + +LF   G V+ V ++    +   +   F+T  N + A +AI++L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 96  NGYALGNRILQV 107
           NG ++    ++V
Sbjct: 58  NGASVDGNCIKV 69

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

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKG----FGFVTMTNYDEAVVA 91
           +++ NL     E  L +LF  +G ++        ++   KG    + FVT    +EA  A
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFD-FLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 92  IQSLNGYALGNRILQVS 108
           ++SLNG     + L V 
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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

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

 Score = 42.2 bits (100), Expect = 2e-06
 Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 17/78 (21%)

Query: 35  CIFVYNLAPETEE-------SVLWQLFGPFGAVQSVKVIRDLQ-----TNKCKGFGFVTM 82
            + V  L P   E        VL ++F  FG       I  +      T K KG+ FV  
Sbjct: 3   VVVVDGL-PVVGEEKLEKLKKVLRKIFSKFGVG----KIVGIYMPVDETGKTKGYAFVEF 57

Query: 83  TNYDEAVVAIQSLNGYAL 100
              +EA  A+++LNGY L
Sbjct: 58  ATPEEAKEAVKALNGYKL 75

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

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

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  LA +  E  L++ F   G V+ V+ I+D  + + KG  +V   + +  + A+  L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-L 150

Query: 96  NGYALGNR--ILQVS 108
            G  L  R  I+Q S
Sbjct: 151 TGQMLLGRPIIVQSS 165

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 41.8 bits (98), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +  E    +LF  +G    V + RD      +GFGF+ + +   A +A   L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 57

Query: 96  NGYALGNRILQVSF 109
           +G  L NR L++ F
Sbjct: 58  DGTILKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.1 bits (97), Expect = 4e-06
 Identities = 19/52 (36%), Positives = 27/52 (51%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
          +FV NL        L + F  FG V+S  V  D +T   KG+GFV+ ++ D 
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDG 53

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 41.2 bits (96), Expect = 4e-06
 Identities = 20/57 (35%), Positives = 33/57 (57%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
          +F+  L+ ET +  L + F  +G +    V+RD QT + +GFGFVT +  +E   A+
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 41.1 bits (96), Expect = 4e-06
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL     E +L++LF   G +  V + +D +  K K FGFV   + +    AI  L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIALL 62

Query: 96  NGYALGNRILQVS 108
           NG  L  R ++V 
Sbjct: 63  NGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 43.4 bits (102), Expect = 5e-06
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L     +  L  +F PFG + + +++ D  T   KG GF+     DEA  AI++L
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 96  NG 97
           NG
Sbjct: 152 NG 153

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

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

 Score = 41.0 bits (96), Expect = 5e-06
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+  E ++++LF   G V  VK+ +D +  K K F FV   +      A+  L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 96  NGYALGNRILQV 107
           NG  L  R L +
Sbjct: 63  NGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 41.0 bits (96), Expect = 5e-06
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          ++V NL  +  E  L ++F  +G +    ++RD  T   +G  FV     +EA  AI SL
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 96 NG 97
          NG
Sbjct: 63 NG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 40.7 bits (96), Expect = 7e-06
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL  +  E  L +LFG  G V+ VK+  D ++ + +G   V     ++A  AI+  
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 96  NGYALGNRILQVSF 109
           NG  L  + +QV  
Sbjct: 62  NGVLLDGQPMQVEL 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 40.7 bits (96), Expect = 7e-06
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL  +     L+ LFG +GA++    IR   T + +G  FV   +  +A  A   L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQ---IRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 96  NGYALGNRILQVSF 109
           +G+ + NR L V +
Sbjct: 62  SGFNVANRYLVVLY 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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.4 bits (95), Expect = 8e-06
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV  ++    +  L +LF     ++   + RD  T K KGF +VT +N   A+ A + 
Sbjct: 2   RLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60

Query: 95  LNG--YALGNRI 104
           LNG  Y  GNR+
Sbjct: 61  LNGFEYPPGNRL 72

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.5 bits (95), Expect = 8e-06
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 44 ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
          +TE+ V  +LF PFG ++   ++R    N  KG  FV  +++ EA  AI +L+G
Sbjct: 13 QTEDDVR-RLFEPFGTIEECTILRGPDGNS-KGCAFVKFSSHAEAQAAINALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 40.5 bits (95), Expect = 9e-06
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +F+  L+ +T    L + F  FG ++   V+RD  T + +GFGFVT ++
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSD 49

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 40.4 bits (94), Expect = 9e-06
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NLA    E +L + F  FG ++ VK ++D        + FV     D AV A+  +
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 96  NGYALGNRILQV 107
           NG  +    +++
Sbjct: 56  NGKEIEGEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 40.6 bits (96), Expect = 1e-05
 Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 18/90 (20%)

Query: 36  IFVYNLAPETE-ESVL--WQLFGPFGAVQSVKVIRDLQTNKCKGFGF---------VTMT 83
           ++V  L P    E VL   + FG +G ++ + +      N+   +           VT +
Sbjct: 8   VYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVI------NRNTSYNGSQGPSASAYVTYS 61

Query: 84  NYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             ++A+  IQ+++G+ L  R+L+ SF T K
Sbjct: 62  RKEDALRCIQAVDGFYLDGRLLKASFGTTK 91

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

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIR--DLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           ++V N  P  ++S +  LF  +G + S   IR   L+ NK + F +V  T+ + A  A+ 
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59

Query: 94  SLNGYALGNRILQV 107
            LNG       L V
Sbjct: 60  LLNGKLGEGYKLVV 73

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 40.4 bits (94), Expect = 1e-05
 Identities = 23/81 (28%), Positives = 40/81 (49%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+A  T    L + FG +G +  V V  D  T + +GF ++   +  +A  A+ +L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 96  NGYALGNRILQVSFKTNKGKT 116
           N   +  R +++ F     KT
Sbjct: 63  NRKWVCGRQIEIQFAQGDRKT 83

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

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

 Score = 40.3 bits (94), Expect = 1e-05
 Identities = 23/81 (28%), Positives = 41/81 (50%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+A +T    L + FG +G +  V V  D  T + +GF +V   +  +A  A+ +L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 96  NGYALGNRILQVSFKTNKGKT 116
           +   +  R +++ F     KT
Sbjct: 63  DRKWICGRQIEIQFAQGDRKT 83

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

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

 Score = 39.9 bits (93), Expect = 1e-05
 Identities = 23/70 (32%), Positives = 32/70 (45%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           + NL P   +    +L  PFG ++   ++    T   KG+GFV     D A  A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 98  YALGNRILQV 107
             LG+R L V
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I + N+ P      L  L   +G V++ + +    T        VT  + ++A  A+  L
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQV---PTKSETATVNVTYESPEQAQQAVNKL 59

Query: 96  NGYALGNRILQVSFKTN 112
           NG+      L+VS+  +
Sbjct: 60  NGHEYEGSKLKVSYIPD 76

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) 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 = 76

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

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 23/69 (33%), Positives = 39/69 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L  +T +S L + F  +G +    V+ D  T + +GFGF+T ++ DEA  A+++ 
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64

Query: 96  NGYALGNRI 104
                GN+I
Sbjct: 65  PHSIDGNQI 73

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

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

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          ++V  L     +  L QLF  +G + + +++RD  T   +G GF+      EA  AI+ L
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 96 NG 97
          NG
Sbjct: 63 NG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 27/61 (44%)

Query: 33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           + +FV NL  +  E  L   F  FG+V+    + D  T + KG GFV   +       +
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 93 Q 93
          +
Sbjct: 61 K 61

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL    +E  L  +  PFG V S +++RD      +G GF  M + ++  V IQ  
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 96  NGYAL 100
           NG  L
Sbjct: 63  NGKYL 67

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
          +F+  L+ ET +  L   F  +G +    V+RD  T + +GFGFVT ++ +E   A+ +
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

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

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L P T  + L + F  FGA++ +           + + ++   + + A  A ++L
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG------RNYAYIEYESIEAAQAAKEAL 54

Query: 96  NGYALGNRILQV 107
            G+ LG    ++
Sbjct: 55  RGFPLGGPGRRL 66

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 39.2 bits (91), Expect = 3e-05
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+  L  +  E  L  L    G +  ++++ D   N  +G+ FVT +N  EA  AI+ L
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQL 62

Query: 96  NGYALGN-RILQV 107
           N Y + N R+L V
Sbjct: 63  NNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 38.9 bits (90), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L+  T  + L  LF  +G V   KV+ + ++   + +GFVTM+  +EA   I  L
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 96  NGYALGNRILQV 107
           +   L  R++ V
Sbjct: 64  HRTELHGRMISV 75

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

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

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 3/59 (5%)

Query: 36 IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          +FV  + P++  E  L + F  FG ++ V +++D  T + KGFG+V      +A VA++
Sbjct: 4  LFV--VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

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

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

 Score = 38.7 bits (91), Expect = 3e-05
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I V NL     E  L + F   G V  VKV+R  +  K + FGFV   + ++A  A++  
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 96  NG-YALGNRILQVSF 109
           N  +   ++I  V  
Sbjct: 62  NKTFIDTSKI-SVEL 75

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

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

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 47  ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ 106
           E ++ Q F PFG +  V+V  D      KG+ FV   +++ A  AI S+NG  +   +++
Sbjct: 14  EQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSVNGTTIEGHVVK 67

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

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

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI-- 92
           +FV NL     E  L +LF   G +  V+++++ +  K KG+ +V   N +    A+  
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59

Query: 93 --QSLNG 97
            + + G
Sbjct: 60 DRELIKG 66

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 38.5 bits (89), Expect = 5e-05
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +F+  L+ +T    L   F  FG ++   V+RD  T + +GFGFVT  +
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD 50

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 38.1 bits (89), Expect = 5e-05
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NLA +  E  + + F     + SV++  D +T + KGFG V   + +E++ A   L
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFAD-EESLDAALKL 59

Query: 96  NGYALGNRILQVS 108
           +G  L  R ++++
Sbjct: 60  DGTVLCGRPIRIA 72

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

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

 Score = 38.5 bits (89), Expect = 5e-05
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+  T    + Q F  FG V    ++ D  TN+ +GFGFVT  + D  V  +  +
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED-IVEKVCEI 60

Query: 96  NGYALGNRILQ 106
           + + + N++++
Sbjct: 61  HFHEINNKMVE 71

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

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

 Score = 38.2 bits (89), Expect = 7e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          IFV  +  +T E+ L + F  +G V+ VK++ D +    KG+GFVT    ++A   +Q  
Sbjct: 5  IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQEA 63

Query: 96 N 96
          N
Sbjct: 64 N 64

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

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 37.9 bits (88), Expect = 7e-05
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVAIQ 93
           +FV N+  +  ES L +LF  +G V+ V+        +    G VT+  YD  +A  A++
Sbjct: 4   LFVINVPRDVTESTLRRLFEVYGDVRGVQT-------ERISEGIVTVHFYDIRDAKRAVR 56

Query: 94  SLNGYALGNRILQVS 108
            L G  +  + L  S
Sbjct: 57  ELCGRHMQQQALGGS 71

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 37.9 bits (89), Expect = 9e-05
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 50  LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           L+ LF  FG V  +      +T K +G  FV   + + A  A+++L G+   ++ +++ +
Sbjct: 20  LYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQY 76

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

 Score = 37.7 bits (87), Expect = 9e-05
 Identities = 19/49 (38%), Positives = 30/49 (61%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT  +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51

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

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

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +     L ++F   G V    ++ D +  K +G G VT     EAV AI   
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILED-KDGKSRGIGTVTFEQPIEAVQAISMF 61

Query: 96  NGYALGNRILQV 107
           NG  L +R + V
Sbjct: 62  NGQLLFDRPMHV 73

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

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

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 8/79 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +++ NL+ +  ES L QLF      V SV V +        G+ FV   +   A  AI+ 
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEK 53

Query: 95  LNGYALGNRILQVSFKTNK 113
           LNG  L  ++++V     K
Sbjct: 54  LNGKILQGKVIEVEHSVPK 72

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

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 38/72 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L+  T+ + L  LFG +G V S KV+ + ++   K +G VTM++  E    I  L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 96  NGYALGNRILQV 107
           +   L  + + V
Sbjct: 62  HRTELHGQQISV 73

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+  E  + +LF  +G    + +      +K KGFGF+ +     A +A   L
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKAEL 57

Query: 96  NGYALGNRILQVSF 109
           +   L  + L+V F
Sbjct: 58  DNMPLRGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 37.3 bits (87), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+   E+  L + F   G V  V++ +D    + KGFG V     + A  A++  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 96  NGYALGNRILQVSFKTNK 113
           +G  L  R ++V   T +
Sbjct: 60  SGEELLGREIRVDLATER 77

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

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 47  ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ 106
           E ++ Q F PFG +  ++V  +      KG+ F+  + ++ A  AI S+NG  +   +++
Sbjct: 14  EQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSVNGTTIEGHVVK 67

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
          +F+  L+ ET E  L   +  +G +    V+RD  + + +GFGFVT +  +E   A+ +
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQS 94
          I V N+  E     L +LF  FG +++V++ + +  T   +GFGFV      +A  A ++
Sbjct: 3  ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 95 L 95
          L
Sbjct: 63 L 63

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

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

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 10/76 (13%)

Query: 36  IFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           ++V NL   T E  + + F     GAV+ VK IRD        + FV  +N ++AV A+ 
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVDAMN 62

Query: 94  SLNGYALGNRILQVSF 109
           +LNG  +    ++V+ 
Sbjct: 63  ALNGKVIDGSPIEVTL 78

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

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

 Score = 36.9 bits (86), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKV-IRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
          I+V  +  +T  S L Q F PFG ++ + +  RD   N    +GFVT     +A  AI+ 
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN----YGFVTYRYACDAFRAIEH 60

Query: 95 LN 96
           N
Sbjct: 61 GN 62

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

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 16/79 (20%), Positives = 41/79 (51%), Gaps = 11/79 (13%)

Query: 36  IFVYNLAPETEESVLWQ-----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           +++ N++   +E  L +         +G ++S++++R+      K   F+   N   A+ 
Sbjct: 5   VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE------KACAFINFMNIPNAIA 58

Query: 91  AIQSLNGYALGNRILQVSF 109
           A+Q+LNG    + I+++++
Sbjct: 59  ALQTLNGKKPYDTIVRINY 77

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 8/71 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL     E  L +    FG +  +K++++      K   FV   +   A+  + +L
Sbjct: 6   VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVTTL 59

Query: 96  --NGYALGNRI 104
                    RI
Sbjct: 60  PCEPDYASRRI 70

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 8/66 (12%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F  N   +  +S + +LFG +G V  V    D+++    GF FV M +  +A  AI+ L
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRVDRV----DMKS----GFAFVYMEDERDAEDAIRGL 54

Query: 96  NGYALG 101
           + +  G
Sbjct: 55  DNFEFG 60

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++ NL    +E  L  +  PFG V S +++RD  +   +G GF  M + ++    I   
Sbjct: 3  LYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIITHF 61

Query: 96 NG 97
          NG
Sbjct: 62 NG 63

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

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.5 bits (85), Expect = 3e-04
 Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+++  L     E  L + F  +G V  V V+ D Q    +G   V     + A  A+  
Sbjct: 9   CVWLDGLDESVTEQYLTRHFSRYGPV--VHVVIDRQ----RGQALVFFDKVEAAQAAVNE 62

Query: 95  LNGYALGNRILQVSF 109
           + G  LG R LQV F
Sbjct: 63  MKGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 36.0 bits (84), Expect = 3e-04
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD--EAVVAIQ 93
           + V+NL     +  L  LF  FG V+ ++      + K   F       YD   A  A+ 
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEF-------YDIRAAEAALD 56

Query: 94  SLNGYALGNRILQV 107
           +LNG       L+V
Sbjct: 57  ALNGRPFLGGRLKV 70

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 36  IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +FV    P  T E  + +LF PFG +    + +         F FV   + ++A  A+++
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEA 53

Query: 95  LNGYALGNRILQVSFKT 111
           L+G  +   +L V F  
Sbjct: 54  LHGSRIDGSVLTVEFVK 70

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241072 cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 36.2 bits (83), Expect = 3e-04
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           + N+ P+    VL  L   +G V++ +    + T+       VT  N ++   AI  LNG
Sbjct: 5   IRNIPPQLRWEVLDGLLAQYGTVENCE---QVNTDSETAVVNVTYGNREQTRQAIMKLNG 61

Query: 98  YALGNRILQVSF 109
           + L N  L+VS+
Sbjct: 62  HQLENHALKVSY 73

This subgroup corresponds to the RRM2 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. It promotes mRNA stabilization and functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD. It stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 76

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

 Score = 36.2 bits (83), Expect = 4e-04
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+  T    + Q F  FG V+   ++ D  TN+ +GFGFVT    ++ V  +  +
Sbjct: 6   IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF-ENEDVVEKVCEI 64

Query: 96  NGYALGNRILQ 106
           + + + N++++
Sbjct: 65  HFHEINNKMVE 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 36.1 bits (83), Expect = 4e-04
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + V NL P+      L+ LFG +G V  VK++ + + N       V M +  +A +A+  
Sbjct: 3   LLVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKEN-----ALVQMADATQAQLAMSH 57

Query: 95  LNGYALGNRILQVSFKTNK 113
           LNG  L  ++++ +   ++
Sbjct: 58  LNGQRLYGKVIRATLSKHQ 76

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

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

 Score = 36.3 bits (84), Expect = 4e-04
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVT 81
          +FV  L+ ET +  L + F  +G V    +++D  TN+ +GFGFV 
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVK 47

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

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

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 50  LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV 107
           L + F   G +  V +  D +T   KGF ++   + D    A++ L+G  LG   L V
Sbjct: 20  LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 36.2 bits (83), Expect = 4e-04
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++ NL    +E  L  +  PFG V S +++RD  +   +G GF  M + ++    I   
Sbjct: 3  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 96 NG 97
          NG
Sbjct: 62 NG 63

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 39  YNLAPETEESVLWQLFGPFGAVQSVKV-IRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG 97
           Y L+ +  +  L   F   G V SV +  +   +        V + N  +A  AI  L+ 
Sbjct: 14  YRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDGSLVAS----VRVPNLQDAQYAISQLHR 69

Query: 98  YALGNRILQVSFKTNKGKTS 117
             +G++ + VS+       S
Sbjct: 70  RKIGSKRILVSYAQGSSNKS 89

This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. Length = 89

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

 Score = 35.9 bits (83), Expect = 5e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I V NL  E  +  +  LF  +G ++SV+V +       +GF FV  +   EA+ A+ +L
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFD-QSARGFAFVEFSTAKEALNAMNAL 61

Query: 96  NGYALGNRILQVSF 109
               L  R L + +
Sbjct: 62  KDTHLLGRRLVLQY 75

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

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 29  MNGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
             G G  + V  L  E      L+ LF  +G V+ VK ++    NK K    + M +  +
Sbjct: 271 GGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMK----NK-KETALIEMADPYQ 325

Query: 88  AVVAIQSLNGYALGNRILQV 107
           A +A+  LNG  L  + L+V
Sbjct: 326 AQLALTHLNGVKLFGKPLRV 345

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). Length = 481

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

 Score = 35.7 bits (82), Expect = 6e-04
 Identities = 21/70 (30%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+ +T E  L + F   G++ + +++ D  T   KGFGFV  ++ ++A  A +++
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 96  -NGYALGNRI 104
            +G   GN++
Sbjct: 60  EDGEIDGNKV 69

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

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 7/78 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV----IRDLQTNKCKGFG--FVTMTNYDEAV 89
           +++ NL+  + E  L +    F  V SV +    +R  ++ + +  G  +   ++ ++A 
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 90  VAIQSLNGYALGNRILQV 107
             ++ LNG    NR L V
Sbjct: 61  KVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 35.2 bits (82), Expect = 6e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NL  ET + +L  LF  F   + V+++        +G  FV     ++A VA+Q+L
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58

Query: 96  NGYAL-GNRILQVS 108
            G+ +     +++S
Sbjct: 59  QGFKITPGHAMKIS 72

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing 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. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V NL P+     +  LF  +GA++ +    DL+  +   F FV   +  +A  A+   
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYGR 57

Query: 96  NGYALGNRILQVSF 109
           +GY      L+V F
Sbjct: 58  DGYDYDGYRLRVEF 71

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 35.4 bits (81), Expect = 7e-04
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV NL  +     L ++F   G V+   +  D +  K +G G VT     EAV AI   
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 96  NGYALGNRILQV 107
           NG  L +R + V
Sbjct: 62  NGQFLFDRPMHV 73

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

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

 Score = 35.4 bits (81), Expect = 7e-04
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL+ +  E+++ QLF   G  +S K+I D   N    + FV    +  A  ++ ++
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGN--DPYCFVEFFEHRHAAASLAAM 59

Query: 96  NGYALGNRILQVSF 109
           NG  +  + ++V++
Sbjct: 60  NGRKIMGKEVKVNW 73

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

>gnl|CDD|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 = 35.2 bits (82), Expect = 7e-04
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 3/75 (4%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
            + +  L     E  +   F         + ++ D    +  G  +V   + ++A  A++
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALR 59

Query: 94  SLNGYALGNRILQVS 108
             N   +G R ++V 
Sbjct: 60  KHNNK-MGGRYIEVF 73

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

 Score = 35.6 bits (82), Expect = 8e-04
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +FV  +    +E+ +   F  +G+V+ VK+I D +T   KG+GFV+  +
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYD 55

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVK--------VIRDLQTNKCKGFGFVTMTNYDE 87
           +FV NL P T E  L + FG  G ++  K        + +D  T + KG   VT  +   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 88  AVVAIQSLNGYALGNRILQVS 108
           A  AI+  N        ++VS
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVS 81

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 35.8 bits (82), Expect = 8e-04
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + V NL PE      L+ LFG +G VQ VK++ + + N       V M + ++A +A+  
Sbjct: 2   LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 56

Query: 95  LNGYALGNRILQVS 108
           LNG  L  + L+++
Sbjct: 57  LNGQKLHGKPLRIT 70

This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 93

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

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 8/70 (11%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKC--KGFGFVTMTNYDEAVVA-- 91
          +FV  +     E  L +LF  +GAV  + V+RD   N    KG  FVT      A+ A  
Sbjct: 4  MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 92 ----IQSLNG 97
              +++L G
Sbjct: 64 ALHNMKTLPG 73

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L  +FG +G +    ++RD  T   +G  FV     +EA  AI +L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 96  N 96
           N
Sbjct: 256 N 256

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 37  FVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN 96
           FV NL   T +  L  +F    +V+SV+++RD +T+K KGF +V   + +    A++  +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 97  GYALGNRILQV 107
           G    +R L+V
Sbjct: 63  GALFDDRSLRV 73

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 34.9 bits (81), Expect = 0.001
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL P   E  + +LF   GA++  +++R        G   V     D+A+ AI   
Sbjct: 3   LVVSNLHPSVTEDDIVELFSAIGALKRARLVR-------PGVAEVVYVRKDDALTAIDKY 55

Query: 96  NGYALGNRILQVS 108
           N   L  + ++  
Sbjct: 56  NNRELDGQPMKCK 68

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

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

 Score = 35.1 bits (80), Expect = 0.001
 Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL+ +  E ++ QLF   G  +S K+I +  +N    + FV    + +A  A+ ++
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 59

Query: 96  NGYALGNRILQVSFKT 111
           NG  +  + ++V++ T
Sbjct: 60  NGRKILGKEVKVNWAT 75

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

>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 36 IFVYNLAPETE-ESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
          I + N+AP T  +S+L  L  P+   +V ++++I+D QT + +GF FV +++  EA   +
Sbjct: 5  IILRNIAPHTVVDSILSAL-APYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLL 63

Query: 93 QSLNG 97
          Q L  
Sbjct: 64 QILQA 68

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 36 IFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          I + N+AP T    +     P+   AV ++++I+D QT + +GF FV +++  EA   +Q
Sbjct: 5  IILRNIAPHTVVDSILTALAPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64

Query: 94 SLNG 97
           L  
Sbjct: 65 ILQS 68

This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 86

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 41  LAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA 99
           L P  +E+ + + F   G  V SVK+IR+  T    G+ FV   +   A   +  LNG  
Sbjct: 7   LEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKP 66

Query: 100 LGNRILQVSFKTN 112
           +        FK N
Sbjct: 67  IPGSNPPKRFKLN 79

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

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCK-GFGFVTMTNYDEAVVAIQS 94
           I+V NL  +  E  +  LF  +G ++++    DL+  +    F FV   +  +A  A++ 
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAI----DLKNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 95  LNGYALGNRILQVSF 109
            +GY      L+V F
Sbjct: 58  RDGYDFDGYRLRVEF 72

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

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL    +E  L +LF  FG +  V++    +  K + FGFV     +EA  A++  
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYT-KDGKFRKFGFVGYKTEEEAQKALKHF 61

Query: 96  NGYALGNRILQVSF 109
           N   +    + V  
Sbjct: 62  NNSFIDTSKITVEI 75

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

>gnl|CDD|241074 cd12630, RRM2_IGF2BP3, RNA recognition motif 2 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 38  VYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN 96
           + N+ P  +  VL  L   +G V+S  +V  D +T        VT  N D+A  A+  LN
Sbjct: 5   IRNIPPHLQWEVLDSLLAQYGTVESCEQVNTDSETAVVN----VTYGNKDQARQALDKLN 60

Query: 97  GYALGNRILQVSF 109
           G+ L N  L+V++
Sbjct: 61  GFQLENYSLKVAY 73

This subgroup corresponds to the RRM2 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 76

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

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFG----AVQSVKVIRDLQT--NKCKGFGFVTMTNYDEAV 89
           +++ NL P+T +  L   F  +G    A  ++K   +     +K    GF    +++EA+
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62

Query: 90  VAIQSLNGYALGNRILQVS 108
            A+ +LNG  LG R ++V 
Sbjct: 63  EAL-ALNGRCLGERAIEVQ 80

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

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

 Score = 34.7 bits (79), Expect = 0.001
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          ++V  L     +  L QLF  +G + + +++ D  T   +G GF+      EA  AI+ L
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 96 NG 97
          NG
Sbjct: 65 NG 66

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

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 36  IFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           ++V NL   T E  +   F  F  G V+ VK +RD        + FV   N ++AV A+ 
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD--------YAFVHFFNREDAVAAMS 55

Query: 94  SLNGYALGNRILQVSF 109
            +NG  +    ++V+ 
Sbjct: 56  VMNGKCIDGASIEVTL 71

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  +    EE  L  LF  FG +  + V++D  T   KG  F+T    + A+ A  +L
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 96  NGYAL---GNRILQV 107
           +        NR +QV
Sbjct: 68  HEQKTLPGMNRPIQV 82

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 8/85 (9%)

Query: 31  GSGWCIFVYNLAPE--TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
           G    + V NL  E  T +S L+ LFG +G VQ VK++     NK K    + M + +++
Sbjct: 11  GGNTVLLVSNLNEEMVTPQS-LFTLFGVYGDVQRVKIL----YNK-KDSALIQMADGNQS 64

Query: 89  VVAIQSLNGYALGNRILQVSFKTNK 113
            +A+  LNG  +  +I++V+   ++
Sbjct: 65  QLAMSHLNGQKMYGKIIRVTLSKHQ 89

This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and 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 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 107

>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 6/56 (10%)

Query: 47  ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN 102
           E  L   FG FG VQS  +      N  K   FV M N  +A  A +++  Y  G+
Sbjct: 17  EYDLRSGFGRFGEVQSCIL------NNDKRHAFVKMYNRRDAENAREAMEQYKSGD 66

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + + NL P+  ES L  L  PFG V +V ++R       K    V M + + A   +   
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRG------KNQALVEMDSVESAKSMVDYY 55

Query: 96  --NGYALGNRILQVSF 109
                 +  R + + +
Sbjct: 56  LTVPALIRGRRVYIQY 71

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 47  ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ 106
           E +L + F PFG + ++ + ++      K  GFVT    + A  AI  LNG  +    L+
Sbjct: 16  EEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIAELNGTTVQGVQLK 69

Query: 107 VSF 109
           VS 
Sbjct: 70  VSL 72

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

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

 Score = 34.4 bits (78), Expect = 0.002
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          ++V  L     +  L QLF  +G + + +++ D  T   +G GF+      EA  AI+ L
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 96 NG 97
          NG
Sbjct: 68 NG 69

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +  E    +LF  +G    V +      NK KGFGF+ + +   A +A   L
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAEL 57

Query: 96  NGYALGNRILQVSF 109
           +   +  R L+V F
Sbjct: 58  DDTPMRGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 20/75 (26%), Positives = 31/75 (41%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +  E  L + F  FG V  V++       +   FGFV   + +     + + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 96  NGYALGNRILQVSFK 110
             Y  G+  L V  K
Sbjct: 66  PIYFRGDHRLNVEEK 80

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

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

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKG---FGFVTMTNYDEAVVAI 92
           I+V NL  +  E  L  LF  +G       IRD++    +G   F FV   +  +A  A+
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGR------IRDIELKNRRGLVPFAFVRFEDPRDAEDAV 55

Query: 93  QSLNGYALGNRILQVSF 109
              NGY  G   L+V F
Sbjct: 56  FGRNGYDFGQCRLRVEF 72

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

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 33.7 bits (78), Expect = 0.003
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + VY L  +      L+ LF  +G V  +K ++    +K  G   V M +   A  AI+ 
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLK----SK-PGTAMVQMGDPQAAERAIEY 56

Query: 95  LNGYALGNRILQVSF 109
           LNG  L  + L+V+F
Sbjct: 57  LNGVVLFGQKLEVNF 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that 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. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 33.8 bits (77), Expect = 0.003
 Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV NL  +    +L   F   G V    +   ++  K KG G V   + + A  A + +
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRMM 59

Query: 96  NGYALGNRILQVSFKTN 112
           NGY L  R + V    N
Sbjct: 60  NGYKLNGREIDVRIDRN 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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 17/86 (19%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVK---VIRDLQTNKCKGF--------------G 78
           +FV NL   T++  L +LF  FG ++SV+   V    +    K                 
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62

Query: 79  FVTMTNYDEAVVAIQSLNGYALGNRI 104
           +V     + A  A++       G+ I
Sbjct: 63  YVVFKEEESAEKALKLNGTEFEGHHI 88

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 33.8 bits (77), Expect = 0.003
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQS--VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          I + NL P +    +     P+  + S  V+VI+D QT   +GF F+ ++   EA   +Q
Sbjct: 5  IILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQ 64

Query: 94 SL 95
           L
Sbjct: 65 IL 66

This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 87

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

 Score = 33.3 bits (76), Expect = 0.004
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 36  IFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +FV N  P  T    L + F P+G + +V++ R+        F FV     ++A  A++S
Sbjct: 2   LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRN--------FAFVQYETQEDATKALES 53

Query: 95  LNGYALGNRILQVSF 109
            N   + +R++ V +
Sbjct: 54  TNMSKVLDRVISVEY 68

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 33.6 bits (77), Expect = 0.004
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 75  KGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK 110
           +G  F    + +EA   +++LNGY +  R L+V +K
Sbjct: 43  RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYK 78

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 33.5 bits (77), Expect = 0.004
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 35  CIFVYNLAP-----ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
           C+FV +L       E E +V  + F  +G +  VKV+RD +    + + FV  TN D+A 
Sbjct: 4   CVFVASLPASKSDDELEAAVT-EHFSKYGTLVFVKVLRDWRQ---RPYAFVQFTNDDDAK 59

Query: 90  VAIQSLNGYALGNR 103
            A+    G  L  R
Sbjct: 60  NALAKGQGTILDGR 73

This subfamily corresponds to the RRM1 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 = 86

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

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 18/62 (29%), Positives = 31/62 (50%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          ++V  L     +  + QLF  +G + + +++ D  T   +G GF+      EA  AI+ L
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 96 NG 97
          NG
Sbjct: 64 NG 65

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

>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate

 Score = 33.5 bits (76), Expect = 0.004
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L P T  + L + F  FG+++++  +      K   F ++   + D A  A   +
Sbjct: 5   LWVGGLGPNTSLAALAREFDRFGSIRTIDYV------KGDSFAYIQYESLDAAQAACAQM 58

Query: 96  NGYALG--NRILQVSFKT 111
            G+ LG  +R L+V F  
Sbjct: 59  RGFPLGGPDRRLRVDFAK 76

This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 76

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	117
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
KOG0122|consensus	270		99.78
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.77
KOG0121|consensus	153		99.74
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.73
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.72
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
KOG0117|consensus	506		99.71
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
KOG0148|consensus	321		99.7
KOG0149|consensus	247		99.68
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
PLN03120	260	nucleic acid binding protein; Provisional	99.68
KOG0107|consensus	195		99.68
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.68
KOG0113|consensus	335		99.67
KOG0145|consensus	360		99.67
KOG0114|consensus	124		99.66
KOG0130|consensus	170		99.66
KOG0145|consensus	360		99.65
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.64
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.64
KOG0126|consensus	219		99.64
KOG0108|consensus	435		99.63
PLN03121	243	nucleic acid binding protein; Provisional	99.63
KOG0125|consensus	376		99.63
smart00362	72	RRM_2 RNA recognition motif.	99.62
KOG4207|consensus	256		99.62
KOG0111|consensus	298		99.62
KOG0131|consensus	203		99.61
KOG0148|consensus	321		99.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.6
smart00360	71	RRM RNA recognition motif.	99.59
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.58
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.57
KOG0105|consensus	241		99.57
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.56
KOG0144|consensus	510		99.56
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.56
KOG0144|consensus	510		99.55
KOG0124|consensus	544		99.51
KOG0117|consensus	506		99.49
KOG1457|consensus	284		99.47
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
KOG0127|consensus	678		99.46
KOG0109|consensus	346		99.44
KOG0127|consensus	678		99.44
smart00361	70	RRM_1 RNA recognition motif.	99.44
KOG0415|consensus	479		99.43
KOG0147|consensus	549		99.42
KOG0146|consensus	371		99.42
KOG0131|consensus	203		99.41
KOG0146|consensus	371		99.39
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.31
KOG4208|consensus	214		99.3
KOG4206|consensus	221		99.3
KOG0132|consensus	894		99.29
KOG4212|consensus	608		99.28
KOG0123|consensus	369		99.22
KOG0153|consensus	377		99.22
KOG0110|consensus	725		99.22
KOG0124|consensus	544		99.21
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.21
KOG4661|consensus	940		99.15
KOG0123|consensus	369		99.14
KOG0109|consensus	346		99.11
KOG0151|consensus	877		99.09
KOG4212|consensus	608		99.08
KOG4205|consensus	311		99.02
KOG0110|consensus	725		99.0
KOG0116|consensus	419		98.99
KOG0533|consensus	243		98.99
KOG1548|consensus	382		98.91
KOG0106|consensus	216		98.87
KOG4205|consensus	311		98.87
KOG4209|consensus	231		98.86
KOG4660|consensus	549		98.86
KOG4454|consensus	267		98.84
KOG0226|consensus	290		98.83
KOG4211|consensus	510		98.82
KOG1190|consensus	492		98.55
KOG0120|consensus	500		98.54
KOG1995|consensus	351		98.42
KOG1457|consensus	284		98.4
KOG4211|consensus	510		98.36
KOG4206|consensus	221		98.28
KOG0147|consensus	549		98.28
KOG1456|consensus	494		98.26
KOG4210|consensus	285		98.2
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.18
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.12
KOG4849|consensus	498		98.05
KOG0106|consensus	216		98.03
KOG4307|consensus	944		98.02
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.01
KOG1190|consensus	492		97.94
KOG0105|consensus	241		97.87
KOG3152|consensus	278		97.85
KOG0129|consensus	520		97.81
KOG2314|consensus	698		97.73
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.73
KOG1456|consensus	494		97.71
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.71
KOG1365|consensus	508		97.66
KOG0129|consensus	520		97.65
KOG2193|consensus	584		97.65
KOG1548|consensus	382		97.62
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.59
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.57
KOG1365|consensus	508		97.53
KOG0120|consensus	500		97.52
KOG0112|consensus	975		97.46
KOG2202|consensus	260		97.3
KOG2416|consensus	718		97.3
KOG1855|consensus	484		97.16
KOG4307|consensus	944		97.15
KOG1996|consensus	378		96.93
KOG4660|consensus	549		96.89
KOG4676|consensus	479		96.73
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.7
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.58
KOG0128|consensus	881		96.48
KOG2068|consensus	327		96.36
KOG0128|consensus	881		96.33
KOG0115|consensus	275		96.07
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.74
KOG0112|consensus	975		95.66
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.62
KOG2591|consensus	684		95.6
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.49
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.39
KOG2253|consensus	668		95.1
KOG2135|consensus	526		94.95
KOG4285|consensus	350		94.47
KOG4410|consensus	396		93.78
KOG0804|consensus	493		92.65
KOG4210|consensus	285		91.86
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.86
KOG4483|consensus	528		89.4
KOG4574|consensus	1007		86.53
KOG2318|consensus	650		81.33
KOG4676|consensus	479		80.9

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

Probab=99.87  E-value=1.7e-20  Score=115.59  Aligned_cols=85  Identities=29%  Similarity=0.463  Sum_probs=80.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ...+++|||+|||+++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|+.|+..+++..+.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      +..+.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.83  E-value=1.3e-19  Score=125.76  Aligned_cols=85  Identities=78%  Similarity=1.359  Sum_probs=80.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..++.|||+|||..+++++|.++|++||.|..++++.++.++.++|||||+|.+.++|..|+..|||..++|+.|+|.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            44568999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      ..+.+
T Consensus       347 ~~~~~  351 (352)
T TIGR01661       347 TNKAY  351 (352)
T ss_pred             cCCCC
Confidence            88765

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=8.8e-19  Score=121.57  Aligned_cols=83  Identities=30%  Similarity=0.489  Sum_probs=78.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +..+|||+|||..+++++|+++|..||.|..++++.++.+|+++|||||+|.+.++|.+|+..|+|..+.|+.|+|.+++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            643

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.79  E-value=2.1e-18  Score=119.43  Aligned_cols=85  Identities=28%  Similarity=0.507  Sum_probs=79.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....+++|||+|||+++++++|+++|..||.|..++++.++.+++++|||||+|.+.++|++|+..|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98753

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).

>KOG0122|consensus

Probab=99.78  E-value=2.5e-18  Score=111.33  Aligned_cols=85  Identities=38%  Similarity=0.555  Sum_probs=81.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .+++..+|.|.||+.+++|.+|+++|.+||.|..+.+.+++.||.++|||||.|.++++|.+|+..|+|.-+++-.|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            45677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99875

>PF00076 RRM_1: RNA recognition motif

Probab=99.77  E-value=1.1e-17  Score=90.90  Aligned_cols=70  Identities=34%  Similarity=0.685  Sum_probs=66.5

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      |||+|||.++++++|+++|..||.+..+.+..+ .++..+++|||+|.+.++|+.|+..++|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 6688899999999999999999999999999999886

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

>KOG0121|consensus

Probab=99.74  E-value=9.6e-18  Score=99.21  Aligned_cols=80  Identities=24%  Similarity=0.375  Sum_probs=76.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+||+..++|++|.++|+.+|.|..+.+-.++.+..++|||||+|.+.++|+.|++.++|..+..+.|++.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            36789999999999999999999999999999999999988899999999999999999999999999999999999874

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.73  E-value=2.1e-16  Score=86.13  Aligned_cols=70  Identities=33%  Similarity=0.657  Sum_probs=64.4

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      |||+|||+++++++|.++|..+|.|..+.+..++. +..+++|||+|.+.++|.+|+..+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 88999999999999999999999998999999875

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 ....

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

Probab=99.72  E-value=1.1e-16  Score=116.91  Aligned_cols=83  Identities=25%  Similarity=0.401  Sum_probs=78.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||.++++++|+++|+.||.|..+++..++.++.++|||||+|.+.++|..|+..+|+..++|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45789999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ..+
T Consensus       283 ~pP  285 (612)
T TIGR01645       283 TPP  285 (612)
T ss_pred             CCc
Confidence            644

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=1.3e-16  Score=110.61  Aligned_cols=84  Identities=27%  Similarity=0.428  Sum_probs=76.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~  109 (117)
                      ...+|||+|||..+++++|+++|.+||.|..+.++.++.+++++|++||+|.+.++|++|++.|++..+.+  +.|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999998899999999999999999999999999998865  6899999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +....+
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            876543

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).

>KOG0117|consensus

Probab=99.71  E-value=1.7e-16  Score=110.19  Aligned_cols=82  Identities=27%  Similarity=0.457  Sum_probs=77.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~  109 (117)
                      +.++-||||.||.++.|++|.-+|.+.|.|.++++|.++.+|.++|||||.|.+.+.|++|++.||+..|. |+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            67889999999999999999999999999999999999999999999999999999999999999999886 88999987


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +-.
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            543

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

Probab=99.70  E-value=1.3e-16  Score=116.43  Aligned_cols=81  Identities=30%  Similarity=0.484  Sum_probs=76.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|++.++|..+.|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy13319        111 T  111 (117)
Q Consensus       111 ~  111 (117)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=99.70  E-value=1e-16  Score=105.35  Aligned_cols=82  Identities=43%  Similarity=0.737  Sum_probs=78.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      ...+||+.|...++-++|++.|.+||+|+.+++++|..|++++||+||.|..+++|++|+..|+|.+|++|.|+-.||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CC
Q psy13319        113 KG  114 (117)
Q Consensus       113 ~~  114 (117)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

>KOG0149|consensus

Probab=99.68  E-value=1.1e-16  Score=103.32  Aligned_cols=78  Identities=31%  Similarity=0.410  Sum_probs=71.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      -.+||||||+|.+..++|++.|..||+|.+..++.|+.+|+++||+||+|.+.++|++|++. ..-.|+||+..+..|.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            35799999999999999999999999999999999999999999999999999999999996 4567899988777654

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

Probab=99.68  E-value=1.1e-15  Score=109.46  Aligned_cols=81  Identities=33%  Similarity=0.619  Sum_probs=77.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|..|+..|+|..+.|+.|+|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999998888999999999999999999999999999999999999976


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            4

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.68  E-value=6.6e-16  Score=102.10  Aligned_cols=75  Identities=16%  Similarity=0.219  Sum_probs=69.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .++|||+|||+.+++++|+++|+.||.|..+.+..++.   .+|||||+|.+.++++.|+. |+|..+.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            57899999999999999999999999999999988743   47899999999999999996 99999999999999876

>KOG0107|consensus

Probab=99.68  E-value=3.6e-16  Score=96.98  Aligned_cols=81  Identities=25%  Similarity=0.402  Sum_probs=72.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....+.|||+||+..+++.+|+..|..||.+..+.+-..     +.|||||+|++..+|+.|+..|+|..+.|..|+|++
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence            345788999999999999999999999999988866543     378999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++..++
T Consensus        82 S~G~~r   87 (195)
T KOG0107|consen   82 STGRPR   87 (195)
T ss_pred             ecCCcc
Confidence            886554

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

Probab=99.68  E-value=1e-15  Score=110.81  Aligned_cols=82  Identities=28%  Similarity=0.391  Sum_probs=77.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +..++|||+|||..+++++|+++|..||.|..+.++.+..+|.++|||||+|.+.+.|..|+..|+|..++|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            64

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

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

Probab=99.68  E-value=5.2e-16  Score=113.69  Aligned_cols=78  Identities=33%  Similarity=0.630  Sum_probs=74.7

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +|||+|||.++++++|+++|..||.|..|++.++..+++++|||||+|.+.++|++|+..+++..+.|+.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999998753

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

>KOG0113|consensus

Probab=99.67  E-value=1.4e-15  Score=101.12  Aligned_cols=87  Identities=24%  Similarity=0.436  Sum_probs=80.7

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .....++=+||||+-|+.+++|..|++.|..||.|..|.++.+..||+++|||||+|....+...|.+..+|..|+|+.|
T Consensus        94 p~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   94 PNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             CcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            34445778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      .|.+-..
T Consensus       174 ~VDvERg  180 (335)
T KOG0113|consen  174 LVDVERG  180 (335)
T ss_pred             EEEeccc
Confidence            9987543

>KOG0145|consensus

Probab=99.67  E-value=2.9e-15  Score=98.38  Aligned_cols=107  Identities=68%  Similarity=1.156  Sum_probs=92.8

Q ss_pred             cccCCCCccccccccC-CCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHH
Q psy13319          8 LQRFSPLTGDLLASSI-LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD   86 (117)
Q Consensus         8 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~   86 (117)
                      .-+|+|++.+.+..-. ..-+.....++.|||-||.++++|..|.++|.+||.|..+++++|..+.+++||+||.+.+.+
T Consensus       252 ~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYd  331 (360)
T KOG0145|consen  252 QARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYD  331 (360)
T ss_pred             hccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchH
Confidence            3478888877665433 233334456899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCcEeCCeEEEEEEecCCC
Q psy13319         87 EAVVAIQSLNGYALGNRILQVSFKTNKG  114 (117)
Q Consensus        87 ~a~~a~~~l~~~~~~g~~l~v~~a~~~~  114 (117)
                      +|..|+..|||..++++.|+|+|...+.
T Consensus       332 EAamAi~sLNGy~lg~rvLQVsFKtnk~  359 (360)
T KOG0145|consen  332 EAAMAIASLNGYRLGDRVLQVSFKTNKA  359 (360)
T ss_pred             HHHHHHHHhcCccccceEEEEEEecCCC
Confidence            9999999999999999999999976653

>KOG0114|consensus

Probab=99.66  E-value=2.5e-15  Score=85.99  Aligned_cols=81  Identities=22%  Similarity=0.428  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .++..+.|||.|||..++.++..++|.+||.|.++++-..+.   .+|-|||.|++..+|..|+..|+|..+.++.+.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            356678899999999999999999999999999999966543   48999999999999999999999999999999998


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      +-.+
T Consensus        91 yyq~   94 (124)
T KOG0114|consen   91 YYQP   94 (124)
T ss_pred             ecCH
Confidence            7543

>KOG0130|consensus

Probab=99.66  E-value=5.3e-16  Score=92.71  Aligned_cols=89  Identities=27%  Similarity=0.439  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe
Q psy13319         24 LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR  103 (117)
Q Consensus        24 ~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~  103 (117)
                      .+.+...-.++.|||.++...+++++|.+.|..||.|..+.+.+++.||..+||+.|+|.+.+.|++|+..+||..+.|+
T Consensus        63 ~pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q  142 (170)
T KOG0130|consen   63 RPGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQ  142 (170)
T ss_pred             CCCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCC
Confidence            34444445789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEecC
Q psy13319        104 ILQVSFKTN  112 (117)
Q Consensus       104 ~l~v~~a~~  112 (117)
                      .|.|.|+.-
T Consensus       143 ~v~VDw~Fv  151 (170)
T KOG0130|consen  143 NVSVDWCFV  151 (170)
T ss_pred             ceeEEEEEe
Confidence            999998763

>KOG0145|consensus

Probab=99.65  E-value=1.7e-15  Score=99.53  Aligned_cols=86  Identities=31%  Similarity=0.506  Sum_probs=80.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+....|.|.=||...++++++.+|...|+|+.|++++|+-+|.+-||+||.|-+.++|++|+..|||..+..+.|+|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34555679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ||++..
T Consensus       117 yARPSs  122 (360)
T KOG0145|consen  117 YARPSS  122 (360)
T ss_pred             eccCCh
Confidence            999765

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

Probab=99.64  E-value=2.1e-15  Score=109.94  Aligned_cols=81  Identities=28%  Similarity=0.494  Sum_probs=73.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~  108 (117)
                      .+.+++|||+|||++++|++|.++|..+|.|..++++.+ .++.++|||||+|.+.++|++|++.|++..+. ++.|.|+
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            456789999999999999999999999999999999999 78999999999999999999999999998875 7777776


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      .+.
T Consensus       134 ~S~  136 (578)
T TIGR01648       134 ISV  136 (578)
T ss_pred             ccc
Confidence            553

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

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

Probab=99.64  E-value=2.9e-15  Score=109.81  Aligned_cols=82  Identities=33%  Similarity=0.554  Sum_probs=77.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+.+|||+||+..+++++|+++|+.||.|..++++.+ .+|.++|+|||+|.+.++|.+|+..++|..++|+.|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            45678999999999999999999999999999999998 67999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ..+
T Consensus       362 ~~k  364 (562)
T TIGR01628       362 QRK  364 (562)
T ss_pred             cCc
Confidence            764

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

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=1.9e-15  Score=106.69  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY--DEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~--~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+.+||||||++.+++++|...|..||.|..+.++  +.+|  ||||||+|...  .++.+|+..|+|..|.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            345789999999999999999999999999999998  4466  99999999976  78999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      -|++.
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            88753

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

Probab=99.64  E-value=4.2e-15  Score=106.47  Aligned_cols=81  Identities=26%  Similarity=0.452  Sum_probs=75.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||..+++++|+++|..+|.|..+.++.++.++.++|||||+|.+.++|.+|+. ++|..+.|+.|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            356799999999999999999999999999999999999999999999999999999999997 8999999999999876


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            53

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.

>KOG0126|consensus

Probab=99.64  E-value=7.5e-17  Score=100.64  Aligned_cols=87  Identities=24%  Similarity=0.435  Sum_probs=80.2

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         25 PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        25 ~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      .......++.-|||||||+..+|.||...|+.||.+..+.+++++.||+++||||..|++....--|+..|||+.+.|+.
T Consensus        27 SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRt  106 (219)
T KOG0126|consen   27 SWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRT  106 (219)
T ss_pred             chhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceeccee
Confidence            44455667888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEec
Q psy13319        105 LQVSFKT  111 (117)
Q Consensus       105 l~v~~a~  111 (117)
                      |+|....
T Consensus       107 irVDHv~  113 (219)
T KOG0126|consen  107 IRVDHVS  113 (219)
T ss_pred             EEeeecc
Confidence            9998643

>KOG0108|consensus

Probab=99.63  E-value=1e-15  Score=108.04  Aligned_cols=81  Identities=36%  Similarity=0.552  Sum_probs=78.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK  113 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  113 (117)
                      +.+||||+|+++++++|..+|...|.|..++++.|+.+|+++||+|++|.+.+.+..|++.|+|..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999997754


Q ss_pred             C
Q psy13319        114 G  114 (117)
Q Consensus       114 ~  114 (117)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.63  E-value=6.6e-15  Score=96.16  Aligned_cols=76  Identities=22%  Similarity=0.364  Sum_probs=69.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ...+++|||+||++.+++++|+++|+.||.|..+.+.++.   ...++|||+|.+.+.++.|+. |+|..|.++.|.|..
T Consensus         2 ~~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~   77 (243)
T PLN03121          2 YPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITR   77 (243)
T ss_pred             CCCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEe
Confidence            3567899999999999999999999999999999999883   445799999999999999996 899999999999875

>KOG0125|consensus

Probab=99.63  E-value=4.3e-15  Score=99.96  Aligned_cols=85  Identities=29%  Similarity=0.395  Sum_probs=75.3

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .++..+..++|+|.|||....+.||+.+|.+||.|..|.++.+  ..-++|||||+|++.++|++|=..|||..+.||+|
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkI  166 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKI  166 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEE
Confidence            3344566788999999999999999999999999999988765  24459999999999999999999999999999999


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      +|..+..
T Consensus       167 EVn~ATa  173 (376)
T KOG0125|consen  167 EVNNATA  173 (376)
T ss_pred             EEeccch
Confidence            9998764

>smart00362 RRM_2 RNA recognition motif

Probab=99.62  E-value=8.5e-15  Score=79.03  Aligned_cols=72  Identities=44%  Similarity=0.712  Sum_probs=66.1

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      +|||+|||..+++++|.++|..+|.+..+.+..++  +.+++++||+|.+.+.|+.|+..+++..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999888775  6778999999999999999999999999999988763

>KOG4207|consensus

Probab=99.62  E-value=9.9e-16  Score=97.43  Aligned_cols=83  Identities=28%  Similarity=0.381  Sum_probs=78.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +.-..|-|.||...++.++|..+|.+||.|-.|.+.+++.|+..+||+||.|....+|+.|+..|+|..++|+.|+|++|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      +-.
T Consensus        91 ryg   93 (256)
T KOG4207|consen   91 RYG   93 (256)
T ss_pred             hcC
Confidence            743

>KOG0111|consensus

Probab=99.62  E-value=4.7e-16  Score=99.86  Aligned_cols=84  Identities=30%  Similarity=0.522  Sum_probs=80.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||++|-.++++.-|...|-+||+|..+.++.+..++++|||+||+|...++|-+|+..+|+..+.|+.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      ++.+
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8754

>KOG0131|consensus

Probab=99.61  E-value=1.6e-15  Score=94.65  Aligned_cols=84  Identities=27%  Similarity=0.393  Sum_probs=79.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+.+.+|||+||+..++++.|.++|-..|.|..+.+.+++-++..+||||++|.++++|+-|++.|+.+.+.|++|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      -+..
T Consensus        85 kas~   88 (203)
T KOG0131|consen   85 KASA   88 (203)
T ss_pred             eccc
Confidence            8763

>KOG0148|consensus

Probab=99.60  E-value=1.4e-14  Score=95.39  Aligned_cols=77  Identities=29%  Similarity=0.577  Sum_probs=72.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+++++||+||++.-.+++++++.|..||.|.++++..+      +||+||.|.+.+.|..|+..+|+..+.|+.+++.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            357899999999999999999999999999999999877      78999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      .+.
T Consensus       235 GKe  237 (321)
T KOG0148|consen  235 GKE  237 (321)
T ss_pred             ccc
Confidence            774

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

Probab=99.60  E-value=3.2e-14  Score=94.43  Aligned_cols=79  Identities=38%  Similarity=0.559  Sum_probs=76.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .++|||+|||..+++++|.++|..||.+..+.+..++.++..+|+|||+|.+.+.+..|+..+++..+.|+.|+|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998899999999999999999999999999999999999999864

>smart00360 RRM RNA recognition motif

Probab=99.59  E-value=1.7e-14  Score=77.56  Aligned_cols=71  Identities=42%  Similarity=0.693  Sum_probs=65.9

Q ss_pred             EeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         38 VYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        38 v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      |+|||..+++++|+++|..+|.+..+.+..++.++.++|+|||+|.+.+.|..|+..+++..+.|+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999998887778889999999999999999999999999999988863

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

Probab=99.58  E-value=4.2e-14  Score=102.13  Aligned_cols=78  Identities=27%  Similarity=0.411  Sum_probs=71.7

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .+++++|||+|||. .+++++|.++|..||.|..++++.++     +|+|||+|.+.++|+.|+..|+|..+.|+.|+|+
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            45778999999998 69999999999999999999998763     6899999999999999999999999999999999


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      +++.
T Consensus       347 ~s~~  350 (481)
T TIGR01649       347 PSKQ  350 (481)
T ss_pred             Eccc
Confidence            9764

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=99.57  E-value=5e-14  Score=102.79  Aligned_cols=76  Identities=29%  Similarity=0.474  Sum_probs=69.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCC--CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...++|||+||+.++++++|+++|..|  |.|..+.++        ++||||+|.+.++|++|+..||+..+.|+.|+|+
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  999988664        4599999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      |+++..
T Consensus       303 ~Akp~~  308 (578)
T TIGR01648       303 LAKPVD  308 (578)
T ss_pred             EccCCC
Confidence            998753

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.

>KOG0105|consensus

Probab=99.57  E-value=9e-15  Score=91.78  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=71.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+|||.++.+.+|+++|.+||.|.++.+...+   ...+|+||+|++..+|+.|+..-+|..++|.+|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            356789999999999999999999999999999886552   33679999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ..-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            754

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

Probab=99.56  E-value=4e-14  Score=102.21  Aligned_cols=75  Identities=19%  Similarity=0.223  Sum_probs=68.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCcEeCCeEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL--NGYALGNRILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~  109 (117)
                      ++++|||+|||+.+++++|+++|+.||.|..+.++.+      +++|||+|.+.++|++|+..+  ++..+.|+.|.|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4678999999999999999999999999999988754      579999999999999999865  67899999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +..
T Consensus        75 s~~   77 (481)
T TIGR01649        75 STS   77 (481)
T ss_pred             cCC
Confidence            864

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

>KOG0144|consensus

Probab=99.56  E-value=4.3e-15  Score=103.03  Aligned_cols=84  Identities=26%  Similarity=0.451  Sum_probs=75.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE-e--CCeEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA-L--GNRILQVS  108 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~-~--~g~~l~v~  108 (117)
                      +.++|||+.|++.++|.+++++|.+||.|++|.++++.. +.+|||+||.|.+++-|..|++.|||.. +  ...+|.|.
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            478899999999999999999999999999999999864 8899999999999999999999999943 3  36799999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      ||+.++.+
T Consensus       202 FADtqkdk  209 (510)
T KOG0144|consen  202 FADTQKDK  209 (510)
T ss_pred             ecccCCCc
Confidence            99987654

>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=99.56  E-value=1.1e-13  Score=75.06  Aligned_cols=74  Identities=46%  Similarity=0.774  Sum_probs=67.4

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      +|+|+|||..+++++++++|+.+|.+..+.+..++.+ .+++++||+|.+.+.|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999988877543 6689999999999999999999999999999998864

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

Probab=99.55  E-value=2.6e-14  Score=99.24  Aligned_cols=84  Identities=29%  Similarity=0.403  Sum_probs=75.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE-eC--CeEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA-LG--NRILQVS  108 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~-~~--g~~l~v~  108 (117)
                      +.-++||+-+|+.++|.||+++|++||.|.+|.+++|+.++.++|||||.|.++++|.+|+..|++.. +.  ...|+|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            44579999999999999999999999999999999999999999999999999999999999998854 43  5689999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +|+..+.
T Consensus       113 ~Ad~E~e  119 (510)
T KOG0144|consen  113 YADGERE  119 (510)
T ss_pred             ccchhhh
Confidence            9886544

>KOG0124|consensus

Probab=99.51  E-value=2.1e-14  Score=98.25  Aligned_cols=79  Identities=32%  Similarity=0.532  Sum_probs=75.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      |++|||.+.+...|+.|+..|.+||.|..+.+.+|+-|++++||+||+|+-.+.|+-|++.+||..++|+.|+|....+
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            6799999999999999999999999999999999999999999999999999999999999999999999999986443

>KOG0117|consensus

Probab=99.49  E-value=1.1e-13  Score=96.44  Aligned_cols=75  Identities=32%  Similarity=0.485  Sum_probs=69.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .-+.|||+||+.+++++.|++.|..||.+..++-++|        |+||+|..+++|.+|++.+||..+.|..|.|.+|+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            4467999999999999999999999999999876654        99999999999999999999999999999999999


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      +.-
T Consensus       330 P~~  332 (506)
T KOG0117|consen  330 PVD  332 (506)
T ss_pred             Chh
Confidence            743

>KOG1457|consensus

Probab=99.47  E-value=1.9e-12  Score=83.57  Aligned_cols=112  Identities=18%  Similarity=0.263  Sum_probs=84.0

Q ss_pred             cccccccCCCCcccccccc-CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCC-CcceEEEEE
Q psy13319          4 INKGLQRFSPLTGDLLASS-ILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN-KCKGFGFVT   81 (117)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~-~~~g~~fv~   81 (117)
                      -.+++..+.+.......+. .......++.-++|||.+||.++...+|+.+|+.|-..+.+.+......+ ..+.++|+.
T Consensus         4 p~Pp~~s~~~~es~hsvs~~~~~~~~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFat   83 (284)
T KOG1457|consen    4 PQPPFYSYQLHESPHSVSPQLPLLADEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFAT   83 (284)
T ss_pred             CCCCccccccccCCCCCCcccccccccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEE
Confidence            3445555555544422222 22234446678999999999999999999999999877777665543333 246899999


Q ss_pred             eCCHHHHHHHHHHhCCcEeC---CeEEEEEEecCCCC
Q psy13319         82 MTNYDEAVVAIQSLNGYALG---NRILQVSFKTNKGK  115 (117)
Q Consensus        82 f~~~~~a~~a~~~l~~~~~~---g~~l~v~~a~~~~~  115 (117)
                      |.+.+.|.+|+..|||+.++   +..|++++++.+.+
T Consensus        84 F~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK  120 (284)
T KOG1457|consen   84 FTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTK  120 (284)
T ss_pred             ecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcc
Confidence            99999999999999999997   88999999887554

>PF13893 RRM_5: RNA recognition motif

Probab=99.47  E-value=1.2e-12  Score=68.33  Aligned_cols=56  Identities=38%  Similarity=0.748  Sum_probs=50.0

Q ss_pred             HHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         50 LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        50 l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      |.++|++||.|..+.+....     ++++||+|.+.++|+.|+..|+|..+.|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            57899999999999886552     579999999999999999999999999999999986

(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 ....

>KOG0127|consensus

Probab=99.46  E-value=5.8e-13  Score=94.98  Aligned_cols=85  Identities=29%  Similarity=0.437  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh-----CC-cEeCC
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL-----NG-YALGN  102 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-----~~-~~~~g  102 (117)
                      ....+.+|||+|||+++++++|.+.|+.||.+....++.++.|+.+.|.|||.|.+..++..|+...     .| +.+.|
T Consensus       288 n~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G  367 (678)
T KOG0127|consen  288 NITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG  367 (678)
T ss_pred             cccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec
Confidence            3456789999999999999999999999999999999999999999999999999999999999976     23 56889


Q ss_pred             eEEEEEEecCC
Q psy13319        103 RILQVSFKTNK  113 (117)
Q Consensus       103 ~~l~v~~a~~~  113 (117)
                      +.|.|..+-.+
T Consensus       368 R~Lkv~~Av~R  378 (678)
T KOG0127|consen  368 RLLKVTLAVTR  378 (678)
T ss_pred             cEEeeeeccch
Confidence            99999876543

>KOG0109|consensus

Probab=99.44  E-value=2.4e-13  Score=90.48  Aligned_cols=74  Identities=31%  Similarity=0.538  Sum_probs=69.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCCC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG  114 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  114 (117)
                      ++||+|||..+++.+|+.+|++||+|.+|.++.+        |+||..++...++.++..|+|..|+|..|.|+-++++.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            5899999999999999999999999999999866        99999999999999999999999999999999988775


Q ss_pred             CC
Q psy13319        115 KT  116 (117)
Q Consensus       115 ~~  116 (117)
                      +.
T Consensus        76 k~   77 (346)
T KOG0109|consen   76 KA   77 (346)
T ss_pred             CC
Confidence            43

>KOG0127|consensus

Probab=99.44  E-value=7.4e-13  Score=94.45  Aligned_cols=81  Identities=26%  Similarity=0.464  Sum_probs=74.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|.|+|||+.+...+|+.+|+.||.+..+.+++.+. |+-+|||||.|....+|..|++.+|+..++|++|.|.||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            467899999999999999999999999999999987655 5556999999999999999999999999999999999976


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus       195 ~K  196 (678)
T KOG0127|consen  195 DK  196 (678)
T ss_pred             cc
Confidence            53

>smart00361 RRM_1 RNA recognition motif

Probab=99.44  E-value=1.6e-12  Score=70.84  Aligned_cols=62  Identities=24%  Similarity=0.361  Sum_probs=54.7

Q ss_pred             HHHHHHhhc----CCCCeEEEE-EEecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         47 ESVLWQLFG----PFGAVQSVK-VIRDLQT--NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        47 ~~~l~~~f~----~~g~i~~~~-~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      +++|+++|+    .||.+..+. +..++.+  +.++|++||.|.+.++|..|+..|+|..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            567888888    999999985 6666656  8889999999999999999999999999999998763

>KOG0415|consensus

Probab=99.43  E-value=4.3e-13  Score=91.52  Aligned_cols=90  Identities=26%  Similarity=0.429  Sum_probs=83.5

Q ss_pred             CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC
Q psy13319         23 ILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN  102 (117)
Q Consensus        23 ~~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g  102 (117)
                      ..+.....++...|||..|.+.++.++|+-+|+.||.|..|.++++..||.+-.|+||+|.+.++++.|.-+|+++.|..
T Consensus       229 DlpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD  308 (479)
T KOG0415|consen  229 DLPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD  308 (479)
T ss_pred             CCcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeecc
Confidence            34556667788899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEEecC
Q psy13319        103 RILQVSFKTN  112 (117)
Q Consensus       103 ~~l~v~~a~~  112 (117)
                      ++|+|.|+.+
T Consensus       309 rRIHVDFSQS  318 (479)
T KOG0415|consen  309 RRIHVDFSQS  318 (479)
T ss_pred             ceEEeehhhh
Confidence            9999998654

>KOG0147|consensus

Probab=99.42  E-value=4.1e-13  Score=95.48  Aligned_cols=79  Identities=37%  Similarity=0.685  Sum_probs=74.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      ..+||+||..+++++++..+|.+||.|..+.++.+..||.++||+|++|.+.+.|+.|++.|||..+.|+.|+|+....
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            3399999999999999999999999999999999988999999999999999999999999999999999999987543

>KOG0146|consensus

Probab=99.42  E-value=3.5e-13  Score=89.00  Aligned_cols=86  Identities=40%  Similarity=0.628  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+++|+|||-.||.+....+|...|-.||.|...++..|+-|..+++|+||.|.+...++.|+..+||..|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ..+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            877654

>KOG0131|consensus

Probab=99.41  E-value=5.5e-13  Score=83.42  Aligned_cols=84  Identities=39%  Similarity=0.640  Sum_probs=76.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE-EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS-VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      -+.+.++||+||.+.++|..|.+.|+.||++.. ..+++++.||.++|++|+.|.+.+.+.+|+..++|..+.++++.|+
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            345688999999999999999999999999755 4888999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      ++..+
T Consensus       173 ya~k~  177 (203)
T KOG0131|consen  173 YAFKK  177 (203)
T ss_pred             EEEec
Confidence            97643

>KOG0146|consensus

Probab=99.39  E-value=9.1e-13  Score=87.07  Aligned_cols=85  Identities=29%  Similarity=0.483  Sum_probs=75.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE-eC--CeEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA-LG--NRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~-~~--g~~l~  106 (117)
                      ..++++||||.|.+.-.|+|++++|+.||.+.+|.+++.+. |.++|++||.|.+..+|+.|+..|+|.. +.  +..|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLV   94 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLV   94 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceE
Confidence            34889999999999999999999999999999999988754 8889999999999999999999999954 33  56799


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.|++..+.
T Consensus        95 VK~ADTdkE  103 (371)
T KOG0146|consen   95 VKFADTDKE  103 (371)
T ss_pred             EEeccchHH
Confidence            999887654

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

Probab=99.31  E-value=2.3e-11  Score=88.32  Aligned_cols=74  Identities=26%  Similarity=0.412  Sum_probs=60.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCC------------CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPF------------GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~------------g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      ....++|||+|||..+++++|.++|..+            +.|..+.+      +..+|||||+|.+.++|..|+. |+|
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            4467899999999999999999999864            22333333      3347899999999999999995 999


Q ss_pred             cEeCCeEEEEEEe
Q psy13319         98 YALGNRILQVSFK  110 (117)
Q Consensus        98 ~~~~g~~l~v~~a  110 (117)
                      ..+.|..|+|...
T Consensus       245 ~~~~g~~l~v~r~  257 (509)
T TIGR01642       245 IIYSNVFLKIRRP  257 (509)
T ss_pred             eEeeCceeEecCc
Confidence            9999999998743

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

>KOG4208|consensus

Probab=99.30  E-value=1.3e-11  Score=78.58  Aligned_cols=81  Identities=22%  Similarity=0.401  Sum_probs=72.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCC-CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPF-GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..-.+|+..+|....+.++...|..+ |.+...++-+++.||.++|||||+|.+.+.|+-|.+.||+..+.++.|.+.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34468999999999999999999998 66788888899999999999999999999999999999999999999999874


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            43

>KOG4206|consensus

Probab=99.30  E-value=1.5e-11  Score=79.33  Aligned_cols=79  Identities=20%  Similarity=0.478  Sum_probs=70.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHH----hhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         33 GWCIFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+|||.||+..+..+++++    +|+.||.|..|....   +.+-+|-|||.|.+.+.|-.|++.|+|..+.|+.++++
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            33999999999999988877    999999999886643   46779999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ||+.+.
T Consensus        86 yA~s~s   91 (221)
T KOG4206|consen   86 YAKSDS   91 (221)
T ss_pred             cccCcc
Confidence            998754

>KOG0132|consensus

Probab=99.29  E-value=1.3e-11  Score=91.13  Aligned_cols=78  Identities=24%  Similarity=0.473  Sum_probs=71.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      -++|||||+|++.+++.+|..+|..||.|..+.+...      +++|||.+..+++|++|+..|.++.+.++.|++.|+-
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            3578999999999999999999999999999988655      7899999999999999999999999999999999987


Q ss_pred             CCCC
Q psy13319        112 NKGK  115 (117)
Q Consensus       112 ~~~~  115 (117)
                      ..+-
T Consensus       494 g~G~  497 (894)
T KOG0132|consen  494 GKGP  497 (894)
T ss_pred             cCCc
Confidence            6553

>KOG4212|consensus

Probab=99.28  E-value=1.8e-11  Score=85.66  Aligned_cols=79  Identities=23%  Similarity=0.346  Sum_probs=72.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcC-CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGP-FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+.+||.|+|+++.+++|++++.. .|.|..|.++.| .+|+.+|++.|+|.+++.+++|++.|+...+.|+.|.|.-.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            4456999999999999999999995 899999999888 56999999999999999999999999999999999999754


Q ss_pred             c
Q psy13319        111 T  111 (117)
Q Consensus       111 ~  111 (117)
                      .
T Consensus       122 ~  122 (608)
T KOG4212|consen  122 H  122 (608)
T ss_pred             C
Confidence            3

>KOG0123|consensus

Probab=99.22  E-value=7.7e-11  Score=82.56  Aligned_cols=74  Identities=31%  Similarity=0.531  Sum_probs=68.5

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +||.||+++++..+|+++|..||.|..|++..+. +| .+|| ||+|.+.+.|++|+..+||..+.++.|-|.....
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            9999999999999999999999999999999884 35 7899 9999999999999999999999999999876543

>KOG0153|consensus

Probab=99.22  E-value=9.9e-11  Score=79.70  Aligned_cols=77  Identities=22%  Similarity=0.338  Sum_probs=67.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL-NGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~  108 (117)
                      +....+|||++|...+++.+|.++|.+||+|..+.++..      +++|||+|.++++|+.|.... +...+.|.+|.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            445678999999999999999999999999999988765      559999999999999988865 4456889999999


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      |..+
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9887

>KOG0110|consensus

Probab=99.22  E-value=1.2e-11  Score=90.36  Aligned_cols=82  Identities=28%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ....|.|+|+|..++-.+++++|..||++..++++.-...+.++|||||.|-+..+|.+|+..|.+..++|++|.++|++
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            35689999999999999999999999999999998765556779999999999999999999999999999999999987


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ..
T Consensus       692 ~d  693 (725)
T KOG0110|consen  692 SD  693 (725)
T ss_pred             cc
Confidence            53

>KOG0124|consensus

Probab=99.21  E-value=5.3e-11  Score=81.86  Aligned_cols=78  Identities=27%  Similarity=0.455  Sum_probs=73.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .+|||..+.++.+++||+..|..||.|..|.+-+.+..+.++||+|++|.+.+....|+..+|-..++|+.|+|..+-
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            579999999999999999999999999999999999888899999999999999999999999999999999997654

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

Probab=99.21  E-value=2.7e-10  Score=65.48  Aligned_cols=82  Identities=18%  Similarity=0.323  Sum_probs=72.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcC--CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC----CeEEEE
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGP--FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG----NRILQV  107 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~--~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~----g~~l~v  107 (117)
                      +||.|+|+|...+.++|.+++..  .|....+.++.|..++.+.|||||.|.+.+.+..-...++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            57999999999999999888875  477888999999999999999999999999999999999998775    567899


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .||+-+++
T Consensus        82 ~yAriQG~   89 (97)
T PF04059_consen   82 SYARIQGK   89 (97)
T ss_pred             ehhHhhCH
Confidence            99886654

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

>KOG4661|consensus

Probab=99.15  E-value=1.7e-10  Score=83.25  Aligned_cols=81  Identities=30%  Similarity=0.466  Sum_probs=74.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      -++.|||.+|...+...+|+.+|++||+|.-.+++.+-.+.-.++|+||++.+..+|.+||..|+...+.|+.|.|.-++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            56789999999999999999999999999998888776666679999999999999999999999999999999999877


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      +
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            5

>KOG0123|consensus

Probab=99.14  E-value=2.7e-10  Score=79.86  Aligned_cols=74  Identities=26%  Similarity=0.499  Sum_probs=68.6

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCCC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG  114 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  114 (117)
                      .||||   +++++..|.++|..+|.+..+++.++. |  +-|||||+|.+..+|++|+..+|...+.|+++++-|+....
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            58998   899999999999999999999999997 5  89999999999999999999999999999999999976543

>KOG0109|consensus

Probab=99.11  E-value=1.9e-10  Score=76.89  Aligned_cols=75  Identities=23%  Similarity=0.440  Sum_probs=69.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ....+++|+|+.+.++.++++..|.+||.+.+|.++.+        |+||.|.-.++|..|++.|++..+.|++++|+.+
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            45678999999999999999999999999999999865        9999999999999999999999999999999987


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ..+
T Consensus       148 tsr  150 (346)
T KOG0109|consen  148 TSR  150 (346)
T ss_pred             ccc
Confidence            754

>KOG0151|consensus

Probab=99.09  E-value=7.3e-10  Score=81.45  Aligned_cols=82  Identities=26%  Similarity=0.438  Sum_probs=72.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT---NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      +....+||+||++.++++.|...|..||.+..++++..+..   ...+-++||.|.++.++++|++.|+|+.+.+..+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            34567999999999999999999999999999998877533   244679999999999999999999999999999999


Q ss_pred             EEecC
Q psy13319        108 SFKTN  112 (117)
Q Consensus       108 ~~a~~  112 (117)
                      .|++.
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99853

>KOG4212|consensus

Probab=99.08  E-value=3.6e-10  Score=79.29  Aligned_cols=76  Identities=24%  Similarity=0.316  Sum_probs=67.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|+|+|||.+++++.|++-|..+|.+....++..   |+.+|  .|.|.+.++|++|+..++|..+.|+.|.|.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~---GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMEN---GKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhcc---CCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            346678999999999999999999999999988877543   76665  8999999999999999999999999999987


Q ss_pred             e
Q psy13319        110 K  110 (117)
Q Consensus       110 a  110 (117)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

>KOG4205|consensus

Probab=99.02  E-value=4.2e-10  Score=76.94  Aligned_cols=81  Identities=27%  Similarity=0.425  Sum_probs=71.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.+++||++|+++++++.|++.|..||.+.+|.+++++.++..+||+||+|.+.+...+++.. ....+.|+.|.+.-+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678899999999999999999999999999999999999999999999999988888888763 4567888888777655


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus        84 ~r   85 (311)
T KOG4205|consen   84 SR   85 (311)
T ss_pred             Cc
Confidence            43

>KOG0110|consensus

Probab=99.00  E-value=2.4e-09  Score=78.63  Aligned_cols=77  Identities=29%  Similarity=0.429  Sum_probs=67.9

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN---KCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +|||.||+++++.+++...|...|.|..+.+...+...   .+.|||||+|.+.+.|+.|++.|+|..++|+.|.|.++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            39999999999999999999999999888776554321   234999999999999999999999999999999999877

>KOG0116|consensus

Probab=98.99  E-value=2.5e-09  Score=75.73  Aligned_cols=80  Identities=30%  Similarity=0.429  Sum_probs=67.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ...+|||+|||.+++..+|+++|..||.|....+.....-++..+|+||+|.+..+++.++.. +...+++++|.|+-.+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            556699999999999999999999999998887766532344449999999999999999995 6888999999998644


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      .
T Consensus       366 ~  366 (419)
T KOG0116|consen  366 P  366 (419)
T ss_pred             c
Confidence            3

>KOG0533|consensus

Probab=98.99  E-value=4.7e-09  Score=69.44  Aligned_cols=80  Identities=26%  Similarity=0.352  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ...+|+|.|||..+.+.||+++|..||.+..+.+..+ .+|.+.|.|-|.|...++|.++++.++++.++|+.+++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            3467999999999999999999999998877777666 468899999999999999999999999999999999887654


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            3

>KOG1548|consensus

Probab=98.91  E-value=1.5e-08  Score=69.24  Aligned_cols=81  Identities=21%  Similarity=0.243  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE--------EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQ--------SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN  102 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g  102 (117)
                      ..+..|||.|||.+++.+++.++|+++|.|.        .|++-++.. |..+|-+.+.|...++..-|+..|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            3456699999999999999999999999763        366767644 8999999999999999999999999999999


Q ss_pred             eEEEEEEecC
Q psy13319        103 RILQVSFKTN  112 (117)
Q Consensus       103 ~~l~v~~a~~  112 (117)
                      ..|+|+.|+-
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998764

>KOG0106|consensus

Probab=98.87  E-value=2.4e-09  Score=69.52  Aligned_cols=70  Identities=23%  Similarity=0.399  Sum_probs=64.2

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .+||++||+.+.+.+++.+|..||++..+.+.        .||+||+|.+..+|..|+..+++..+.+-.+.+.++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            58999999999999999999999999888664        45889999999999999999999999988899999874

>KOG4205|consensus

Probab=98.87  E-value=9.3e-09  Score=70.42  Aligned_cols=81  Identities=28%  Similarity=0.365  Sum_probs=73.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ....+||++||.++++.++++.|..||.|..+.++.+..+.+.++|+||.|.+.+....++. ..-..+.++.+.|.-|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            34589999999999999999999999999999999999999999999999999999999877 36688999999998766


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus       175 pk  176 (311)
T KOG4205|consen  175 PK  176 (311)
T ss_pred             ch
Confidence            54

>KOG4209|consensus

Probab=98.86  E-value=9.7e-09  Score=67.85  Aligned_cols=80  Identities=21%  Similarity=0.305  Sum_probs=73.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+...+||+|+...++.+++...|+.||.+..+.++.++.++.++|++||+|.+.+..+.++. |++..+.|+.+.+.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            456779999999999988899999999999989899999888899999999999999999999 9999999999999875


Q ss_pred             c
Q psy13319        111 T  111 (117)
Q Consensus       111 ~  111 (117)
                      +
T Consensus       178 r  178 (231)
T KOG4209|consen  178 R  178 (231)
T ss_pred             e
Confidence            4

>KOG4660|consensus

Probab=98.86  E-value=2.1e-09  Score=77.07  Aligned_cols=72  Identities=19%  Similarity=0.432  Sum_probs=64.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .....+|+|-|||..+++++|.++|..||+|..++.-     -..+|..||+|.+..+|++|++.|++..+.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4467789999999999999999999999999886543     33478999999999999999999999999998887

>KOG4454|consensus

Probab=98.84  E-value=1.3e-09  Score=70.44  Aligned_cols=79  Identities=24%  Similarity=0.252  Sum_probs=70.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+.+++|||+|+...++|+-|.++|-..|.|.++.+...+. +..+ |+||.|.++....-|++.+||..+.++.+++.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            46688999999999999999999999999999998877754 5556 999999999999999999999999999888876


Q ss_pred             e
Q psy13319        110 K  110 (117)
Q Consensus       110 a  110 (117)
                      -
T Consensus        84 r   84 (267)
T KOG4454|consen   84 R   84 (267)
T ss_pred             c
Confidence            3

>KOG0226|consensus

Probab=98.83  E-value=4.6e-09  Score=69.16  Aligned_cols=80  Identities=34%  Similarity=0.556  Sum_probs=73.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+++.+||.+.|.-+++.+.+-+.|.+|-....-++++++.||+++||+||-|.+..++.+|++.++|..++++.|++.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            45788999999999999999999999998877788899999999999999999999999999999999999999988754

>KOG4211|consensus

Probab=98.82  E-value=2.8e-08  Score=70.63  Aligned_cols=77  Identities=14%  Similarity=0.310  Sum_probs=65.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+....|.+++|||++++++|.+||..++ |..+.+.  +.+|++.|-|||+|.+.++++.|+++ +...+..+.|.|--
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFT   82 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEc
Confidence            45566788999999999999999999987 6665444  45799999999999999999999995 78888888888865


Q ss_pred             e
Q psy13319        110 K  110 (117)
Q Consensus       110 a  110 (117)
                      +
T Consensus        83 ~   83 (510)
T KOG4211|consen   83 A   83 (510)
T ss_pred             c
Confidence            4

>KOG1190|consensus

Probab=98.55  E-value=6.8e-07  Score=62.62  Aligned_cols=74  Identities=30%  Similarity=0.504  Sum_probs=67.6

Q ss_pred             CcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +..|.|.||..+ ++.+.|..+|..||.|.+++++..+.     .-+.|+|.+...|+-|++.|+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            578899999877 89999999999999999999987753     479999999999999999999999999999999876

>KOG0120|consensus

Probab=98.54  E-value=1.2e-07  Score=68.42  Aligned_cols=84  Identities=29%  Similarity=0.383  Sum_probs=76.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ......+||++||...++.++.+++..||.+....++.+..+|.++||+|.+|.+......|+..|||..+++..|.|+.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34566799999999999999999999999999999999988899999999999999999999999999999999999987


Q ss_pred             ecCC
Q psy13319        110 KTNK  113 (117)
Q Consensus       110 a~~~  113 (117)
                      |...
T Consensus       366 A~~g  369 (500)
T KOG0120|consen  366 AIVG  369 (500)
T ss_pred             hhcc
Confidence            6643

>KOG1995|consensus

Probab=98.42  E-value=7.1e-07  Score=61.42  Aligned_cols=85  Identities=21%  Similarity=0.256  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE--------EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQ--------SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ......++||.++|..++++++.++|..+|.|.        .+.+-.++.|+..++-+.|.|.+...|+.|+..+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            345667899999999999999999999999762        345667778999999999999999999999999999999


Q ss_pred             CCeEEEEEEecCC
Q psy13319        101 GNRILQVSFKTNK  113 (117)
Q Consensus       101 ~g~~l~v~~a~~~  113 (117)
                      .++.|+|..+..+
T Consensus       142 ~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  142 CGNTIKVSLAERR  154 (351)
T ss_pred             cCCCchhhhhhhc
Confidence            9999999887643

>KOG1457|consensus

Probab=98.40  E-value=4.4e-07  Score=59.10  Aligned_cols=67  Identities=22%  Similarity=0.342  Sum_probs=56.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      ....++||.||..+++|++|+.+|..|.....+++...  .|  -.++|++|++.+.|..|+..|+|..+.
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            45668999999999999999999999988776666432  23  458999999999999999999997654

>KOG4211|consensus

Probab=98.36  E-value=2.1e-06  Score=61.36  Aligned_cols=77  Identities=17%  Similarity=0.230  Sum_probs=62.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE-EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQS-VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+..|.+++||+.+++++|.+||+..--+.. +.++.++ .+++.|-+||+|.+.+.++.|+.. +.-.|+.+-|.|-.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            35678999999999999999999998765544 4445443 477889999999999999999985 66678888787754

>KOG4206|consensus

Probab=98.28  E-value=7.4e-06  Score=53.30  Aligned_cols=78  Identities=26%  Similarity=0.481  Sum_probs=67.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQV  107 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v  107 (117)
                      ..++..++++.|||..++.+.+..+|..|....+++++...     .+.+||+|.+...+..|...+++..+. ...+++
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            35678899999999999999999999999988888887543     569999999999999999999998877 778888


Q ss_pred             EEec
Q psy13319        108 SFKT  111 (117)
Q Consensus       108 ~~a~  111 (117)
                      .+++
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            8764

>KOG0147|consensus

Probab=98.28  E-value=3.3e-07  Score=66.00  Aligned_cols=78  Identities=24%  Similarity=0.378  Sum_probs=71.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +-+++|+-.+.....+.+|+++|..+|.|..++++.++.++..+|.+||+|.+.+....|+. |.|..+.|.+|.|...
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLS  255 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEeccc
Confidence            55788888999999999999999999999999999999999999999999999999999986 8999999999988753

>KOG1456|consensus

Probab=98.26  E-value=1.8e-05  Score=55.25  Aligned_cols=81  Identities=25%  Similarity=0.338  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         28 TMNGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .-..+++.++|.+|... .+.+.+..+|--||.|..++++..+     .|-+.|++.+..+.++++..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            34567899999999887 6778899999999999999999875     46899999999999999999999999999999


Q ss_pred             EEEecCC
Q psy13319        107 VSFKTNK  113 (117)
Q Consensus       107 v~~a~~~  113 (117)
                      |++++..
T Consensus       357 v~~SkQ~  363 (494)
T KOG1456|consen  357 VCVSKQN  363 (494)
T ss_pred             Eeecccc
Confidence            9987753

>KOG4210|consensus

Probab=98.20  E-value=1.6e-06  Score=59.13  Aligned_cols=84  Identities=23%  Similarity=0.320  Sum_probs=74.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .....+|++++..+++++|+..|..+|.+..+++..++.++...|++|+.|.....+..++.. +...+.++.+.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            334444999999999999999999999999999999999999999999999999999999886 7888999999999877


Q ss_pred             CCCCC
Q psy13319        112 NKGKT  116 (117)
Q Consensus       112 ~~~~~  116 (117)
                      +.+..
T Consensus       263 ~~~~~  267 (285)
T KOG4210|consen  263 PRPKS  267 (285)
T ss_pred             CCccc
Confidence            76543

>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=98.18  E-value=1e-05  Score=47.37  Aligned_cols=59  Identities=24%  Similarity=0.328  Sum_probs=37.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      ++.|++.+++..++.++|++.|+.+|.|..|.+...      ..-|||.|.+.+.|+.++..+..
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHH
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHh
Confidence            467899999999999999999999999988877543      33799999999999999887643

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

>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=98.12  E-value=2e-05  Score=43.89  Aligned_cols=68  Identities=26%  Similarity=0.300  Sum_probs=46.2

Q ss_pred             cEEEEeCCCCCCCHHHH----HHhhcCCCC-eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         34 WCIFVYNLAPETEESVL----WQLFGPFGA-VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l----~~~f~~~g~-i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..|+|.|||.+.+...|    ++++..+|. +..+  .        .+.|++.|.+.+.|.+|.+.|+|-.+.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            35899999999887654    456667764 4433  1        3479999999999999999999999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            864

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

>KOG4849|consensus

Probab=98.05  E-value=5.7e-06  Score=57.21  Aligned_cols=75  Identities=15%  Similarity=0.260  Sum_probs=65.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCC--CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ....+|||||-|+++.+||.+.+...|  ++..+++..++.+|.++||+.+...+..+.+..++.|....+.|+.-.
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~  155 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPT  155 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCe
Confidence            445699999999999999999999766  567778888889999999999999999999999999988888876433

>KOG0106|consensus

Probab=98.03  E-value=4e-06  Score=54.71  Aligned_cols=71  Identities=27%  Similarity=0.385  Sum_probs=61.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ...+.+.|.+++..+.+++|.+.|..+|.+.....        ..+.+||+|...+++..|+..+++..+.++.|.+..
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            35678999999999999999999999999843322        255899999999999999999999999999998843

>KOG4307|consensus

Probab=98.02  E-value=4e-05  Score=57.30  Aligned_cols=77  Identities=18%  Similarity=0.273  Sum_probs=64.6

Q ss_pred             CCc-EEEEeCCCCCCCHHHHHHhhcCCCCe-EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         32 SGW-CIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        32 ~~~-~l~v~~Lp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++ .|-+.|+|++++-+||.+||..|-.+ ..+.+ +..+.|+..|-|.|.|++.++|++|...+++..|.++.+.+..
T Consensus       865 pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~-r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  865 PGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRI-RRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCeEEEecCCCccccHHHHHHHhcccccCCCceeE-eecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            444 78899999999999999999999765 33333 3345699999999999999999999999999999999887753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.01  E-value=2.6e-05  Score=53.83  Aligned_cols=78  Identities=19%  Similarity=0.434  Sum_probs=59.2

Q ss_pred             cEEEEeCCCCCCCHHH----H--HHhhcCCCCeEEEEEEecCCCC-Ccce--EEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         34 WCIFVYNLAPETEESV----L--WQLFGPFGAVQSVKVIRDLQTN-KCKG--FGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~----l--~~~f~~~g~i~~~~~~~~~~~~-~~~g--~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      .-+||-+||+.+..++    |  .++|..||.|..+.+.....+- ...+  ..|+.|.+.++|.+++...+|..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            4589999998865543    2  3789999999988664332111 1122  3499999999999999999999999999


Q ss_pred             EEEEEec
Q psy13319        105 LQVSFKT  111 (117)
Q Consensus       105 l~v~~a~  111 (117)
                      |+..|..
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9998854

>KOG1190|consensus

Probab=97.94  E-value=4.7e-05  Score=53.70  Aligned_cols=78  Identities=26%  Similarity=0.362  Sum_probs=64.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCe-EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v  107 (117)
                      .+++.++++.|+|.+++|++++..|..-|.. ...++-     ++.+-++++.+.+.++|-.|+..++...++ +..++|
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff-----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRv  485 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF-----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRV  485 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec-----CCCcceeecccCChhHhhhhccccccccCCCCceEEE
Confidence            4677899999999999999999999987754 333332     333569999999999999999999998887 558999


Q ss_pred             EEecC
Q psy13319        108 SFKTN  112 (117)
Q Consensus       108 ~~a~~  112 (117)
                      +|++.
T Consensus       486 SFSks  490 (492)
T KOG1190|consen  486 SFSKS  490 (492)
T ss_pred             Eeecc
Confidence            99875

>KOG0105|consensus

Probab=97.87  E-value=9.8e-05  Score=47.11  Aligned_cols=68  Identities=22%  Similarity=0.250  Sum_probs=58.5

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      .+.+.....|.|.+||+..++++|++++.+.|.++...+.++       |++.|+|...++.+-|+..|....+.
T Consensus       109 ppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  109 PPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             CcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            344556678999999999999999999999999999888766       37999999999999999999876554

>KOG3152|consensus

Probab=97.85  E-value=8.3e-06  Score=54.07  Aligned_cols=71  Identities=18%  Similarity=0.284  Sum_probs=59.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCC--------C----CcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT--------N----KCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~--------~----~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      -.||++++|+..+..-++++|..||.|-.+.+.....+        |    ....-|+|+|.+...|..+...||+..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            57999999999999999999999999998887655443        2    22345789999999999999999999998


Q ss_pred             CeE
Q psy13319        102 NRI  104 (117)
Q Consensus       102 g~~  104 (117)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            764

>KOG0129|consensus

Probab=97.81  E-value=0.00016  Score=52.29  Aligned_cols=68  Identities=26%  Similarity=0.246  Sum_probs=60.3

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhc-CCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFG-PFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS   94 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   94 (117)
                      +..-++.+|||||+||.-.+.++|-.+|. -||.|..+.+-.|++-+.++|-|-|.|.+..+--+|+..
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            33457889999999999999999999999 599999998888877788999999999999998888874

>KOG2314|consensus

Probab=97.73  E-value=0.00034  Score=51.37  Aligned_cols=77  Identities=26%  Similarity=0.303  Sum_probs=61.8

Q ss_pred             CCCcEEEEeCCCCCCCH------HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-Ce
Q psy13319         31 GSGWCIFVYNLAPETEE------SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NR  103 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~------~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~  103 (117)
                      .-+..|.|.|+|---..      ..|.++|+++|++....++.+.. |..+||.|++|.+...|+.|++.|||..++ ++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            34567889999876433      35678899999999888887765 448999999999999999999999998887 55


Q ss_pred             EEEEE
Q psy13319        104 ILQVS  108 (117)
Q Consensus       104 ~l~v~  108 (117)
                      ...|.
T Consensus       135 tf~v~  139 (698)
T KOG2314|consen  135 TFFVR  139 (698)
T ss_pred             eEEee
Confidence            55553

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

Probab=97.73  E-value=0.00039  Score=42.81  Aligned_cols=76  Identities=25%  Similarity=0.372  Sum_probs=51.8

Q ss_pred             CCCCcEEEEeCCCC------CCCH---HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         30 NGSGWCIFVYNLAP------ETEE---SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~------~~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      .+++.+|.|.=+.+      ...+   .++.+.|..||.+.-+++..+        .-+|.|.+-+.|-+|+. ++|..+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            34556666654441      2222   377788989999888887654        58999999999999999 799999


Q ss_pred             CCeEEEEEEecCCC
Q psy13319        101 GNRILQVSFKTNKG  114 (117)
Q Consensus       101 ~g~~l~v~~a~~~~  114 (117)
                      .|+.|+|....+.+
T Consensus        95 ~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   95 NGRTLKIRLKTPDW  108 (146)
T ss_dssp             TTEEEEEEE-----
T ss_pred             CCEEEEEEeCCccH
Confidence            99999998866554

; PDB: 1UFW_A 2DNR_A.

>KOG1456|consensus

Probab=97.71  E-value=0.00065  Score=47.73  Aligned_cols=82  Identities=16%  Similarity=0.222  Sum_probs=64.5

Q ss_pred             CCCCCCcEEEEeCC--CCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe--
Q psy13319         28 TMNGSGWCIFVYNL--APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR--  103 (117)
Q Consensus        28 ~~~~~~~~l~v~~L--p~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~--  103 (117)
                      +...+++.|.+.=|  -+.++.+.|+.+-...|++..+.+...  +|.   -+.|+|.+.+.|++|...|||..|+..  
T Consensus       115 es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCC  189 (494)
T KOG1456|consen  115 ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCC  189 (494)
T ss_pred             CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccce
Confidence            33445566655544  445788999999999999999977654  455   599999999999999999999988744  


Q ss_pred             EEEEEEecCCC
Q psy13319        104 ILQVSFKTNKG  114 (117)
Q Consensus       104 ~l~v~~a~~~~  114 (117)
                      .|+|+||++.+
T Consensus       190 TLKIeyAkP~r  200 (494)
T KOG1456|consen  190 TLKIEYAKPTR  200 (494)
T ss_pred             eEEEEecCcce
Confidence            68889998764

>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=97.71  E-value=0.0003  Score=40.79  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=51.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEE-EEecC------CCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe-
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVK-VIRDL------QTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR-  103 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~-~~~~~------~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~-  103 (117)
                      ..+-|.|-+.|+. ....+.+.|+.||.|.+.. ...+.      .......+..+.|.+..+|.+|+.. ||..+.|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            3455888899998 5678999999999986653 00000      0012245899999999999999995 99999876 


Q ss_pred             EEEEEEec
Q psy13319        104 ILQVSFKT  111 (117)
Q Consensus       104 ~l~v~~a~  111 (117)
                      .+-|.+++
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            55566764

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.

>KOG1365|consensus

Probab=97.66  E-value=0.00011  Score=51.64  Aligned_cols=76  Identities=20%  Similarity=0.288  Sum_probs=62.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCC-eEE--EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGA-VQS--VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~-i~~--~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      -.|.+++||+..+.++|..||..|.. |..  +.++.+ ..|++.|-+||+|.+.+.|.+|....+.....++.|.|--+
T Consensus       281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            35889999999999999999998864 322  555555 45889999999999999999999988877777888887543

>KOG0129|consensus

Probab=97.65  E-value=0.00068  Score=49.14  Aligned_cols=65  Identities=20%  Similarity=0.255  Sum_probs=48.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecC--CCC-Ccce---EEEEEeCCHHHHHHHHHHh
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL--QTN-KCKG---FGFVTMTNYDEAVVAIQSL   95 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~--~~~-~~~g---~~fv~f~~~~~a~~a~~~l   95 (117)
                      ..-++.||||+||++++|+.|...|..||.+ .+.+....  ... -++|   |+|+.|+++...+.-+..+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3456789999999999999999999999964 34454211  111 2356   9999999998888766654

>KOG2193|consensus

Probab=97.65  E-value=3.7e-05  Score=54.51  Aligned_cols=76  Identities=25%  Similarity=0.343  Sum_probs=59.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-cEeCCeEEEEEEecCC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG-YALGNRILQVSFKTNK  113 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~-~~~~g~~l~v~~a~~~  113 (117)
                      .+|++||.+..+..++..+|....-...-.++..      .||+||.+.+..++.++++.++| ..+.|.++.+...-++
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            5899999999999999999986421111122222      56999999999999999999998 5688999999887665


Q ss_pred             CCC
Q psy13319        114 GKT  116 (117)
Q Consensus       114 ~~~  116 (117)
                      +++
T Consensus        77 kqr   79 (584)
T KOG2193|consen   77 KQR   79 (584)
T ss_pred             HHH
Confidence            544

>KOG1548|consensus

Probab=97.62  E-value=0.00052  Score=47.58  Aligned_cols=79  Identities=24%  Similarity=0.269  Sum_probs=60.9

Q ss_pred             CCCCCcEEEEeCCCC----CCC-------HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         29 MNGSGWCIFVYNLAP----ETE-------ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~----~~~-------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      .....++|.+.|+-.    ..+       .++|.+--.+||.+..+.+...    .+.|.+-|.|.+.++|..|++.|+|
T Consensus       261 k~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~G  336 (382)
T KOG1548|consen  261 KARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDG  336 (382)
T ss_pred             cccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcC
Confidence            345677888888732    122       2455666778999999866432    3478999999999999999999999


Q ss_pred             cEeCCeEEEEEEec
Q psy13319         98 YALGNRILQVSFKT  111 (117)
Q Consensus        98 ~~~~g~~l~v~~a~  111 (117)
                      .+++|+.|..+...
T Consensus       337 R~fdgRql~A~i~D  350 (382)
T KOG1548|consen  337 RWFDGRQLTASIWD  350 (382)
T ss_pred             eeecceEEEEEEeC
Confidence            99999999887644

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

Probab=97.59  E-value=0.0003  Score=36.01  Aligned_cols=52  Identities=17%  Similarity=0.314  Sum_probs=40.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI   92 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~   92 (117)
                      +.|-|.|.+.+.. +.+.+.|..+|.|....+..      .....|+.|.++.+|+.|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            3567888887754 55677899999999987752      2448999999999999884

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

Probab=97.57  E-value=0.0011  Score=36.93  Aligned_cols=57  Identities=32%  Similarity=0.513  Sum_probs=42.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN   96 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   96 (117)
                      ..++..||. +|..+...||.++|++||.| .+.++.+.       -|||....++.+..++..+.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            345566676 99999999999999999976 46676652       59999999999999988775

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG1365|consensus

Probab=97.53  E-value=0.00017  Score=50.64  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=55.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcC----CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGP----FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~----~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ..-.|..++||.++++.++.+||..    -|....+.++..+ .|+..|-+||.|..++.|+.|+.+ |...++.+.|
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            3446788899999999999999973    2345666666654 488899999999999999999986 5555554433

>KOG0120|consensus

Probab=97.52  E-value=0.00064  Score=49.62  Aligned_cols=64  Identities=25%  Similarity=0.362  Sum_probs=51.8

Q ss_pred             HHHHhhcCCCCeEEEEEEecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         49 VLWQLFGPFGAVQSVKVIRDLQT---NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        49 ~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +++.-+.+||.|..|.+.++...   .-+.|-.||+|.+.+++++|+..|+|..+.++.+..+|...
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            45555778999999888766211   23467899999999999999999999999999999888653

>KOG0112|consensus

Probab=97.46  E-value=0.0002  Score=54.90  Aligned_cols=77  Identities=19%  Similarity=0.269  Sum_probs=65.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC--CeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG--NRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~--g~~l~v~  108 (117)
                      .....+++++|+.++....+...|..||.|..+.+-.      ...|+|+.|++...+++|+..+.|.-++  .++++|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            4567899999999999999999999999998876632      2459999999999999999999999888  4578888


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      |+...
T Consensus       527 la~~~  531 (975)
T KOG0112|consen  527 LASPP  531 (975)
T ss_pred             cccCC
Confidence            87754

>KOG2202|consensus

Probab=97.30  E-value=9.1e-05  Score=49.23  Aligned_cols=63  Identities=14%  Similarity=0.292  Sum_probs=49.1

Q ss_pred             HHHHHhhc-CCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         48 SVLWQLFG-PFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        48 ~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +++...+. +||.|..+.+-.+ ..-.-.|-+||.|...++|++|+..||+.++.|++|...++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34445555 8999988755433 223347899999999999999999999999999999988753

>KOG2416|consensus

Probab=97.30  E-value=0.00029  Score=51.96  Aligned_cols=80  Identities=19%  Similarity=0.229  Sum_probs=62.8

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHhhcC-CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC---
Q psy13319         26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGP-FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG---  101 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~---  101 (117)
                      ++.....+..|||.||-.-++..+|+.+++. .|.|... |+.     +.+..|||.|.+.++|-+....|||+.|-   
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD-----kIKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD-----KIKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHH-----HhhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            3345667889999999999999999999995 5555544 432     23668999999999999999999998764   


Q ss_pred             CeEEEEEEec
Q psy13319        102 NRILQVSFKT  111 (117)
Q Consensus       102 g~~l~v~~a~  111 (117)
                      .+.|-+.|..
T Consensus       511 PK~L~adf~~  520 (718)
T KOG2416|consen  511 PKHLIADFVR  520 (718)
T ss_pred             CceeEeeecc
Confidence            5567777754

>KOG1855|consensus

Probab=97.16  E-value=0.00064  Score=48.36  Aligned_cols=67  Identities=21%  Similarity=0.281  Sum_probs=55.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEec---CCCCC----------cceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRD---LQTNK----------CKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~---~~~~~----------~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      -++++|.+.|||.+-.-+-|.++|..+|.|..|++...   +.+..          .+-+++|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            37899999999999888999999999999999988765   22211          255799999999999999998754

>KOG4307|consensus

Probab=97.15  E-value=0.00058  Score=51.36  Aligned_cols=85  Identities=20%  Similarity=0.227  Sum_probs=66.4

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE-EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC
Q psy13319         24 LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS-VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN  102 (117)
Q Consensus        24 ~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g  102 (117)
                      .+.....+.+..|||.+||..+.+.++.++|.+.-.|+. +.+-.. -+++.++.+||.|...+++..|...-+...++.
T Consensus       425 q~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~  503 (944)
T KOG4307|consen  425 QNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGH  503 (944)
T ss_pred             CCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCc
Confidence            344455677889999999999999999999998766655 555444 457778999999999888777766556667778


Q ss_pred             eEEEEEE
Q psy13319        103 RILQVSF  109 (117)
Q Consensus       103 ~~l~v~~  109 (117)
                      +.|+|.-
T Consensus       504 r~irv~s  510 (944)
T KOG4307|consen  504 RIIRVDS  510 (944)
T ss_pred             eEEEeec
Confidence            8888864

>KOG1996|consensus

Probab=96.93  E-value=0.0055  Score=41.93  Aligned_cols=64  Identities=20%  Similarity=0.250  Sum_probs=51.7

Q ss_pred             HHHHHhhcCCCCeEEEEEEecCCCCCc-ceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         48 SVLWQLFGPFGAVQSVKVIRDLQTNKC-KGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        48 ~~l~~~f~~~g~i~~~~~~~~~~~~~~-~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +++++...+||.|..|.+...+..... .--.||+|...+.|.+|+..|||..++|+.+..+|-+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            467778889999998877665433222 3458999999999999999999999999999988754

>KOG4660|consensus

Probab=96.89  E-value=0.0019  Score=47.30  Aligned_cols=59  Identities=19%  Similarity=0.358  Sum_probs=49.0

Q ss_pred             CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC----CeEEEEEEecCCCC
Q psy13319         57 FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG----NRILQVSFKTNKGK  115 (117)
Q Consensus        57 ~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~----g~~l~v~~a~~~~~  115 (117)
                      .|....+.++.|-.+.+.-|||||+|-+.+++....+.++|..|.    .+.+.+.||+-+++
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk  475 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGK  475 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhch
Confidence            677778888888888888999999999999999999999997554    45677888876654

>KOG4676|consensus

Probab=96.73  E-value=0.0037  Score=44.23  Aligned_cols=73  Identities=21%  Similarity=0.348  Sum_probs=57.4

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ---TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .|.|.||.+.++.++++.+|...|.|.++.+.....   .......|||.|.+...+..|.. |.+..+-+..|.|-
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            799999999999999999999999999998765322   23346799999999999988866 55655555554443

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

Probab=96.70  E-value=0.016  Score=30.60  Aligned_cols=54  Identities=13%  Similarity=0.137  Sum_probs=42.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCC---CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPF---GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL   95 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~---g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   95 (117)
                      ..|+|.|+.. .+.++|+.+|..|   .....+.|..+.       -|-|.|.+...|.+|+..|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4589999854 5678899999988   235678888774       3889999999999998753

>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=96.58  E-value=0.012  Score=37.62  Aligned_cols=81  Identities=12%  Similarity=0.194  Sum_probs=50.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcC-CCCe---EEEEEEecCC-CC-CcceEEEEEeCCHHHHHHHHHHhCCcEeC---
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGP-FGAV---QSVKVIRDLQ-TN-KCKGFGFVTMTNYDEAVVAIQSLNGYALG---  101 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~-~g~i---~~~~~~~~~~-~~-~~~g~~fv~f~~~~~a~~a~~~l~~~~~~---  101 (117)
                      .....|-|++||+..+++++.+.+.. ++..   ..+....... .. ....-||+.|.+.++.......++|..+.   
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999999998887 6655   2332112211 12 23567999999999999999999997764   


Q ss_pred             C--eEEEEEEec
Q psy13319        102 N--RILQVSFKT  111 (117)
Q Consensus       102 g--~~l~v~~a~  111 (117)
                      |  ....|.+|-
T Consensus        85 g~~~~~~VE~Ap   96 (176)
T PF03467_consen   85 GNEYPAVVEFAP   96 (176)
T ss_dssp             S-EEEEEEEE-S
T ss_pred             CCCcceeEEEcc
Confidence            2  244555543

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.

>KOG0128|consensus

Probab=96.48  E-value=0.0014  Score=50.10  Aligned_cols=78  Identities=15%  Similarity=0.082  Sum_probs=64.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ...++|.|.|+..+.+.++.++.+.|.+..++++..+ .|+++|.++|.|.+...+.++........+.-+.+.+..++
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccC
Confidence            4568999999999999999999999999888877664 59999999999999999998887776666665555555533

>KOG2068|consensus

Probab=96.36  E-value=0.0016  Score=45.01  Aligned_cols=79  Identities=18%  Similarity=0.344  Sum_probs=58.4

Q ss_pred             cEEEEeCCCCCCCHHHHH---HhhcCCCCeEEEEEEecCC--CC-CcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         34 WCIFVYNLAPETEESVLW---QLFGPFGAVQSVKVIRDLQ--TN-KCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~---~~f~~~g~i~~~~~~~~~~--~~-~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      .-+||-+|+.....+.+.   +.|..||.|..+..-.+..  .+ .+..-+||.|...++|..++...+|..+.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            457888888876544433   5688899998887766541  11 12345999999999999999999999999888777


Q ss_pred             EEecC
Q psy13319        108 SFKTN  112 (117)
Q Consensus       108 ~~a~~  112 (117)
                      ++...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            66543

>KOG0128|consensus

Probab=96.33  E-value=0.00014  Score=55.40  Aligned_cols=68  Identities=25%  Similarity=0.411  Sum_probs=57.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      .++||.||+..+.+.++...|..+|.+..+.+..+..+++.+|+||+.|...+.+.+++....+..++
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            56899999999999999999999998877766656677889999999999999999998865554444

>KOG0115|consensus

Probab=96.07  E-value=0.01  Score=39.81  Aligned_cols=63  Identities=22%  Similarity=0.243  Sum_probs=52.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      ..|||.||+..++.+.+...|+.||.+..-.+..| .-++..+-++|.|.....+.+|+..+..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhcc
Confidence            66999999999999999999999999966544444 2377788899999999999999987743

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

Probab=95.74  E-value=0.05  Score=35.07  Aligned_cols=61  Identities=20%  Similarity=0.182  Sum_probs=44.3

Q ss_pred             CHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CcEeCCeEEEEEEecC
Q psy13319         46 EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN--GYALGNRILQVSFKTN  112 (117)
Q Consensus        46 ~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~a~~  112 (117)
                      ....|+++|..++.+..+..+..      -+-..|.|.+.+.|.++...|+  +..+.|..+++.|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999998877766544      2358899999999999999999  8999999999998753

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.

>KOG0112|consensus

Probab=95.66  E-value=0.0018  Score=49.97  Aligned_cols=78  Identities=22%  Similarity=0.285  Sum_probs=64.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...+||++||+..+++.+|...|..+|.+..|.+...+. +...-|+|+.|.+...+..++..+.+..|....+++.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            567899999999999999999999999999998866532 344569999999999999999888888777555555443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.62  E-value=0.11  Score=32.13  Aligned_cols=73  Identities=19%  Similarity=0.237  Sum_probs=53.4

Q ss_pred             CCCCcEEEEeCCCCCCC----HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         30 NGSGWCIFVYNLAPETE----ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~----~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .++=.+|-|+=|.++..    -..+...++.||.|..+.+.     |  +--+.|.|.+..+|=.|+..++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            34556777876666643    24566677889999887653     3  33699999999999999998866 5667788


Q ss_pred             EEEEe
Q psy13319        106 QVSFK  110 (117)
Q Consensus       106 ~v~~a  110 (117)
                      +++|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            88773

>KOG2591|consensus

Probab=95.60  E-value=0.039  Score=40.97  Aligned_cols=67  Identities=15%  Similarity=0.136  Sum_probs=53.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcC--CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGP--FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRIL  105 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~--~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l  105 (117)
                      .-|.+.++-||..+-.++++.+|..  +-.+..|.+-.+.       -.||.|++..+|+.|.+.|..  ..|.|+.|
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            4467889999999999999999996  6677888775442       489999999999999998865  34666654

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.49  E-value=0.25  Score=29.14  Aligned_cols=68  Identities=15%  Similarity=0.255  Sum_probs=48.6

Q ss_pred             CCcEEEEeCCCCCCCH-HHHHHhhcCC-CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         32 SGWCIFVYNLAPETEE-SVLWQLFGPF-GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~-~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      .+..+.+-..|+.... +++..+...+ ..|.++++.++.  ..++-.+.+.|.+.+.|......+||..+.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3445555555666554 5555555554 457888888873  235778999999999999999999998765

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

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=95.39  E-value=0.18  Score=26.92  Aligned_cols=54  Identities=9%  Similarity=0.079  Sum_probs=41.7

Q ss_pred             CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         45 TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        45 ~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ++-.+++..+..|+ ...+  ..+      +..-||.|.+..+|+++....+|..+.+..+.+
T Consensus        12 ~~v~d~K~~Lr~y~-~~~I--~~d------~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   12 VTVEDFKKRLRKYR-WDRI--RDD------RTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             ccHHHHHHHHhcCC-cceE--Eec------CCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            56789999999987 3333  333      225789999999999999999998887777654

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

>KOG2253|consensus

Probab=95.10  E-value=0.026  Score=42.47  Aligned_cols=80  Identities=20%  Similarity=0.168  Sum_probs=63.9

Q ss_pred             cccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Q psy13319         20 ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA   99 (117)
Q Consensus        20 ~~~~~~~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~   99 (117)
                      ..+..+.....++..++||+|+...+..+-+..++..+|-|..+..  .       -|||..|.......+++..+....
T Consensus        27 ~~p~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr--~-------~fgf~~f~~~~~~~ra~r~~t~~~   97 (668)
T KOG2253|consen   27 VVPIQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKR--D-------KFGFCEFLKHIGDLRASRLLTELN   97 (668)
T ss_pred             ccCCcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhh--h-------hhcccchhhHHHHHHHHHHhcccC
Confidence            3444556666778889999999999999999999999998755422  1       289999999999999999888888


Q ss_pred             eCCeEEEEE
Q psy13319        100 LGNRILQVS  108 (117)
Q Consensus       100 ~~g~~l~v~  108 (117)
                      ++|..+.+.
T Consensus        98 ~~~~kl~~~  106 (668)
T KOG2253|consen   98 IDDQKLIEN  106 (668)
T ss_pred             CCcchhhcc
Confidence            887766543

>KOG2135|consensus

Probab=94.95  E-value=0.019  Score=41.61  Aligned_cols=74  Identities=19%  Similarity=0.176  Sum_probs=58.3

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETE-ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~-~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +.+.+-+...|...+ -++|...|..||.|..|.+-..      .-.|.|+|.+..+|-+|.. .++..|.++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEe
Confidence            455666666777654 5789999999999988866333      3479999999999866755 5899999999999997


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      ++
T Consensus       444 np  445 (526)
T KOG2135|consen  444 NP  445 (526)
T ss_pred             cC
Confidence            76

>KOG4285|consensus

Probab=94.47  E-value=0.21  Score=34.50  Aligned_cols=71  Identities=18%  Similarity=0.258  Sum_probs=51.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe-EEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR-ILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~-~l~v~~a~  111 (117)
                      +.=|-|-++|+.. ...+...|..||.|.+....   .+   -.+-+|.|.++.+|++|+.+ +|..|+|. .|-|.-+.
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~---~n---gNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP---SN---GNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC---CC---CceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            3446677888774 35688899999998654222   22   34899999999999999995 89888865 35554433

>KOG4410|consensus

Probab=93.78  E-value=0.26  Score=33.94  Aligned_cols=50  Identities=18%  Similarity=0.056  Sum_probs=38.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCe-EEEEEEecCCCCCcceEEEEEeCCHH
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYD   86 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~~~   86 (117)
                      +....+|++||+.++...||+..+.+.+.+ ..+.|.-      +.|-||..|.+..
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg------~~~k~flh~~~~~  378 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKG------HFGKCFLHFGNRK  378 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCCCceeEeeec------CCcceeEecCCcc
Confidence            344569999999999999999999988754 4454532      3667999997653

>KOG0804|consensus

Probab=92.65  E-value=0.95  Score=33.09  Aligned_cols=67  Identities=12%  Similarity=0.258  Sum_probs=57.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCC-CCeEEEEEEecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPF-GAVQSVKVIRDLQTNK-CKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      ++..|+|-.+|...+.-|+..|...+ ..|..++++++   |. ++-...+.|.+..+|....+.+||..+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd---~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRD---GMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeec---CCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            37889999999999999999999875 45789999986   33 3557889999999999999999997765

>KOG4210|consensus

Probab=91.86  E-value=0.17  Score=34.88  Aligned_cols=76  Identities=18%  Similarity=0.065  Sum_probs=57.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ....+.|++++...+.+.+...++..+|............+...++++++.|...+.+..++.........+..+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~  161 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGE  161 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhcccccccccc
Confidence            3567899999999999888888888888765555544445577799999999999999999985433344444433

>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=91.86  E-value=1.2  Score=24.12  Aligned_cols=58  Identities=14%  Similarity=0.214  Sum_probs=33.5

Q ss_pred             CCCHHHHHHhhcCCCC-----eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         44 ETEESVLWQLFGPFGA-----VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        44 ~~~~~~l~~~f~~~g~-----i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .++..+|..++..-+.     |-.+.+...        |+||+-... .+..++..|++..+.|+.++|+.|
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3577788888876543     455656433        899888764 678888999999999999998864

; PDB: 2G0C_A 3MOJ_B.

>KOG4483|consensus

Probab=89.40  E-value=2  Score=31.13  Aligned_cols=58  Identities=14%  Similarity=0.231  Sum_probs=48.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCC-eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS   94 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   94 (117)
                      .+-.+.|-|.++|.....+||...|..|+. -..|.|+.+.       +++..|.+...|..|+..
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            345678899999999999999999999864 4677888763       799999999999999885

>KOG4574|consensus

Probab=86.53  E-value=0.66  Score=36.46  Aligned_cols=72  Identities=25%  Similarity=0.331  Sum_probs=56.8

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe--CCeEEEEEEecC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL--GNRILQVSFKTN  112 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~--~g~~l~v~~a~~  112 (117)
                      +.++.|.+-..+-..|..++..||.+.....+++      --.+.|.|...+.|-.|...++|..+  .|-+.+|.+|+.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            3445555556666788899999999988766665      23799999999999999999999764  477889998875

>KOG2318|consensus

Probab=81.33  E-value=19  Score=27.56  Aligned_cols=80  Identities=19%  Similarity=0.252  Sum_probs=58.3

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHhhcCC----CCeEEEEEEecC----------CC-----------------------
Q psy13319         30 NGSGWCIFVYNLAPE-TEESVLWQLFGPF----GAVQSVKVIRDL----------QT-----------------------   71 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~----g~i~~~~~~~~~----------~~-----------------------   71 (117)
                      ....++|-|-|+.|+ +...+|..+|..|    |.|..|.+....          -+                       
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456778999999998 6778999888764    467777653221          00                       


Q ss_pred             --------------CCcceEEEEEeCCHHHHHHHHHHhCCcEeC--CeEEEEEE
Q psy13319         72 --------------NKCKGFGFVTMTNYDEAVVAIQSLNGYALG--NRILQVSF  109 (117)
Q Consensus        72 --------------~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~--g~~l~v~~  109 (117)
                                    ....=||.|+|.+...|......++|+.+.  +..+-+.|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                          112347789999999999999999999887  45555555

>KOG4676|consensus

Probab=80.90  E-value=0.14  Score=36.61  Aligned_cols=65  Identities=11%  Similarity=-0.047  Sum_probs=48.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      -.++++|++|+..+...++.+.|..+|.+....+-    .+....+|-+.|........++. .+|..+.
T Consensus       150 irRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  150 IRRTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             HHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            34789999999999999999999999987655442    23334567789988777777777 4666554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	117
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		9e-13
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		6e-12
2khc_A	118	Bruno Rrm3+ Length = 118		1e-11
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		5e-11
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-10
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		2e-10
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-09
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-09
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		7e-09
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		3e-08
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		1e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-07
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-07
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-07
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-07
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		2e-07
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-07
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-07
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		4e-07
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		6e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		8e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		9e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-06
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-06
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		1e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-06
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-06
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		4e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		4e-06
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		5e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		5e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		6e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		6e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		6e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		7e-06
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		7e-06
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		7e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		9e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		9e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		9e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-06
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		1e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		1e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		3e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		4e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		6e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		6e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		6e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		6e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		6e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		6e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		7e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		7e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		8e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		9e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-04
2adc_A	229	Solution Structure Of Polypyrimidine Tract Binding		3e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		4e-04
1qm9_A	198	Nmr, Representative Structure Length = 198		4e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		6e-04
2lkz_A	95	Solution Structure Of The Second Rrm Domain Of Rbm5		8e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		8e-04

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 49/81 (60%)
Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  +  L Q+F PFG V S KV  D QTN  K FGFV+  N   A  AI
Sbjct: 25  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 93  QSLNGYALGNRILQVSFKTNK 113
           QS+NG+ +G + L+V  K +K
Sbjct: 85  QSMNGFQIGMKRLKVQLKRSK 105

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 4/83 (4%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           IF+ NL PE +E +L+  F  FG + Q+ K++RD  T   KG+ F+   ++D +  AI++
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 95  LNGYALGNRILQVSF---KTNKG 114
           +NG  L NR + VS+   K +KG
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKG 90

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 48/78 (61%)
Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  ++ L   F PFG V S KV  D QT+  K FGFV+  N D A VAI
Sbjct: 40  GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 93  QSLNGYALGNRILQVSFK 110
           +++NG+ +G + L+V  K
Sbjct: 100 KAMNGFQVGTKRLKVQLK 117

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 46/78 (58%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L+PE     +   F PFG +   +V++D+ T K KG+GFV+  N  +A  AIQ +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 96  NGYALGNRILQVSFKTNK 113
            G  LG R ++ ++ T K
Sbjct: 78  GGQWLGGRQIRTNWATRK 95

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 46/72 (63%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+ +T E  L Q+F  +G +  V V++D +T + +GFGFVT  N D+A  A+ ++
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 96  NGYALGNRILQV 107
           NG ++  R ++V
Sbjct: 75  NGKSVDGRQIRV 86

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 50/83 (60%)
Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           GS + +FV +L+PE   + +   F PFG +   +V++D+ T K KG+GFV+  N  +A  
Sbjct: 4   GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           AIQ + G  LG R ++ ++ T K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L+PE     +   F PFG +   +V++D+ T K KG+GFV+  N  +A  AI  +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 96  NGYALGNRILQVSFKTNK 113
            G  LG R ++ ++ T K
Sbjct: 78  GGQWLGGRQIRTNWATRK 95

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 49/78 (62%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L     E +L  +F PFG ++S++++ D +T + KG+GF+T ++ + A  A++ L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 96  NGYALGNRILQVSFKTNK 113
           NG+ L  R ++V   T +
Sbjct: 89  NGFELAGRPMKVGHVTER 106

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 49/86 (56%), Gaps = 3/86 (3%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            I V NL+ +T E+ L +LF PFG++  + + +D  T + KGF F++    ++A  AI  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 95  LNGYALGNRILQVSF---KTNKGKTS 117
           ++G+   + IL V +    TN G +S
Sbjct: 77  VSGFGYDHLILNVEWAKPSTNSGPSS 102

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 95  LNGYALGNRILQVSFKTNK 113
            NG  L  R ++V F   K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 47/78 (60%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L     E +L  +F PFG + ++ +++D  T + KG+GF+T ++ + A  A++ L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 96  NGYALGNRILQVSFKTNK 113
           NG+ L  R ++V   T +
Sbjct: 68  NGFELAGRPMRVGHVTER 85

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 95  LNGYALGNRILQVSFKTNK 113
            NG  L  R ++V F   K
Sbjct: 77  ANGMELDGRRIRVDFSITK 95

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 14  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 95  LNGYALGNRILQVSFKTNK 113
            NG  L  R ++V F   K
Sbjct: 74  ANGMELDGRRIRVDFSITK 92

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 95  LNGYALGNRILQVS 108
            NG  L  R ++VS
Sbjct: 77  ANGMELDGRRIRVS 90

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 44/81 (54%)
Query: 28  TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
           +M  +   ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 88  AVVAIQSLNGYALGNRILQVS 108
           A  AI ++N   L  R ++V+
Sbjct: 62  AAAAIDNMNESELFGRTIRVN 82

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 24  LPANTMNGSGWCI--FVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
           +P   MN     +   + N  P T +E  L QLF  +G ++SVK++ D +T + +G+GFV
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Query: 81  TMTNYDEAVVAIQSLNGYALGNRILQVSF 109
              +   A  AI  LNG+ + N+ L+V+ 
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVAL 118

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 43/81 (53%)
Query: 29  MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
           M  +   ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 89  VVAIQSLNGYALGNRILQVSF 109
             AI ++N   L  R ++V+ 
Sbjct: 68  AAAIDNMNESELFGRTIRVNL 88

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 42/77 (54%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A  A
Sbjct: 1   SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 92  IQSLNGYALGNRILQVS 108
           I ++N   L  R ++V+
Sbjct: 61  IDNMNESELFGRTIRVN 77

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 44  ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
           +TEE +L  L    G V ++K++ D QT + KG+ F+   + + +  A+++LNGY LG+R
Sbjct: 16  QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 74
Query: 104 ILQVSFKTN 112
            L+  + +N
Sbjct: 75  FLKCGYSSN 83

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L  ET E +L  +FG  G +  V +I+D +T+K +GF F+T  N  +A  A + +
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 96  NGYALGNRILQV 107
           NG +L  + ++V
Sbjct: 69  NGKSLHGKAIKV 80

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 44  ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
           +TEE +L  L    G V ++K++ D QT + KG+ F+   + + +  A+++LNGY LG+R
Sbjct: 15  QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 73
Query: 104 ILQVSFKTN 112
            L+  + +N
Sbjct: 74  FLKCGYSSN 82

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 44  ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
           +TEE +L  L    G V ++K++ D QT + KG+ F+   + + +  A+++LNGY LG+R
Sbjct: 14  QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 72
Query: 104 ILQVSFKTN 112
            L+  + +N
Sbjct: 73  FLKCGYSSN 81

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL    ++  L + F PFG + S KV+  ++  + KGFGFV  ++ +EA  A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 96  NGYALGNRILQVSFKTNK 113
           NG  +  + L V+    K
Sbjct: 76  NGRIVATKPLYVALAQRK 93

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A  AI +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 95  LNGYALGNRILQVS 108
           +N   L  R ++V+
Sbjct: 67  MNESELFGRTIRVN 80

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+  E  E  L  +F   G V S +++ D +T K KG+GF    + + A+ A+++L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 96  NGYALGNRILQVS 108
           NG     R L+V 
Sbjct: 71  NGREFSGRALRVD 83

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A  AI ++
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96  NGYALGNRILQVSF 109
           N   L  R ++V+ 
Sbjct: 126 NESELFGRTIRVNL 139

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +++  L P T +  L +L  P+G + S K I D  TNKCKG+GFV   +   A  A+ +L
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 96 N 96
Sbjct: 68 K 68

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 44/81 (54%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V ++  E  E  + Q F PFG ++S+ +  D  T K KGF FV     + A +A++ +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 96  NGYALGNRILQVSFKTNKGKT 116
           N   LG R ++V   +N G+ 
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQA 111

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 21/89 (23%), Positives = 46/89 (51%)
Query: 21  SSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
             + P    +  GW +FV ++  E +E  + + F  +G ++++ +  D +T   KG+  V
Sbjct: 60  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119
Query: 81  TMTNYDEAVVAIQSLNGYALGNRILQVSF 109
               + +A+ A ++LNG  +  + +QV +
Sbjct: 120 EYETHKQALAAKEALNGAEIMGQTIQVDW 148

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 44/81 (54%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V ++  E  E  + Q F PFG ++S+ +  D  T K KGF FV     + A +A++ +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 96  NGYALGNRILQVSFKTNKGKT 116
           N   LG R ++V   +N G+ 
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQA 96

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 37  FVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
            + N  P+   +     LFG  G ++S K++RD  T +  G+GFV  ++ ++A  AI +L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 96  NGYALGNRILQVSF 109
           NG  L  + ++VS+
Sbjct: 67  NGLKLQTKTIKVSY 80

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  AI+ +
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 71
Query: 96  NGYALGNRILQV-SFKTNKGKTS 117
           NG  L +R + V  FK+ K + +
Sbjct: 72  NGMLLNDRKVFVGRFKSRKEREA 94

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 31  GSGWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
           G G    + N  P+   +  L  LF   G V+S K+IRD       G+GFV      +A 
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 90  VAIQSLNGYALGNRILQVSF 109
            AI +LNG  L ++ ++VS+
Sbjct: 61  RAINTLNGLRLQSKTIKVSY 80

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/94 (24%), Positives = 48/94 (51%)
Query: 21  SSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFV 80
             + P    +  GW +FV ++  E +E  + + F  +G ++++ +  D +T   KG+  V
Sbjct: 14  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73
Query: 81  TMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
               + +A+ A ++LNG  +  + +QV +   KG
Sbjct: 74  EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 37/57 (64%)
Query: 53  LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           LFG  G ++S K++RD  T +  G+GFV  ++ ++A  AI +LNG  L  + ++VS+
Sbjct: 24  LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSY 80

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 4/88 (4%)
Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           GSG  IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  
Sbjct: 4   GSGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60
Query: 91  AIQSLNGYALGNRILQV-SFKTNKGKTS 117
           AI+ +NG  L +R + V  FK+ K + +
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREA 88

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  AI+ +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 158
Query: 96  NGYALGNRILQV-SFKTNKGKTS 117
           NG  L +R + V  FK+ K + +
Sbjct: 159 NGMLLNDRKVFVGRFKSRKEREA 181

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  AI+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 96  NGYALGNRILQV-SFKTNKGKTS 117
           NG  L +R + V  FK+ K + +
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREA 186

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L    ++  L   F  F +  S  V+ D+QT   +G+GFV+ T+ D+A  A+ S+
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96  NGYALGNRILQVSF 109
            G  L  R L++++
Sbjct: 64  QGQDLNGRPLRINW 77

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+P+T E  + + FG FG V+S+++  D +TNK +GF F+T    +E V  I   
Sbjct: 4   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE-EEPVKKIMEK 62
Query: 96  NGYALG 101
             + +G
Sbjct: 63  KYHNVG 68

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 42/81 (51%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V ++  E  E  + Q F PFG ++S+    D  T K KGF FV     + A +A++  
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 96  NGYALGNRILQVSFKTNKGKT 116
           N   LG R ++V   +N G+ 
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQA 95

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+P+T E  + + FG FG V+S+++  D +TNK +GF F+T    +E V  I   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE-EEPVKKIMEK 60
Query: 96  NGYALG 101
             + +G
Sbjct: 61  KYHNVG 66

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 37  FVYNLAPE--TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + N  P+  T+E     LFG  G ++S K++RD  T +  G+GFV   +  +A  AI +
Sbjct: 5   LIVNYLPQNMTQEE-FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 95  LNGYALGNRILQVSF 109
           LNG  L  + ++VS+
Sbjct: 64  LNGLRLQTKTIKVSY 78

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 33  GWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           G    + N  P+   +  L  LF   G V+S K+IRD       G+GFV      +A  A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 92  IQSLNGYALGNRILQVSF 109
           I +LNG  L ++ ++VS+
Sbjct: 61  INTLNGLRLQSKTIKVSY 78

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L    ++  L   F  F +  S  V+ D+QT   +G+GFV+ T+ D+A  A+ S+
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96  NGYALGNRILQVSF 109
            G  L  R L++++
Sbjct: 150 QGQDLNGRPLRINW 163

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 33  GWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           G    + N  P+   +  L  LF   G V+S K+IRD       G+GFV      +A  A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 92  IQSLNGYALGNRILQVSF 109
           I +LNG  L ++ ++VS+
Sbjct: 61  INTLNGLRLQSKTIKVSY 78

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 38/77 (49%)
Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  + V  L     +  L  LF   G V+S K+IRD       G+GFV      +A  AI
Sbjct: 19  GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 93  QSLNGYALGNRILQVSF 109
            +LNG  L ++ ++VS+
Sbjct: 79  NTLNGLRLQSKTIKVSY 95

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 40/85 (47%)
Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P    +  GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    
Sbjct: 15  PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
           Y EA  A++ LNG  L  + + V +
Sbjct: 75  YKEAQAAMEGLNGQDLMGQPISVDW 99

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 40/85 (47%)
Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P    +  GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    
Sbjct: 14  PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 73
Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
           Y EA  A++ LNG  L  + + V +
Sbjct: 74  YKEAQAAMEGLNGQDLMGQPISVDW 98

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 40/85 (47%)
Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P    +  GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    
Sbjct: 1   PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
           Y EA  A++ LNG  L  + + V +
Sbjct: 61  YKEAQAAMEGLNGQDLMGQPISVDW 85

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 23 ILPANTMNGSGWC-IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVT 81
          ++P  +  GS  C +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT
Sbjct: 14 LVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
Query: 82 MTN 84
            +
Sbjct: 74 FMD 76

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 45/90 (50%)
Query: 27  NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
           N    S   + V  L  +  +  L+ LF   G + + ++ RD +T    G+ FV  T+  
Sbjct: 8   NDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX 67
Query: 87  EAVVAIQSLNGYALGNRILQVSFKTNKGKT 116
           ++  AI+ LNG  + N+ L+VS+    G++
Sbjct: 68  DSQRAIKVLNGITVRNKRLKVSYARPGGES 97

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 33/61 (54%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          IFV  L   T ++ L + F  FG ++   VI D QT K +G+GFVTM +   A  A +  
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 96 N 96
          N
Sbjct: 80 N 80

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   +FV     + +ES L ++FGPFG ++ VK++         GF FV     + A  A
Sbjct: 30  SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKA 81
Query: 92  IQSLNGYALGNRILQVSF 109
           I+ ++G +  N+ L+V +
Sbjct: 82  IEEVHGKSFANQPLEVVY 99

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 41/83 (49%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +++ NL+P   E  L  LF  F   +   +   + T + +G  F+T  N + A  A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 95  LNGYALGNRILQVSFKTNKGKTS 117
           +NGY L  +IL + F  NK + S
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRS 109

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 40/82 (48%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+  + E  L +LF  +G +  +    D  T K KGF FVT    + AV A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G     R+L V   T K + S
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEAS 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 45/86 (52%)
Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
            S   + V  L  +  +  L+ LF   G + + +++RD +T    G+ FV  T+  ++  
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 91  AIQSLNGYALGNRILQVSFKTNKGKT 116
           AI+ LNG  + N+ L+VS+    G++
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGES 86

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 38/78 (48%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    Y EA  A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 92  IQSLNGYALGNRILQVSF 109
           ++ LNG  L  + + V +
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 42/76 (55%)
Query: 41  LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL 100
           L  +  +  L+ LF   G + + +++RD +T    G+ FV  T+  ++  AI+ LNG  +
Sbjct: 11  LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 101 GNRILQVSFKTNKGKT 116
            N+ L+VS+    G++
Sbjct: 71  RNKRLKVSYARPGGES 86

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 38/78 (48%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    Y EA  A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 92  IQSLNGYALGNRILQVSF 109
           ++ LNG  L  + + V +
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   +FV     + +ES L ++FGPFG ++ VK++         GF FV     + A  A
Sbjct: 3   SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
Query: 92  IQSLNGYALGNRILQVSF 109
           I+ ++G +  N+ L+V +
Sbjct: 55  IEEVHGKSFANQPLEVVY 72

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 38/78 (48%)
Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    Y EA  A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 92  IQSLNGYALGNRILQVSF 109
           ++ LNG  L  + + V +
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV-AIQS 94
           I+V NL        + +LF  FG V +VK+I D +T K KGFGFV M   +E+V  AI  
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ--EESVSEAIAK 61
Query: 95  LNGYALGNRILQVS 108
           L+      R ++V+
Sbjct: 62  LDNTDFMGRTIRVT 75

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL     E +L++LF   G +  V + +D +  K K FGFV   + +    AI  L
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVSYAIALL 77
Query: 96  NGYALGNRILQVS 108
           NG  L  R + VS
Sbjct: 78  NGIRLYGRPINVS 90

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 30/54 (55%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
          + V  L  +T E  L + F  FG V  V+V +DL+T   KGFGFV  T Y+  V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL P   +    +L  PFG+++   ++   +T + KG+GF      D A  A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96  NGYALGNRILQVSFKTNKGK 115
            G  LG R L V + T+ G+
Sbjct: 158 LGKPLGPRTLYVHW-TDAGQ 176

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL P   +    +L  PFG+++   ++   +T + KG+GF      D A  A   L
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 96  NGYALGNRILQVSFKTNKGK 115
            G  LG R L V + T+ G+
Sbjct: 156 LGKPLGPRTLYVHW-TDAGQ 174

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV NLA    E +L + F  FG ++ VK ++D        + F+     D AV A++ 
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 95  LNGYALGNRILQVSF 109
           +NG  L    +++ F
Sbjct: 65  MNGKDLEGENIEIVF 79

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N+     +  L Q+FG FG +  V++I        KGFGFVT  N  +A  A + L
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 75
Query: 96  NGYALGNRILQVS 108
           +G  +  R ++V+
Sbjct: 76  HGTVVEGRKIEVN 88

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N+     +  L Q+FG FG +  V++I        KGFGFVT  N  +A  A + L
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 89
Query: 96  NGYALGNRILQVS 108
           +G  +  R ++V+
Sbjct: 90  HGTVVEGRKIEVN 102

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL P   +    +L  PFG+++   ++   +T + KG+GF      D A  A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96  NGYALGNRILQVSFKTNKGK 115
            G  LG R L V + T+ G+
Sbjct: 158 LGKPLGPRTLYVHW-TDAGQ 176

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 168 YHTVNGH 174

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 166 YHTVNGH 172

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 167 YHTVNGH 173

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 159
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 160 YHTVNGH 166

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 164
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 165 YHTVNGH 171

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE----AVVA 91
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D      +  
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 92  IQSLNGY 98
             ++NG+
Sbjct: 167 YHTVNGH 173

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV  L+ +T E  L + F   G+V+  +++ D +T   KGFGFV   + ++A  A ++
Sbjct: 17  TLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 95  L-NGYALGNRI 104
           + +G   GN++
Sbjct: 74  MEDGEIDGNKV 84

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTM---TNYDEAVVAI 92
           +F+  L  +T E  L + FG +G V  +K+++D  T + +GFGF++    ++ DE V   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 93  QSLNGYAL 100
             L+G  +
Sbjct: 66  HILDGKVI 73

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
          +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT  +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 19  LASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFG 78
           + S + P          +FV NL  +  E    +LF  +G    V + RD      +GFG
Sbjct: 8   IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFG 61
Query: 79  FVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN 112
           F+ + +   A +A   L+G  L +R L++ F T+
Sbjct: 62  FIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein Rbd34 Complexed With Cucucu Rna Length = 229

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 8/81 (9%)
Query: 35  CIFVYNLAPE--TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
            + V NL PE  T +S L+ LFG +G VQ VK++ + + N       V M + ++A +A+
Sbjct: 36  VLLVSNLNPERVTPQS-LFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAM 89
Query: 93  QSLNGYALGNRILQVSFKTNK 113
             LNG+ L  + ++++   ++
Sbjct: 90  SHLNGHKLHGKPIRITLSKHQ 110

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L  +FG +G++    ++RD  T + +G  FV     +EA  AI +L
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 96  NGYAL--GNRILQVSFKTNKGK 115
           N      G++ L V      GK
Sbjct: 76  NNVIPEGGSQPLSVRLAEEHGK 97

>pdb|1QM9|A Chain A, Nmr, Representative Structure Length = 198

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 8/81 (9%)
Query: 35  CIFVYNLAPE--TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
            + V NL PE  T +S L+ LFG +G VQ VK++ + + N       V M + ++A +A+
Sbjct: 5   VLLVSNLNPERVTPQS-LFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAM 58
Query: 93  QSLNGYALGNRILQVSFKTNK 113
             LNG+ L  + ++++   ++
Sbjct: 59  SHLNGHKLHGKPIRITLSKHQ 79

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+  E  + +LF  +G    V + +D      KGFGF+ +     A +A   L
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 96  NGYALGNRILQVSF 109
           +   L  + L+V F
Sbjct: 72  DNMPLRGKQLRVRF 85

>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5 Length = 95

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 35 CIFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           I + N+AP T    +     P+   AV ++++I+D QT + +GF FV +++  +A   +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 93 QSLNG 97
          Q L  
Sbjct: 71 QILQS 75

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 3/86 (3%)
Query: 30  NGSGWCIFVYNLAPETEESVLWQLF-GPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
           +G  + +FV +L P+ ++ +L++ F   + + +  KV+ D QT   KG+GFV  T+  E 
Sbjct: 6   SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQ 64
Query: 89  VVAIQSLNG-YALGNRILQVSFKTNK 113
             A+    G   LG++ +++S    K
Sbjct: 65  KRALTECQGAVGLGSKPVRLSVAIPK 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	117
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-37
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-37
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-35
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-33
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-30
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-30
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-29
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-29
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-29
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-28
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-28
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-28
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-28
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-27
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-27
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-27
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-27
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-27
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-26
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-22
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-26
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-26
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-26
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-26
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-26
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-26
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-26
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-26
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-25
2div_A	99	TRNA selenocysteine associated protein; structural	1e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-25
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-25
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-25
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-24
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-25
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-25
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-25
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-24
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-24
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-24
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-17
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-24
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-24
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-24
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-24
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-24
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-23
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-23
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-23
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-23
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-23
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-23
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-23
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-23
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-22
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-20
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-22
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-22
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-22
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-22
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-19
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-22
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-21
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-21
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-21
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-18
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-21
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-21
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-14
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-21
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-21
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-19
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-21
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-21
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-21
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-21
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-21
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-17
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-20
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-20
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-20
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-20
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-20
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-20
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	9e-20
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-19
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-19
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-19
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-19
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-19
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-19
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-19
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-18
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-17
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-17
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-17
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-17
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-17
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-17
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-17
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-17
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-17
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-17
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-16
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-17
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-16
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-16
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-15
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-15
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-14
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-14
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-14
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-13
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-11
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-08
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-07
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	2e-04

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  121 bits (306), Expect = 2e-37
 Identities = 40/104 (38%), Positives = 57/104 (54%), Gaps = 3/104 (2%)

Query: 10  RFSPLTGDLL--ASSILPANTMNG-SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI 66
             SPL    L  A++      + G  G  +F+Y+L  E  ++ L   F PFG V S KV 
Sbjct: 14  STSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVF 73

Query: 67  RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK 110
            D QT+  K FGFV+  N D A VAI+++NG+ +G + L+V  K
Sbjct: 74  IDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 =  120 bits (303), Expect = 5e-37
 Identities = 37/83 (44%), Positives = 49/83 (59%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            G  +F+Y+L  E  +  L Q+F PFG V S KV  D QTN  K FGFV+  N   A  A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83

Query: 92  IQSLNGYALGNRILQVSFKTNKG 114
           IQS+NG+ +G + L+V  K +K 
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKN 106

>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 =  116 bits (292), Expect = 2e-35
 Identities = 29/89 (32%), Positives = 49/89 (55%), Gaps = 3/89 (3%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
               I V NL+ +T E+ L +LF PFG++  + + +D  T + KGF F++    ++A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 92  IQSLNGYALGNRILQVSF---KTNKGKTS 117
           I  ++G+   + IL V +    TN G +S
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTNSGPSS 102

>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 =  109 bits (276), Expect = 3e-33
 Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 5/84 (5%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
            + +       +++  L P T +  L +L  P+G + S K I D  TNKCKG+GFV   +
Sbjct: 2   SSGSSG-----LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 56

Query: 85  YDEAVVAIQSLNGYALGNRILQVS 108
              A  A+ +L    +  ++ + S
Sbjct: 57  PSAAQKAVTALKASGVQAQMAKQS 80

>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 =  101 bits (255), Expect = 6e-30
 Identities = 31/83 (37%), Positives = 50/83 (60%)

Query: 31  GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
           GS + +FV +L+PE   + +   F PFG +   +V++D+ T K KG+GFV+  N  +A  
Sbjct: 4   GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           AIQ + G  LG R ++ ++ T K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>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 =  103 bits (259), Expect = 9e-30
 Identities = 22/83 (26%), Positives = 45/83 (54%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV ++  E +E  + + F  +G ++++ +  D +T   KG+  V    + +A+ A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 92  IQSLNGYALGNRILQVSFKTNKG 114
            ++LNG  +  + +QV +   KG
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKG 153

>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 =  102 bits (257), Expect = 1e-29
 Identities = 25/80 (31%), Positives = 45/80 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  +    +E  L QLF  +G ++SVK++ D +T + +G+GFV   +   A  AI  L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 96  NGYALGNRILQVSFKTNKGK 115
           NG+ + N+ L+V+   +  +
Sbjct: 105 NGFNILNKRLKVALAASGHQ 124

>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 =  100 bits (251), Expect = 6e-29
 Identities = 23/86 (26%), Positives = 40/86 (46%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    Y EA  A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 92  IQSLNGYALGNRILQVSFKTNKGKTS 117
           ++ LNG  L  + + V +   +G   
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPK 106

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 99.3 bits (248), Expect = 9e-29
 Identities = 24/90 (26%), Positives = 42/90 (46%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P    +  GW +FV  +  E  E  +   F  +G ++++ +  D +T   KG+  V    
Sbjct: 15  PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
           Y EA  A++ LNG  L  + + V +   +G
Sbjct: 75  YKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>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 = 98.5 bits (246), Expect = 3e-28
 Identities = 24/79 (30%), Positives = 39/79 (49%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +++ NL+P   E  L  LF  F   +   +   + T + +G  F+T  N + A  A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 95  LNGYALGNRILQVSFKTNK 113
           +NGY L  +IL + F  NK
Sbjct: 87  VNGYKLYGKILVIEFGKNK 105

>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 = 98.1 bits (245), Expect = 3e-28
 Identities = 22/83 (26%), Positives = 45/83 (54%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            GW +FV ++  E +E  + + F  +G ++++ +  D +T   KG+  V    + +A+ A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 92  IQSLNGYALGNRILQVSFKTNKG 114
            ++LNG  +  + +QV +   KG
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKG 107

>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 = 96.8 bits (242), Expect = 5e-28
 Identities = 24/78 (30%), Positives = 42/78 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L    ++  L   F  F +  S  V+ D+QT   +G+GFV+ T+ D+A  A+ S+
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 96  NGYALGNRILQVSFKTNK 113
            G  L  R L++++    
Sbjct: 64  QGQDLNGRPLRINWAAKL 81

>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 = 97.4 bits (243), Expect = 7e-28
 Identities = 29/78 (37%), Positives = 46/78 (58%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L+PE     +   F PFG +   +V++D+ T K KG+GFV+  N  +A  AIQ +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 96  NGYALGNRILQVSFKTNK 113
            G  LG R ++ ++ T K
Sbjct: 78  GGQWLGGRQIRTNWATRK 95

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 97.9 bits (244), Expect = 8e-28
 Identities = 23/75 (30%), Positives = 37/75 (49%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V NL   T    L ++F  +G V  V + RD  T + +GF FV   +  +A  A+ +
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108

Query: 95  LNGYALGNRILQVSF 109
           ++G  L  R L+V  
Sbjct: 109 MDGAVLDGRELRVQM 123

>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 = 96.7 bits (241), Expect = 2e-27
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 95  LNGYALGNRILQVSF 109
            NG  L  R ++V F
Sbjct: 108 ANGMELDGRRIRVDF 122

>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 = 95.8 bits (239), Expect = 2e-27
 Identities = 21/82 (25%), Positives = 46/82 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ ++  +  E  +  L    G V ++K++ D QT + KG+ F+   + + +  A+++L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NGY LG+R L+  + +N   + 
Sbjct: 65  NGYQLGSRFLKCGYSSNSDISG 86

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 96.4 bits (240), Expect = 4e-27
 Identities = 24/74 (32%), Positives = 41/74 (55%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A  AI ++
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

Query: 96  NGYALGNRILQVSF 109
           N   L  R ++V+ 
Sbjct: 126 NESELFGRTIRVNL 139

>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 = 94.1 bits (235), Expect = 6e-27
 Identities = 25/81 (30%), Positives = 44/81 (54%)

Query: 28  TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
           +M  +   ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 88  AVVAIQSLNGYALGNRILQVS 108
           A  AI ++N   L  R ++V+
Sbjct: 62  AAAAIDNMNESELFGRTIRVN 82

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 94.2 bits (235), Expect = 9e-27
 Identities = 28/82 (34%), Positives = 40/82 (48%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+  + E  L +LF  +G +  +    D  T K KGF FVT    + AV A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G     R+L V   T K + S
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEAS 92

>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 = 96.1 bits (240), Expect = 1e-26
 Identities = 23/82 (28%), Positives = 44/82 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L  +  +  L+ LF   G + + +++RD +T    G+ FV  T+  ++  AI+ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NG  + N+ L+VS+    G++ 
Sbjct: 66  NGITVRNKRLKVSYARPGGESI 87

>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 = 84.9 bits (211), Expect = 2e-22
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L  +FG +G++    ++RD  T + +G  FV     +EA  AI +L
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 96  NGYAL--GNRILQVSF 109
           N      G++ L V  
Sbjct: 152 NNVIPEGGSQPLSVRL 167

>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 = 94.3 bits (235), Expect = 1e-26
 Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 5/89 (5%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
            A  M      ++V +L     E +L  +F PFG ++S++++ D +T + KG+GF+T ++
Sbjct: 23  SAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
            + A  A++ LNG+ L  R ++V   T +
Sbjct: 78  SECAKKALEQLNGFELAGRPMKVGHVTER 106

>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 = 95.7 bits (238), Expect = 1e-26
 Identities = 23/75 (30%), Positives = 37/75 (49%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V NL   T    L ++F  +G V  V + RD  T + +GF FV   +  +A  A+ +
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131

Query: 95  LNGYALGNRILQVSF 109
           ++G  L  R L+V  
Sbjct: 132 MDGAVLDGRELRVQM 146

>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 = 93.4 bits (233), Expect = 2e-26
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 95  LNGYALGNRILQVSF 109
            NG  L  R ++VS 
Sbjct: 77  ANGMELDGRRIRVSG 91

>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 = 93.4 bits (233), Expect = 2e-26
 Identities = 24/74 (32%), Positives = 41/74 (55%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A  AI ++
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 96  NGYALGNRILQVSF 109
           N   L  R ++V+ 
Sbjct: 75  NESELFGRTIRVNL 88

>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 = 93.4 bits (233), Expect = 2e-26
 Identities = 23/74 (31%), Positives = 45/74 (60%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L     E +L  +F PFG + ++ +++D  T + KG+GF+T ++ + A  A++ L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

Query: 96  NGYALGNRILQVSF 109
           NG+ L  R ++V  
Sbjct: 68  NGFELAGRPMRVGH 81

>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 = 92.7 bits (231), Expect = 3e-26
 Identities = 21/78 (26%), Positives = 39/78 (50%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   ++V NL      + L+++F  +G V  V +++D  T K KG  F+   + D A   
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 92  IQSLNGYALGNRILQVSF 109
            +++N   L  R+++ S 
Sbjct: 75  TRAINNKQLFGRVIKASI 92

>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 = 97.4 bits (243), Expect = 4e-26
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 35  CIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           C+ V  L P   +   L +      +    ++    Q  + KGF  +     + A  A Q
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQ 244

Query: 94  SLNGYALGNRILQVSFKTNK 113
             +G +LG   L+VSF    
Sbjct: 245 QADGLSLGGSHLRVSFCAPG 264

>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 = 96.2 bits (240), Expect = 1e-25
 Identities = 24/82 (29%), Positives = 36/82 (43%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL P   +    +L  PFG+++   ++   +T + KG+GF      D A  A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
            G  LG R L V +      T 
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTP 179

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 75.0 bits (185), Expect = 1e-17
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I +  L  +     +  L   +  ++   V +       KG  FVT+ N ++A  AI + 
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY------KGTAFVTLLNGEQAEAAINAF 77

Query: 96  NGYALGNRILQVSFKTNK 113
           +   L  R L V  +   
Sbjct: 78  HQSRLRERELSVQLQPTD 95

>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 = 92.7 bits (231), Expect = 4e-26
 Identities = 22/75 (29%), Positives = 35/75 (46%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V NL   T    L ++F  +G V  V + R+  T   +GF FV   +  +A  A  +
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 95  LNGYALGNRILQVSF 109
           ++G  L  R L+V  
Sbjct: 75  MDGAELDGRELRVQV 89

>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 = 92.3 bits (230), Expect = 5e-26
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL    ++  L + F PFG + S KV+ +    + KGFGFV  ++ +EA  A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 96  NGYALGNRILQVSFKTNK 113
           NG  +  + L V+    K
Sbjct: 76  NGRIVATKPLYVALAQRK 93

>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 = 92.3 bits (230), Expect = 7e-26
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  AI+ +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 96  NGYALGNRILQVSFKTNK 113
           NG  L +R + V    ++
Sbjct: 66  NGMLLNDRKVFVGRFKSR 83

>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 = 94.7 bits (236), Expect = 8e-26
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L     +  + +L   FG +++  +++D  T   KG+ F    + +    AI  L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NG  LG++ L V   +   K +
Sbjct: 177 NGMQLGDKKLLVQRASVGAKNA 198

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 74.3 bits (183), Expect = 7e-18
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 6/85 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVK-----VIRDLQTNKCKGFGFVTMTNYDEAVV 90
           ++V N+     E  +   F     +  +       +  +Q N+ K F F+   + DE   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 91  AIQSLNGYALGNRILQVSFKTNKGK 115
           A+   +G     + L++    +   
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQP 90

>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 = 93.3 bits (232), Expect = 1e-25
 Identities = 20/75 (26%), Positives = 39/75 (52%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V NL+  T E  +++LF   G ++ + +  D       GF FV   +  +A  A++ 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 95  LNGYALGNRILQVSF 109
           +NG  L +RI++  +
Sbjct: 101 INGTRLDDRIIRTDW 115

>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 = 91.6 bits (228), Expect = 1e-25
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 26  ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTN 84
           ++  +G    +++ +L P  +E+ + + F   G  V SVK+IR+  T    G+ FV   +
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTN 112
              A   +  +NG  L        FK N
Sbjct: 62  LATAEKCLHKINGKPLPGATPAKRFKLN 89

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 93.0 bits (232), Expect = 1e-25
 Identities = 24/74 (32%), Positives = 39/74 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L     +     LFG  G ++S K++RD  T +  G+GFV   +  +A  AI +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 96  NGYALGNRILQVSF 109
           NG  L  + ++VS+
Sbjct: 65  NGLRLQTKTIKVSY 78

>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 = 81.5 bits (202), Expect = 5e-21
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L     +  L QLF  +G + + +++ D  T   +G GF+      EA  AI+ L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 96  NGYAL--GNRILQVSF 109
           NG         + V F
Sbjct: 151 NGQKPSGATEPITVKF 166

>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 = 90.8 bits (226), Expect = 2e-25
 Identities = 27/75 (36%), Positives = 46/75 (61%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV  L+ +T E  L Q+F  +G +  V V++D +T + +GFGFVT  N D+A  A+ +
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 95  LNGYALGNRILQVSF 109
           +NG ++  R ++V  
Sbjct: 74  MNGKSVDGRQIRVDQ 88

>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 = 90.8 bits (226), Expect = 2e-25
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V  L  +  E +LW+LF   G V +  + +D  T + +G+GFV   + ++A  AI+ 
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76

Query: 95  LNGYALGNRILQV 107
           ++   L  + ++V
Sbjct: 77  MDMIKLYGKPIRV 89

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 91.2 bits (227), Expect = 2e-25
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L  ET E +L  +FG  G +  V +I+D +T+K +GF F+T  N  +A  A + +
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68

Query: 96  NGYALGNRILQV 107
           NG +L  + ++V
Sbjct: 69  NGKSLHGKAIKV 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 90.9 bits (226), Expect = 3e-25
 Identities = 14/74 (18%), Positives = 31/74 (41%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +    L     E+ L  +   +G V+ V+++   +T K  G   V  T+   A   +++L
Sbjct: 9   VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68

Query: 96  NGYALGNRILQVSF 109
           +  ++   I+    
Sbjct: 69  HLTSVMGNIIHAQL 82

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.5 bits (233), Expect = 3e-25
 Identities = 21/82 (25%), Positives = 39/82 (47%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V ++  +  +  +  +F  FG ++S  + RD  T K KG+GF+       +  A+ S+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           N + LG + L+V          
Sbjct: 188 NLFDLGGQYLRVGKAVTPPMPL 209

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 91.2 bits (227), Expect = 3e-24
 Identities = 26/80 (32%), Positives = 44/80 (55%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V ++  E  E  + Q F PFG ++S+ +  D  T K KGF FV     + A +A++ +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 96  NGYALGNRILQVSFKTNKGK 115
           N   LG R ++V   +N G+
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQ 110

>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 = 89.6 bits (223), Expect = 7e-25
 Identities = 25/78 (32%), Positives = 42/78 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+  E  E  L  +F   G V S +++ D +T K KG+GF    + + A+ A+++L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 96  NGYALGNRILQVSFKTNK 113
           NG     R L+V    ++
Sbjct: 71  NGREFSGRALRVDNAASE 88

>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 = 89.2 bits (222), Expect = 7e-25
 Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 3/93 (3%)

Query: 20  ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
           +S + PA         +FV NL     E +L++LF   G +  V + +D +  K K FGF
Sbjct: 5   SSGMFPAQEEADR--TVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGF 61

Query: 80  VTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN 112
           V   + +    AI  LNG  L  R + VS  ++
Sbjct: 62  VCFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94

>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 = 89.2 bits (222), Expect = 7e-25
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+  E  + +LF  +G    V + +D      KGFGF+ +     A +A   L
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +   L  + L+V F  +    +
Sbjct: 72  DNMPLRGKQLRVRFACHSASLT 93

>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 = 89.2 bits (222), Expect = 1e-24
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL    +E  L  +  PFG V S +++RD  +   +G GF  M + ++    I   
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 96  NGYALGNRILQVS 108
           NG  +       +
Sbjct: 87  NGKFIKTPPGVSA 99

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 88.9 bits (221), Expect = 2e-24
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 20  ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
            SS LP++   G    +F+ NL+ ++EE  L ++   FG ++ V+V+    T   KG  F
Sbjct: 4   GSSGLPSDVTEGK--TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 80  VTMTNYDEAVVAIQSLN------GYALGNRILQVSF 109
                 + A   + + +      G  L  R L+V  
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97

>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 = 89.9 bits (224), Expect = 2e-24
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV +L    ++  L   F  F +  S  V+ D+QT   +G+GFV+ T+ D+A  A+ S+
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 96  NGYALGNRILQVSF 109
            G  L  R L++++
Sbjct: 150 QGQDLNGRPLRINW 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 = 81.0 bits (201), Expect = 6e-21
 Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     E +L Q F   G + ++K++ D + NK   + FV      +A +A+Q+L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NG  + N I+++++     ++S
Sbjct: 62  NGKQIENNIVKINWAFQSQQSS 83

>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 = 90.0 bits (224), Expect = 2e-24
 Identities = 19/73 (26%), Positives = 35/73 (47%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L     +  + +L   FG +++  +++D  T   KG+ F    + +    AI  L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 96  NGYALGNRILQVS 108
           NG  LG++ L V 
Sbjct: 157 NGMQLGDKKLLVQ 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 = 72.6 bits (179), Expect = 1e-17
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVK-----VIRDLQTNKCKGFGFVTMTNYDEAVV 90
           ++V N+     E  +   F     +  +       +  +Q N+ K F F+   + DE   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 91  AIQSLNGYALGNRILQV 107
           A+   +G     + L++
Sbjct: 67  AMA-FDGIIFQGQSLKI 82

>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 = 87.6 bits (218), Expect = 3e-24
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V NL        + +LF  FG V +VK+I D +T K KGFGFV M   +    AI  L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62

Query: 96  NGYALGNRILQVS 108
           +      R ++V+
Sbjct: 63  DNTDFMGRTIRVT 75

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 87.7 bits (218), Expect = 3e-24
 Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L     +  L ++    G V+ ++++ + +  K KG  +V   N  +A  A+  +
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKM 78

Query: 96  NGYALGNRILQVSF---KTNKG 114
           +G  +   I++V+      + G
Sbjct: 79  DGMTIKENIIKVAISNSGPSSG 100

>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 = 87.3 bits (217), Expect = 5e-24
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N+     +  L Q+FG FG +  V++I +      KGFGFVT  N  +A  A + L
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKL 75

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G  +  R ++V+  T +  T+
Sbjct: 76  HGTVVEGRKIEVNNATARVMTN 97

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 87.3 bits (217), Expect = 5e-24
 Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           IF+ NL PE +E +L+  F  FG +    K++RD  T   KG+ F+   ++D +  AI++
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 95  LNGYALGNRILQVSFKTNK 113
           +NG  L NR + VS+   K
Sbjct: 68  MNGQYLCNRPITVSYAFKK 86

>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 = 86.4 bits (215), Expect = 7e-24
 Identities = 12/75 (16%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRD-LQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + +  L     +  + ++F  +G ++ + +  + +  +  KG+ +V   N DEA  A++ 
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 95  LNGYALGNRILQVSF 109
           ++G  +  + +  + 
Sbjct: 67  MDGGQIDGQEITATA 81

>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 = 86.5 bits (215), Expect = 9e-24
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V NL+ +  E ++ QLF   G  +S K+I +  +N    + FV    + +A  A+ +
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74

Query: 95  LNGYALGNRILQVSFKTNKGKTS 117
           +NG  +  + ++V++ T      
Sbjct: 75  MNGRKILGKEVKVNWATTPSSQK 97

>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 = 86.6 bits (215), Expect = 1e-23
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVV 90
           +   I V N+  +  +  + +LF  FG +++V++ + +  T   +GFGFV      +A  
Sbjct: 14  TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73

Query: 91  AIQSL-NGYALGNRILQVSFKTNKGKTS 117
           A  +L +   L  R L + +  ++    
Sbjct: 74  AFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 86.6 bits (215), Expect = 1e-23
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  +    +E  L  LF  FG +  + V++D  T   KG  F+T    + A+ A  +L
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 96  NGYAL---GNRILQVSFKTNKGK 115
           +        NR +QV    ++ +
Sbjct: 76  HEQKTLPGMNRPIQVKPADSESR 98

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 86.2 bits (214), Expect = 2e-23
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V N+     +  L Q+FG FG +  V++I +      KGFGFVT  N  +A  A + 
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREK 88

Query: 95  LNGYALGNRILQVSF 109
           L+G  +  R ++V+ 
Sbjct: 89  LHGTVVEGRKIEVNN 103

>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 = 85.4 bits (212), Expect = 3e-23
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKC---KGFGFVTMTNYDEAVVAI 92
           +F+ NL   T E  L  +F   GA++S  + +           GFGFV     ++A  A+
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 93  QSLNGYALGNRILQVSFKTNKGK 115
           + L G+ +    L+V       K
Sbjct: 68  KQLQGHTVDGHKLEVRISERATK 90

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 85.1 bits (211), Expect = 3e-23
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 12/99 (12%)

Query: 11  FSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ 70
            +P   D +  S  P  T        ++ N+     E+ L  LF  FG +   K   +  
Sbjct: 11  VNPQAVDHIIRSAPPRVTT------AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-- 62

Query: 71  TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
               KG  F+    +++A V I +L  +    R L+  +
Sbjct: 63  ----KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 84.7 bits (210), Expect = 4e-23
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           I + N+AP T    +     P+ +  V ++++I+D QT + +GF FV +++  +A   +Q
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 94  SLNG----YALGNRILQVSF 109
            L        +  + + V F
Sbjct: 72  ILQSLHPPLKIDGKTIGVDF 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 = 85.1 bits (211), Expect = 5e-23
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +     L ++F   G V    ++ D +  K +G G VT     EAV AI   
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 96  NGYALGNRILQVSFKTNK 113
           NG  L +R + V      
Sbjct: 77  NGQLLFDRPMHVKMDERA 94

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 84.5 bits (210), Expect = 5e-23
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 26  ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY 85
            ++ +     IFV NL  +    +L   F   G V    +  +    K KG G V   + 
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58

Query: 86  DEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           + A  A + +NG  L  R + V    N   
Sbjct: 59  EVAERACRMMNGMKLSGREIDVRIDRNASG 88

>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 = 84.3 bits (209), Expect = 1e-22
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +G  + V NL     ++ + +LF  FG ++   V  D ++ +  G   V      +A+ A
Sbjct: 34  TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKA 92

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           ++   G  L  R + +    ++
Sbjct: 93  MKQYKGVPLDGRPMDIQLVASQ 114

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 83.8 bits (208), Expect = 1e-22
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV  L+ +T E  L + F         +++ D +T   KGFGFV   + ++A  A ++
Sbjct: 17  TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 95  LNGYALGNRILQVSFKTNKGK 115
           +    +    + + +   KG+
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGE 94

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 86.6 bits (215), Expect = 1e-22
 Identities = 18/81 (22%), Positives = 43/81 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L P+  E++L++ F P G + S++V RD+ T +  G+ +V      +A  A+ ++
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 96  NGYALGNRILQVSFKTNKGKT 116
           N   +  + +++ +       
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSL 98

>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 = 81.2 bits (201), Expect = 2e-20
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IF+ NL    +   L+  F  FG + S KV+ D   N  KG+GFV     + A  AI+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 96  NGYALGNRILQVSFKTNK 113
           NG  L +R + V    ++
Sbjct: 164 NGMLLNDRKVFVGRFKSR 181

>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 = 83.1 bits (206), Expect = 2e-22
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +G  + V NL     ++ + +LF  FG ++   V  D ++ +  G   V      +A+ A
Sbjct: 28  TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKA 86

Query: 92  IQSLNGYALGNRILQVSF 109
           ++  NG  L  R + +  
Sbjct: 87  MKQYNGVPLDGRPMNIQL 104

>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 = 82.6 bits (205), Expect = 3e-22
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V N+        L   F   G+V  V ++ D  +   KGF ++  ++  E+V    +L
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLAL 67

Query: 96  NGYALGNRILQVSFK-TNK 113
           +      R ++V  K TN+
Sbjct: 68  DESLFRGRQIKVIPKRTNR 86

>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 = 86.3 bits (213), Expect = 3e-22
 Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 2/85 (2%)

Query: 27  NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTN 84
            T  G    +++ NL   T +  L +     G   +  +K   +    + KGF  V + +
Sbjct: 62  YTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS 121

Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
              +   +  L    L  +   V+ 
Sbjct: 122 EASSKKLMDLLPKRELHGQNPVVTP 146

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 84.9 bits (210), Expect = 3e-22
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +G  + V NL     ++ + +LF  FG ++   V  D ++ +  G   V      +A+ A
Sbjct: 87  TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKA 145

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           ++   G  L  R + +    ++
Sbjct: 146 MKQYKGVPLDGRPMDIQLVASQ 167

>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 = 82.8 bits (205), Expect = 4e-22
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++   +A    + ++ Q F PFG +  ++V  +      KG+ FV  + ++ A  AI S+
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81

Query: 96  NGYALGNRILQVSF 109
           NG  +   +++  +
Sbjct: 82  NGTTIEGHVVKCYW 95

>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 = 83.2 bits (206), Expect = 4e-22
 Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V N+   +    L   F   G++  + ++ D  +   KG+ ++       +V A  ++
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVAM 97

Query: 96  NGYALGNRILQVSFK 110
           +      R ++V  K
Sbjct: 98  DETVFRGRTIKVLPK 112

>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 = 85.9 bits (213), Expect = 7e-22
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL  +  E    +LF  +G    V + RD      +GFGF+ + +   A +A   L
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78

Query: 96  NGYALGNRILQVSFKTNKGK 115
           +G  L +R L++ F T+   
Sbjct: 79  DGTILKSRPLRIRFATHGAA 98

>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 = 77.8 bits (192), Expect = 9e-19
 Identities = 21/83 (25%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL+P     +L Q F  FG V+   V+ D    +  G GFV       A  A++  
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157

Query: 96  NGYAL----GNRILQVSFKTNKG 114
              A       R + V       
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFD 180

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 81.7 bits (202), Expect = 8e-22
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + + N+ P  +  VL  L   +G V+S + +             VT ++ D+A  A+  L
Sbjct: 18  LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKL 74

Query: 96  NGYALGNRILQVSFKTNK 113
           NG+ L N  L+V++  ++
Sbjct: 75  NGFQLENFTLKVAYIPDE 92

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 83.0 bits (205), Expect = 1e-21
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 2/103 (1%)

Query: 9   QRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGA--VQSVKVI 66
           Q  SP   +   + +   + +      ++V + +  T +  L Q+    G   V  +K  
Sbjct: 31  QEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFA 90

Query: 67  RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
            +    + KG+  V + + +     ++ L G  L    + V  
Sbjct: 91  ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP 133

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 81.6 bits (202), Expect = 1e-21
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV     + +ES L ++FGPFG ++ VK++         GF FV     + A  AI+ +
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85

Query: 96  NGYALGNRILQVSF 109
           +G +  N+ L+V +
Sbjct: 86  HGKSFANQPLEVVY 99

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 81.2 bits (201), Expect = 1e-21
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + + NL+    E  L ++F     +     +   Q  K KG+ F+   ++++A  A+ S
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 95  LNGYALGNRILQVSFKTNKGK 115
            N   +  R +++  +  +G 
Sbjct: 73  CNKREIEGRAIRLELQGPRGS 93

>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 = 81.6 bits (202), Expect = 1e-21
 Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F   LA       L   F   G V+ V++I D  + + KG  +V         +AI  L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 96  NGYALGNRILQVSFK-TNKGKTS 117
            G  L    + V      K + S
Sbjct: 87  TGQRLLGVPIIVQASQAEKNRLS 109

>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 = 84.3 bits (208), Expect = 2e-21
 Identities = 27/110 (24%), Positives = 41/110 (37%), Gaps = 12/110 (10%)

Query: 5   NKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVK 64
           N  L RF         +   P+ T       + + N+ P   E  L  LF   G V    
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSAT-------LHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182

Query: 65  VIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-RILQVSFKTNK 113
                   K +    + M + +EAV A+  L+ + LG    L+VSF  + 
Sbjct: 183 KFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 71.6 bits (175), Expect = 1e-16
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + V NL PE      L+ LFG +G VQ VK++        K    V M + ++A +A+  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMSH 91

Query: 95  LNGYALGNRILQVSFKTNKGKTS 117
           LNG+ L  + ++++   ++    
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQL 114

>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 = 84.7 bits (210), Expect = 3e-21
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 36  IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQ 93
           I + NL+ E  +E++L + F  FG+++ + +    +  +      F+   N D A  A+Q
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272

Query: 94  SLNGYALGNRILQVSFKTNK 113
            +N   LGNR + VS    K
Sbjct: 273 -MNRSLLGNREISVSLADKK 291

>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 = 80.8 bits (200), Expect = 1e-19
 Identities = 13/75 (17%), Positives = 30/75 (40%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ N  P   +  +  L      V     +  L+ N  + F ++ +T+ ++A   ++ L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 96  NGYALGNRILQVSFK 110
           NG  +    L     
Sbjct: 180 NGLKIEGYTLVTKVS 194

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 75.4 bits (186), Expect = 7e-18
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 2/69 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL     ++ +++ F   G +  V V       K   F  +    YD A+ AI   
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101

Query: 96  NGYALGNRI 104
           +     N I
Sbjct: 102 HKVVGQNEI 110

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 80.5 bits (199), Expect = 3e-21
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYDE 87
           IFV  L        +   F   G +++        + +  D +T K KG   V+  +   
Sbjct: 10  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69

Query: 88  AVVAIQSLNGYALGNRILQVSFKTNKGK 115
           A  AI   +G       ++VSF T +  
Sbjct: 70  AKAAIDWFDGKEFSGNPIKVSFATRRAD 97

>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 = 80.4 bits (199), Expect = 3e-21
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NLA    E +L + F  FG ++ VK ++D        + F+     D AV A++ +
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65

Query: 96  NGYALGNRILQVSF 109
           NG  L    +++ F
Sbjct: 66  NGKDLEGENIEIVF 79

>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 = 80.5 bits (199), Expect = 3e-21
 Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 34  WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
             +++ NL  +     ++ +FG +G ++ ++V    +T   +G  +V   +  +A  A+ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65

Query: 94  SLNGYALGNRILQVSFKTNK 113
            L+G+ + NR L V +    
Sbjct: 66  HLSGFNVSNRYLVVLYYNAN 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 = 82.8 bits (204), Expect = 3e-21
 Identities = 12/85 (14%), Positives = 28/85 (32%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
             N +      +  +N   E  E   +++    G  +   V      ++    G +   +
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDS 174

Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
             +A+  +  LN Y + N      +
Sbjct: 175 KSDALETLGFLNHYQMKNPNGPYPY 199

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 65.9 bits (160), Expect = 1e-14
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 36  IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + VY L         ++ +F  +G V+ VK ++        G   V M +      AI  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61

Query: 95  LNGYALGNRILQVSF 109
           LN   +  + + V  
Sbjct: 62  LNNNFMFGQKMNVCV 76

>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 = 80.1 bits (198), Expect = 5e-21
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 8/92 (8%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMT 83
               I+V  L        L   F   G V+         + +  D +T K KG   V+  
Sbjct: 14  DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73

Query: 84  NYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           +   A  A++  +G       L+VS    K  
Sbjct: 74  DPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 81.5 bits (202), Expect = 5e-21
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN--KCKGFGFVTMTNYDEAVVAIQ 93
           +FV  +     E  L +LF  +GAV  + V+RD   N  + KG  FVT      A+ A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 94  SLNGYALGNRILQVSF 109
           +L+   +   +     
Sbjct: 66  ALHNMKVLPGMHHPIQ 81

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 76.5 bits (189), Expect = 4e-19
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  ++ +  E+ +  +F  FG ++  +++R       +G  FVT T    A  AI+++
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 96  NGY---ALGNRILQVSF 109
           +        +  + V F
Sbjct: 157 HQAQTMEGCSSPMVVKF 173

>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 = 79.6 bits (197), Expect = 5e-21
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  +    +E+ +   F  +G+V+ VK+I D +T   KG+GFV+  N  +    ++  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE-- 68

Query: 96  NGYALGNRILQV 107
           +      + L++
Sbjct: 69  SQINFHGKKLKL 80

>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 = 79.6 bits (197), Expect = 5e-21
 Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L  +  E  + +LF PFG +    V+R       KG  FV  +++ EA  AI +L
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 96  NG---YALGNRILQVSFKTNKGK 115
           +G       +  L V F     +
Sbjct: 77  HGSQTMPGASSSLVVKFADTDKE 99

>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 = 79.2 bits (196), Expect = 5e-21
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           +++ NL   T +  L +     G   +  +K   +    + KGF  V + +   +   + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 94  SLNGYALGNRILQVSF 109
            L    L  +   V+ 
Sbjct: 64  LLPKRELHGQNPVVTP 79

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 79.6 bits (197), Expect = 6e-21
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 36  IFVYNLAPETEESVLWQLFG-PFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +FV +L P+ ++ +L++ F   + + +  KV+ D QT   KG+GFV  T+  E   A+  
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTE 70

Query: 95  LNG-YALGNRILQVSFKTNK 113
             G   LG++ +++S    K
Sbjct: 71  CQGAVGLGSKPVRLSVAIPK 90

>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 = 79.2 bits (196), Expect = 6e-21
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N++P      L   F  +G V    +++         + FV M   ++AV AI+ L
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGL 64

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +      + + V   T++ +T+
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTA 86

>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 = 78.9 bits (195), Expect = 9e-21
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYD 86
            IFV  L        +   F   G +++        + +  D +T K KG   V+  +  
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 87  EAVVAIQSLNGYALGNRILQVSFKT 111
            A  AI   +G       ++VSF T
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 78.0 bits (193), Expect = 1e-20
 Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 8/88 (9%)

Query: 30  NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
           +G+ W IFV N++       L  LF   G V    V+        K + FV M    +A 
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57

Query: 90  VAIQSLNGYALGNRILQVSFKTNKGKTS 117
            AI  LNG  +  + + V   T   K S
Sbjct: 58  AAIAQLNGKEVKGKRINVELSTKGQKKS 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 = 80.7 bits (199), Expect = 2e-20
 Identities = 27/110 (24%), Positives = 41/110 (37%), Gaps = 12/110 (10%)

Query: 5   NKGLQRFSPLTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVK 64
           N  L RF         +   P+ T       + + N+ P   E  L  LF   G V    
Sbjct: 99  NSPLHRFKKPGSKNFQNIFPPSAT-------LHLSNIPPSVSEEDLKVLFSSNGGVVKGF 151

Query: 65  VIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-RILQVSFKTNK 113
                   K +    + M + +EAV A+  L+ + LG    L+VSF  + 
Sbjct: 152 KFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 71.5 bits (175), Expect = 8e-17
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + V NL PE      L+ LFG +G VQ VK++ +      K    V M + ++A +A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 95  LNGYALGNRILQVSFKTNKGKTS 117
           LNG+ L  + ++++   ++    
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQL 83

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 78.4 bits (193), Expect = 2e-20
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 36  IFVYNLAPE-TEESVL--WQLFGPFGAVQSVKVIRDLQTNKCK---GFGFVTMTNYDEAV 89
           +FV  L+    +  VL   + FG FG +  V +         +      +VT    ++A+
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 90  VAIQSLNGYALGNRILQVSFKTNK 113
            AIQ +N   +  R L+ S  T K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 77.7 bits (192), Expect = 2e-20
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL+P      L QLFG         +    Q     G+ FV   + + A+ AI++L
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64

Query: 96  NGYA-LGNRILQVSFKTNKGKTS 117
           +G   L  +I++V +  +K   S
Sbjct: 65  SGKVELHGKIMEVDYSVSKKLRS 87

>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 = 77.7 bits (192), Expect = 3e-20
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V NL   T E ++ + F         +V       K + + FV  +N ++AV A+++
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70

Query: 95  LNGYALGNRILQVSF 109
           LNG  L    ++V+ 
Sbjct: 71  LNGKVLDGSPIEVTL 85

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 77.7 bits (192), Expect = 3e-20
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NL P    + L        A   +  + D++T   + FG+V   + ++   A++ L
Sbjct: 20  LFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77

Query: 96  NGYALGNRILQVSFKTNKGKT 116
            G  +    +++     +  T
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGT 98

>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 = 76.9 bits (190), Expect = 6e-20
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            G  ++VY    +   ++L   F PFG +  + +         +   FVT    + A  A
Sbjct: 14  KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 65

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           +  LNG  + +  L+V+    +
Sbjct: 66  VAELNGTQVESVQLKVNIARKQ 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 76.9 bits (190), Expect = 6e-20
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
            +V NL   T +  +  +F     ++SV+++RD  T+K KGF +V     D    A+ + 
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 96  NGYALGNRILQVSFKTNK 113
           +G  LG+R L+V     +
Sbjct: 76  DGALLGDRSLRVDIAEGR 93

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 78.8 bits (195), Expect = 6e-20
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NL P    + L        A   + V+   +T   + FG+V   + ++   A++ L
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-L 73

Query: 96  NGYALGNRILQVSFKTNKGK 115
            G  +    +++     +  
Sbjct: 74  TGLKVFGNEIKLEKPKGRDS 93

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 78.8 bits (195), Expect = 8e-20
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +   NL+    E  L ++F         ++    Q  K KG  ++   +  +A   ++  
Sbjct: 102 LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156

Query: 96  NGYALGNRILQVSFKTNKG 114
            G  +  R + + +   KG
Sbjct: 157 QGAEIDGRSVSLYYTGEKG 175

>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 = 76.2 bits (188), Expect = 9e-20
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +   NL+    E  L ++F         ++    Q  K KG  ++   +  +A   ++  
Sbjct: 19  LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
            G  +  R + + +   KG T 
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTR 95

>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 = 75.7 bits (187), Expect = 1e-19
 Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+ NL  E  E  +  LF  +G V    +I        K +GFV + +   A  AI++L
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           + Y L    + V    NK K S
Sbjct: 63  HHYKLHGVNINVEASKNKSKAS 84

>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 = 75.7 bits (187), Expect = 2e-19
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT-NKCKGFGFVTMTNYDEAVVAIQS 94
            F+ NL  +  E  + + F     + +V++ R+     + KGFG+    + D  + A+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79

Query: 95  LNGYALGNRILQVSF 109
           LN  +LGNR ++V  
Sbjct: 80  LNEESLGNRRIRVDV 94

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 75.6 bits (186), Expect = 5e-19
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV-----IRDLQTNKCKGFGFVTMTNYDEAVV 90
           I+V NLA   +E  L  +FG +    S        IR ++  + KG  F+ + N   A  
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           A++  NGY L  + + V F  + 
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSA 130

>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 = 74.2 bits (183), Expect = 6e-19
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V  L P T  + L + F  FG+++++  ++         F ++   + D A  A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 95  LNGYALGN--RILQVSF 109
           + G+ LG   R L+V F
Sbjct: 73  MRGFPLGGPDRRLRVDF 89

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 74.2 bits (183), Expect = 7e-19
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  +     E+ L + F  FG V  V +I D +  + +GFGF+T  + +++V    ++
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED-EQSVDQAVNM 71

Query: 96  NGYALGNRILQV 107
           + + +  + ++V
Sbjct: 72  HFHDIMGKKVEV 83

>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 = 74.3 bits (183), Expect = 8e-19
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +   I+V NL P+     +  +F  +GA++ + +           F FV   +  +A  A
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDA 77

Query: 92  IQSLNGYALGNRILQVSFKTNKGKTS 117
           +   +GY      L+V F  +   T 
Sbjct: 78  VYGRDGYDYDGYRLRVEFPRSGRGTG 103

>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 = 74.2 bits (183), Expect = 8e-19
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQS 94
            F+ NL  +  E  + + F     + +V++ R+     + KGFG+    + D  + A+ S
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 95  LNGYALGNRILQVSF 109
           LN  +LGN+ ++V  
Sbjct: 76  LNEESLGNKRIRVDV 90

>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 = 78.4 bits (192), Expect = 2e-18
 Identities = 20/120 (16%), Positives = 46/120 (38%), Gaps = 19/120 (15%)

Query: 3   AINKGLQRFSP-----LTGDLLASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPF 57
            +   L+ + P       GD          T       +FV  +  +T ES L + F  +
Sbjct: 81  EVETELKMWDPHNDPNAQGD-------AFKT-------LFVARVNYDTTESKLRREFEVY 126

Query: 58  GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           G ++ + ++   ++ K +G+ F+   +  +   A +  +G  +  R + V  +  +    
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKG 186

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 73.1 bits (180), Expect = 3e-18
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L   T ++ L + F  FG ++   VI D QT K +G+GFVTM +   A  A +  
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 96  NGYALGNRILQV 107
           N   +  R   V
Sbjct: 80  NPI-IDGRKANV 90

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.1 bits (177), Expect = 4e-18
 Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 31  GSGWCIFVYNL------APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           GS   I V              +  L  LF   G V +++   D  T K KGF FV   +
Sbjct: 4   GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS 63

Query: 85  YDEAVVAIQSLNGYAL-GNRILQV 107
            ++A   I+S +G  L     L +
Sbjct: 64  MNDAKKIIKSFHGKRLDLKHRLFL 87

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 72.9 bits (180), Expect = 1e-17
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  + P+       + F  +G +   +++ D  T + +GFGFVT  + D      Q  
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-N 148

Query: 96  NGYALGNRILQVSF 109
                 +R +++  
Sbjct: 149 KFIDFKDRKIEIKR 162

>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 = 71.4 bits (176), Expect = 5e-17
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L  +T E  L + FG +G V  +K+++D  T + +GFGF++          ++  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63

Query: 96  NGYALGNRILQV 107
             + L  +++  
Sbjct: 64  TQHILDGKVIDP 75

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.2 bits (175), Expect = 1e-17
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L + F  +G +++V + R+       GF FV   +  +A  A++ L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G  +    ++V   T   + S
Sbjct: 58  DGKVICGSRVRVELSTGMPRRS 79

>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 = 70.5 bits (173), Expect = 1e-17
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I V NL  ++    +  L   +        ++    ++ K   FVT+ N ++A  AIQ  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           + Y+   + L V  +       
Sbjct: 61  HQYSFRGKDLIVQLQPTDALLC 82

>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 = 70.8 bits (174), Expect = 1e-17
 Identities = 15/77 (19%), Positives = 30/77 (38%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            I V N+        +   F  +  +     ++  +     G   V   + DEA  A+  
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 95  LNGYALGNRILQVSFKT 111
           LN   +G+R +++S  +
Sbjct: 77  LNDRPIGSRKVKLSGPS 93

>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 = 71.0 bits (174), Expect = 1e-17
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 6/78 (7%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   I   NL   T  + + + F  FG++  V +       +      V      EA  A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKA 62

Query: 92  IQSLNGYALGNRILQVSF 109
            + L      +  L + +
Sbjct: 63  FRHLAYSKFHHVPLYLEW 80

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 71.8 bits (176), Expect = 2e-17
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     ++ L + FG +G ++SV V R+       GF FV   +  +A  A++ L
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130

Query: 96  NGYALGNRILQVSFKTNKGK 115
           +G  L    ++V     + +
Sbjct: 131 DGRTLCGCRVRVELSNGEKR 150

>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 = 70.6 bits (173), Expect = 2e-17
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 7/78 (8%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   + V  L P      L       G V    V RD       G G V     ++   A
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66

Query: 92  IQSLNGYALGNRILQVSF 109
           ++ L+     +   + ++
Sbjct: 67  VRKLDNTKFRSHEGETAY 84

>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 = 69.6 bits (171), Expect = 4e-17
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEESVL----WQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           I++ NL  + ++  L      +F  FG +  + V R L+    +G  FV       A  A
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           ++S+ G+   ++ +++ +    
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTD 89

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 69.9 bits (171), Expect = 5e-17
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           + + N+ PE  +  L      L    G +  + V     ++   G  ++     + A   
Sbjct: 32  VLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAF 88

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           +++  GY      L ++F    
Sbjct: 89  VEAFQGYPFQGNPLVITFSETP 110

>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 = 68.9 bits (169), Expect = 8e-17
 Identities = 14/75 (18%), Positives = 28/75 (37%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            I V N+        +   F  +  +     ++  +     G   V   + DEA  A+  
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 95  LNGYALGNRILQVSF 109
           LN   +G+R +++  
Sbjct: 77  LNDRPIGSRKVKLVL 91

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 71.2 bits (175), Expect = 8e-17
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ ET +  L   F  +G +    V+RD  T + +GFGFVT    +E   A+ + 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74

Query: 96  NGYALGNRILQV 107
             + +  R+++ 
Sbjct: 75  RPHKVDGRVVEP 86

>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 = 70.0 bits (172), Expect = 2e-16
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D     +   
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ- 165

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
             + +     +V    +K + +
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMA 187

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 69.0 bits (169), Expect = 9e-17
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 30  NGSGWCIFVYNLAPETEE------SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMT 83
           +G    I V N+     +      +V+ ++F  FG + +     +    K KG+ F+   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYA 69

Query: 84  NYDEAVVAIQSLNGYAL-GNRILQV 107
           +   AV A+++ +GY L      +V
Sbjct: 70  SPAHAVDAVKNADGYKLDKQHTFRV 94

>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 = 68.1 bits (167), Expect = 1e-16
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-S 94
           ++V  L     E+ L   F  FG ++++ V++       +   F+       A VA + S
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 95  LNGYALGNRILQVSF 109
            N   +  R L V +
Sbjct: 69  FNKLIVNGRRLNVKW 83

>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 = 70.7 bits (172), Expect = 4e-16
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEE----SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           I++ NL  + ++      L+ +F  FG +  + V R   + K +G  FV       A  A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           ++S+ G+   ++ +++ +    
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTD 90

>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 = 70.3 bits (171), Expect = 8e-16
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 34  WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
             +F+ NL  ET E +L  LF  F   + V+++            FV   N  +A  A  
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARD 262

Query: 94  SLNGYAL-GNRILQVSF 109
           +L G+ +  N  +++SF
Sbjct: 263 ALQGFKITQNNAMKISF 279

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 66.0 bits (162), Expect = 6e-16
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI--- 92
          IFV  L+P+T E  + + FG FG V+S+++  D +TNK +GF F+T    +     +   
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 93 -QSLNG 97
            ++  
Sbjct: 62 YHNVGL 67

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 66.8 bits (163), Expect = 9e-16
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 7/78 (8%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   + V  L P      L       G V    V RD       G G V     ++   A
Sbjct: 15  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 67

Query: 92  IQSLNGYALGNRILQVSF 109
           ++ L+     +   + ++
Sbjct: 68  VRKLDNTKFRSHEGETAY 85

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.7 bits (161), Expect = 2e-15
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          + V  L  +T E  L + F  FG V  V+V +DL+T   KGFGFV  T Y+  V  +   
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 96 N 96
          +
Sbjct: 78 H 78

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 64.4 bits (158), Expect = 2e-15
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+  T    +   F  FG V    ++ D  TN+ +GFGFVT  + ++ V  +  +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60

Query: 96  NGYALGNRILQV 107
           + + + N++++ 
Sbjct: 61  HFHEINNKMVEC 72

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 64.7 bits (158), Expect = 2e-15
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 11/81 (13%)

Query: 35  CIFVYNLAPETEES-------VLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDE 87
            I V N+ P+           V+ ++F  FG + +     +    K KG+ F+   +   
Sbjct: 3   VIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59

Query: 88  AVVAIQSLNGYAL-GNRILQV 107
           AV A+++ +GY L      +V
Sbjct: 60  AVDAVKNADGYKLDKQHTFRV 80

>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 = 64.7 bits (158), Expect = 4e-15
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 36  IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +F+ NL     ++S +  +F  +G V    V         KG+ FV  +N   A  A+  
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLG 81

Query: 95  LNGYALGNRILQVSFKTNKGKT 116
            NG  L  + L ++        
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPD 103

>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 = 64.6 bits (157), Expect = 7e-15
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
           I +  L  +  E  +  L  PFG V ++ +++       K   F+ M   + A   +   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 87

Query: 94  SLNGYALGNRILQVSFKTNK 113
           +     L  + + + F  +K
Sbjct: 88  TSVTPVLRGQPIYIQFSNHK 107

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 63.5 bits (155), Expect = 1e-14
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
          +F+  L+ ET E  L   +  +G +    V+RD  + + +GFGFVT ++  E   A+ +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 62.1 bits (152), Expect = 2e-14
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT  +       + 
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 62.7 bits (153), Expect = 3e-14
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI--- 92
          +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT  +       +   
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 93 -QSLNG 97
             L+ 
Sbjct: 88 RHELDS 93

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 62.2 bits (151), Expect = 3e-14
 Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P          ++V NL  +   S L +     G+V      +       +   F+   +
Sbjct: 11  PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ-----GPRRRAFLHYPD 65

Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
              A  A+  L G  LG   L+V+ 
Sbjct: 66  SAAAQQAVSCLQGLRLGTDTLRVAL 90

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 62.5 bits (152), Expect = 4e-14
 Identities = 14/81 (17%), Positives = 24/81 (29%), Gaps = 3/81 (3%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
             + I + NL        L  L               + T    G G +   + +  V A
Sbjct: 27  KRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEA 83

Query: 92  IQSLNGYALGNRILQVSFKTN 112
           ++ LN       ++ V    N
Sbjct: 84  LERLNNIEFRGSVITVERDDN 104

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 62.2 bits (151), Expect = 4e-14
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
           I +  L  +  E  +  L  PFG V ++ +++       K   F+ M   + A   +   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72

Query: 94  SLNGYALGNRILQVSFKTNKGKTS 117
           +     L  + + + F  +K   +
Sbjct: 73  TSVTPVLRGQPIYIQFSNHKELKT 96

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 62.1 bits (151), Expect = 4e-14
 Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 8/81 (9%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + +  L     E+ L +    FG +  V V+        K    V   +   A  A+  
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNY 76

Query: 95  LNGYA--LGNRILQVSFKTNK 113
                  +      V++ T++
Sbjct: 77  AADNQIYIAGHPAFVNYSTSQ 97

>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 = 61.7 bits (150), Expect = 6e-14
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQ 93
           +F+  +    +   + +        V  V V        K +GF FV   ++  A +A +
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 94  SLN--GYALGNRILQVSF 109
            L      L    + V +
Sbjct: 71  KLMPGRIQLWGHQIAVDW 88

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 61.0 bits (149), Expect = 7e-14
 Identities = 17/69 (24%), Positives = 27/69 (39%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+ +T +  L   F  FG V    +  D  T + +GFGF+   +       +   
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 96  NGYALGNRI 104
                G  I
Sbjct: 74  EHRLDGRVI 82

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 61.1 bits (149), Expect = 1e-13
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
          +FV  L   T +  L   F  +G V    +++D  TN+ +GFGFV   + +     + S
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77

>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 = 60.5 bits (147), Expect = 1e-13
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV-----IRDLQTNKCKGFGFVTMTNYDEAVV 90
           ++V N+     E  +   F     +  +       +  +Q N+ K F F+   + DE   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 91  AIQSLNGYALGNRILQV 107
           A+   +G     + L++
Sbjct: 69  AMA-FDGIIFQGQSLKI 84

>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 = 60.0 bits (146), Expect = 2e-13
 Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 20  ASSILPANTMNGSGWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFG 78
           +S ++P  +   S   +F+ NL  +   +  L+++F P+G +  + +           FG
Sbjct: 11  SSGLVPRGSHMKS--RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFG 60

Query: 79  FVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGK 115
           F+   N      AI+  +      + L +   ++  +
Sbjct: 61  FIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.1 bits (146), Expect = 2e-13
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++     +     + +     G V ++++ R       KG  FV   + + A   ++  
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-T 71

Query: 96  NGYALGNRILQVSFK 110
            G       L + FK
Sbjct: 72  PGQKYKETDLLILFK 86

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 59.0 bits (143), Expect = 5e-13
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 8/81 (9%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ- 93
            + V  L     E+ L +    FG +  V ++        K    V   N D A   +  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70

Query: 94  -SLNGYALGNRILQVSFKTNK 113
            +     +  +    ++ T+K
Sbjct: 71  AADVPVYIAGQQAFFNYSTSK 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.5 bits (142), Expect = 9e-13
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV       + + L + F  FG V SV + +D        F  V M +   A  A+ S 
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD--KGV---FAIVEMGDVG-AREAVLSQ 64

Query: 96  NGYALGNRILQVSFKTNK 113
           + ++LG   L+V  +  K
Sbjct: 65  SQHSLGGHRLRVRPREQK 82

>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 = 58.7 bits (142), Expect = 9e-13
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ-- 93
           + +  L  E  E+ +  L  PFG V ++ +++       K   F+ +   + A+  +   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71

Query: 94  SLNGYALGNRILQVSFKTNK 113
           S     L N+ + + +  +K
Sbjct: 72  SAVTPHLRNQPIYIQYSNHK 91

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.0 bits (141), Expect = 1e-12
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 9/82 (10%)

Query: 36  IFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           +F+ NL  +   +  L+++F P+G +  + +           FGF+   N      AI+ 
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIEC 64

Query: 95  LNGYALGNRILQVSFKTNKGKT 116
            +      + L +   ++  + 
Sbjct: 65  ESQEMNFGKKLILEVSSSNARP 86

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 61.0 bits (147), Expect = 1e-12
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 40  NLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA 99
           +L P   ES +  +F   G +  ++ +        K  GFV       A  A ++++   
Sbjct: 150 HLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT 203

Query: 100 LGNRILQVSFKTNKGKT 116
           L     +      +G  
Sbjct: 204 LLLPSDKEWDDRREGTG 220

>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 = 57.1 bits (138), Expect = 5e-12
 Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 3/89 (3%)

Query: 26  ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTN 84
              +N +  C  + N+     +  + Q          +V V+ D    +  G   V   N
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKN 66

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
            D+A  + + L+   L  R   V   T +
Sbjct: 67  EDDARKSER-LHRKKLNGREAFVHVVTLE 94

>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 = 57.2 bits (138), Expect = 6e-12
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
                + +G C+ +  L  +  E+ ++  F P   V  V +       +  G   V    
Sbjct: 38  EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIG-PDGRVTGEADVEFAT 95

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
           ++EAV A+ S +   + +R +++   +  G
Sbjct: 96  HEEAVAAM-SKDRANMQHRYIELFLNSTTG 124

>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 = 56.8 bits (137), Expect = 8e-12
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
            + + + +G+C+++  L  E E   +   F     V+    I      K  G GFV   N
Sbjct: 17  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             +   A+   +   +GNR +QV   T K
Sbjct: 77  EADYKAALC-RHKQYMGNRFIQVHPITKK 104

>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 = 55.9 bits (135), Expect = 1e-11
 Identities = 15/95 (15%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 20  ASSILPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGF 79
           +S    ++  + +G C+ +  L     E+ ++  F P      V +       +  G   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEAD 59

Query: 80  VTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG 114
           V    +++AV A+ + +   + +R +++   +  G
Sbjct: 60  VEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAG 93

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 54.6 bits (131), Expect = 3e-11
 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 7/96 (7%)

Query: 26  ANTMNGSGWCIFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVT 81
           ++  +G+G  + V N+        L Q     F   G V+SV++         +    V 
Sbjct: 2   SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQ 58

Query: 82  MTNYDEAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
           M N  +A+ A+ SL+ Y +G++ + VS  T     S
Sbjct: 59  MENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPS 94

>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 = 54.2 bits (131), Expect = 3e-11
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 30  NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
             +   + +        E  + +   P     +++++R+       G+ FV  +N +E  
Sbjct: 7   GTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRN-AHGNKTGYIFVDFSNEEEVK 64

Query: 90  VAIQSLNGYALGNRILQVSFKTNKGKTS 117
            A++  N   +G R ++V F+   G +S
Sbjct: 65  QALK-CNREYMGGRYIEV-FREKSGPSS 90

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 53.8 bits (130), Expect = 5e-11
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          +FV     +  E  L + F  +G V  V + +       + F FVT  +   A     
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG 60

>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 = 53.6 bits (129), Expect = 1e-10
 Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 3/89 (3%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
               +N     + V+ +     E+ +   F     V +V +++D    +  G G V   +
Sbjct: 8   KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKD-HVGRNNGNGLVKFLS 65

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
             +   A++  N   +  R ++VS  T +
Sbjct: 66  PQDTFEALK-RNRMLMIQRYVEVSPATER 93

>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 = 53.7 bits (129), Expect = 1e-10
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 1/74 (1%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + +  L     +  + Q F     V +   +      K  G  FV   + + A  A+  
Sbjct: 44  FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG- 102

Query: 95  LNGYALGNRILQVS 108
            +   +G+R ++V 
Sbjct: 103 KHKERIGHRYIEVF 116

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.4 bits (128), Expect = 1e-10
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 8/74 (10%)

Query: 35  CIFVYN--LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
            + V N  L      + L  +    G V ++ +  +      K + F      +E+  A 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80

Query: 93  QSLNGYALGNRILQ 106
            +LNG  + + + Q
Sbjct: 81  VTLNGKEVVDDLGQ 94

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 51.8 bits (125), Expect = 3e-10
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 5/58 (8%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
          +FV     +     L Q F  +G V  V + +       + F FVT  +   A     
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG 66

>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 = 52.4 bits (126), Expect = 3e-10
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + +  L     +  + Q F     V +   +      +  G  FV   + + A  A++ 
Sbjct: 17  FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK- 75

Query: 95  LNGYALGNRILQV 107
            +   +G+R +++
Sbjct: 76  KHKERIGHRYIEI 88

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.9 bits (124), Expect = 5e-10
 Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKC--KGFGFVTMTNYDEAVVAIQ 93
           +FV  L P+ +E  +   F  FG +      +    +    KG+ F+     + +V A+ 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF-QEESSVQALI 69

Query: 94  SLNGYALGNRILQVSFKTNKGK 115
                  G   L VS  T K K
Sbjct: 70  DACLEEDGKLYLCVSSPTIKDK 91

>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 Length = 136

 Score = 50.0 bits (119), Expect = 4e-09
 Identities = 11/91 (12%), Positives = 31/91 (34%), Gaps = 3/91 (3%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL--QTNKCKGFGFVTM 82
                 G G+ + +  L        +               +  +  +  +  G  FV +
Sbjct: 36  MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVEL 95

Query: 83  TNYDEAVVAIQSLNGYALGNRILQVSFKTNK 113
            + D+  +A++  +  ++G+R ++V      
Sbjct: 96  GSEDDVKMALK-KDRESMGHRYIEVFKSHRT 125

>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 = 49.1 bits (117), Expect = 6e-09
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 30  NGSGWCIFVYNLAPETEESVLWQLFGPF---GAVQSVKVIRDLQTNKCKGFGFVTMTNYD 86
            G G+ + +  L        +            V  V  I   +  +  G  FV + + D
Sbjct: 14  GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQSGEAFVELESED 72

Query: 87  EAVVAIQSLNGYALGNRILQV 107
           +  +A++  +  ++G+R ++V
Sbjct: 73  DVKLALK-KDRESMGHRYIEV 92

>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 = 48.3 bits (115), Expect = 1e-08
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 3/83 (3%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIR--DLQTNKCKGFGFVTMTNYDEAVV 90
            + I    L        +   F           I     +  K +G   + M +  +   
Sbjct: 11  VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           A++  +   +G R ++V    N+
Sbjct: 71  ALE-KHRMYMGQRYVEVYEINNE 92

>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 = 49.3 bits (117), Expect = 1e-08
 Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 8/79 (10%)

Query: 34  WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGF-GFVTMTNYDEAVVAI 92
             I V NL       VL Q+F  FG V      + +   K   F   +   +   A  A 
Sbjct: 47  LRIIVENLFYPVTLDVLHQIFSKFGTVL-----KIITFTKNNQFQALLQYADPVSAQHAK 101

Query: 93  QSLNGYAL--GNRILQVSF 109
            SL+G  +      L++ F
Sbjct: 102 LSLDGQNIYNACCTLRIDF 120

>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 = 47.2 bits (112), Expect = 3e-08
 Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 1/66 (1%)

Query: 44  ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR 103
           E  E V  ++   +G V+ + V  +   +   G  +V     ++A  A+  LN      +
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 104 ILQVSF 109
            +    
Sbjct: 97  PIHAEL 102

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 46.9 bits (111), Expect = 6e-08
 Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            I V NL       VL Q+F  FG V  +           +    +   +   A  A  S
Sbjct: 30  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLS 85

Query: 95  LNGYAL--GNRILQVSF 109
           L+G  +      L++ F
Sbjct: 86  LDGQNIYNACCTLRIDF 102

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 45.3 bits (107), Expect = 2e-07
 Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 7/83 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFG----AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVV 90
            + +  L        +   FG         + +  +      +  G  FV     + A  
Sbjct: 25  IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQN 83

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           A++  +   LG R +++ F++  
Sbjct: 84  ALR-KHKDLLGKRYIEL-FRSTA 104

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 44.3 bits (104), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 7/86 (8%)

Query: 26  ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY 85
                GS W + + NL  + +   L  L    G + S            +G      T  
Sbjct: 1   GAMAWGSSW-LLLKNLTAQIDGPTLRTLCMQHGPLVS------FHPYLNQGIALCKYTTR 53

Query: 86  DEAVVAIQSLNGYALGNRILQVSFKT 111
           +EA  A  +LN   L N  +     +
Sbjct: 54  EEANKAQMALNNCVLANTTIFAESPS 79

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 46.0 bits (108), Expect = 2e-07
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 2/76 (2%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +++     +     + +     G V ++++ R       KG  FV   + + A   +++
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVET 169

Query: 95  LNGYALGNRILQVSFK 110
                     L + FK
Sbjct: 170 PGQKYKE-TDLLILFK 184

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.9 bits (103), Expect = 7e-07
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + + N        VL+ +  P G VQ     R +   +      V   +   A  A  +
Sbjct: 27  LLSIQNPLYPITVDVLYTVCNPVGKVQ-----RIVIFKRNGIQAMVEFESVLCAQKAKAA 81

Query: 95  LNGYAL--GNRILQVSFKTNK 113
           LNG  +  G   L++ +    
Sbjct: 82  LNGADIYAGCCTLKIEYARPT 102

>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 = 43.0 bits (101), Expect = 1e-06
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 36  IFVYNL-APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ- 93
           I + NL      +S + +L  P+G +++  ++R       K   F+ M   ++A+  +  
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH 81

Query: 94  -SLNGYALGNRILQVSFKTNKGKTS 117
                     R ++V       K  
Sbjct: 82  CLKKALWFQGRCVKVDLSEKYKKLV 106

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.8 bits (93), Expect = 1e-05
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 57  FGAVQSVKVIR--DLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           +G V+S+++ R  D       G  FV  T+  +   A+Q L G    NR++   +
Sbjct: 39  YGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93

>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 Length = 112

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 57  FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           FG ++ + +          G   V+  + +EA   IQ+L+G   G R +    
Sbjct: 50  FGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98

>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 Length = 114

 Score = 37.3 bits (87), Expect = 1e-04
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 14/85 (16%)

Query: 35  CIFVYNL-APETEESVLWQL---------FGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           C  + N+  P+TEE V W               G V  + V +    N  +G  +V   +
Sbjct: 9   CFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDK----NSAQGNVYVKCPS 64

Query: 85  YDEAVVAIQSLNGYALGNRILQVSF 109
              A+ A+ +L+G     +++  ++
Sbjct: 65  IAAAIAAVNALHGRWFAGKMITAAY 89

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)

Query: 57  FGAVQSVKVIRDLQTNKCKGFG----FVTMTNYDEAVVAIQSLNGYALGNRILQVSF 109
           FGAV  V + ++ Q  +         FV  +   E   AIQ+LNG     R +    
Sbjct: 49  FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	117
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.93
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.9
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.9
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.9
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.9
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.89
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.89
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.89
2div_A	99	TRNA selenocysteine associated protein; structural	99.89
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.89
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.89
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.89
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.89
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.89
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.89
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.89
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.88
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.88
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.88
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.88
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.88
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.88
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.88
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.87
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.87
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.87
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.87
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.87
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.87
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.87
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.87
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.86
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.86
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.86
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.86
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.86
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.85
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.85
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.85
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.85
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.85
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.85
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.84
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.84
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.84
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.84
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.84
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.84
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.84
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.84
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.84
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.84
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.84
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.84
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.83
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.83
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.83
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.83
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.83
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.83
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.83
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.83
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.83
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.82
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	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
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.82
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.82
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.82
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.81
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.81
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.81
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.69
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.8
1x5p_A	97	Negative elongation factor E; structure genomics,	99.8
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.8
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.8
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.8
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.79
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.79
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.79
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.78
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.78
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.78
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.77
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.75
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.75
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.75
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.75
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.74
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.73
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.73
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.72
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.72
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.72
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.72
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.71
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.67
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.66
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.6
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.6
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.59
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.54
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.49
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.45
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.39
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.33
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.14
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.09
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.78
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.09
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.0
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.89
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.64
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.62
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.41
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.8
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.05
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.5
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.96
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.17

>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=9e-25  Score=126.27  Aligned_cols=82  Identities=32%  Similarity=0.489  Sum_probs=78.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      -.+++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.||
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            35778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            76

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.90  E-value=7.3e-23  Score=120.30  Aligned_cols=83  Identities=17%  Similarity=0.189  Sum_probs=79.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ++.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..|||..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=2.3e-22  Score=116.66  Aligned_cols=87  Identities=29%  Similarity=0.512  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            35678999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>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=99.90  E-value=1.4e-22  Score=113.15  Aligned_cols=82  Identities=29%  Similarity=0.509  Sum_probs=78.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .++|||+|||.++++++|+++|..||.|..+.++.++.++.++|+|||+|.+.++|++|+..|+|..+.|+.|+|.++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13319        113 KG  114 (117)
Q Consensus       113 ~~  114 (117)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=9.4e-23  Score=114.82  Aligned_cols=85  Identities=36%  Similarity=0.632  Sum_probs=77.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||.++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|+..|+|..+.|+.|+|.+
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            35678999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      +++++
T Consensus        83 a~~kp   87 (87)
T 3bs9_A           83 ATRKP   87 (87)
T ss_dssp             EC---
T ss_pred             cCCCC
Confidence            98753

>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=3.7e-22  Score=115.17  Aligned_cols=87  Identities=17%  Similarity=0.328  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567889999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      ++++++.+
T Consensus        92 ~a~~~~~~   99 (100)
T 2do4_A           92 ISNSGPSS   99 (100)
T ss_dssp             ECCCCSCC
T ss_pred             ECCCCCCC
Confidence            99987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.90  E-value=3.8e-22  Score=117.80  Aligned_cols=87  Identities=33%  Similarity=0.574  Sum_probs=81.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++..
T Consensus        91 ~a~~~~~   97 (115)
T 2dgo_A           91 WATRKPP   97 (115)
T ss_dssp             ESSCCCC
T ss_pred             EccCCCC
Confidence            9886543

>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=2.5e-22  Score=114.74  Aligned_cols=86  Identities=29%  Similarity=0.485  Sum_probs=80.6

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ....++.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|+|||+|.+.++|++|+..|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456788999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEecC
Q psy13319        107 VSFKTN  112 (117)
Q Consensus       107 v~~a~~  112 (117)
                      |.++++
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999875

>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=2.1e-22  Score=116.04  Aligned_cols=87  Identities=22%  Similarity=0.340  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+. +++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34677899999999999999999999999999999999998889999999999999999999999 99999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      +++++..+
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=8e-24  Score=120.52  Aligned_cols=84  Identities=14%  Similarity=0.303  Sum_probs=77.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CcEeCCeEEEEEEe
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN-GYALGNRILQVSFK  110 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~-~~~~~g~~l~v~~a  110 (117)
                      +.+|||+|||+++++++|+++|+.|| .|..++++.++.+|.++|||||+|.+.++|++|++.++ +..+.|+.|+|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36799999999999999999999999 79999999999999999999999999999999999774 56799999999999


Q ss_pred             cCCCCC
Q psy13319        111 TNKGKT  116 (117)
Q Consensus       111 ~~~~~~  116 (117)
                      +++++.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887653

>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=1.2e-22  Score=118.19  Aligned_cols=89  Identities=24%  Similarity=0.395  Sum_probs=82.7

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34567889999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q psy13319        108 SFKTNKGKT  116 (117)
Q Consensus       108 ~~a~~~~~~  116 (117)
                      .+++++.++
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999876543

>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=99.89  E-value=2.2e-22  Score=118.88  Aligned_cols=88  Identities=42%  Similarity=0.601  Sum_probs=81.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++..
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99987654

>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=2.4e-22  Score=115.77  Aligned_cols=86  Identities=31%  Similarity=0.391  Sum_probs=81.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            46778999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++++..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987654

>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=99.89  E-value=1.7e-22  Score=113.32  Aligned_cols=82  Identities=29%  Similarity=0.505  Sum_probs=78.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|+|||+|.+.++|++|+..|+|..+.|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45788999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ec
Q psy13319        110 KT  111 (117)
Q Consensus       110 a~  111 (117)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=117.28  Aligned_cols=88  Identities=28%  Similarity=0.467  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45678899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      +++++..+
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99876543

>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=5.4e-22  Score=115.39  Aligned_cols=87  Identities=29%  Similarity=0.436  Sum_probs=79.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC---eEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN---RIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g---~~l  105 (117)
                      ..++.++|||+|||..+++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|++|+..|++..+.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34578899999999999999999999999999999999987 78999999999999999999999999999887   999


Q ss_pred             EEEEecCCCCC
Q psy13319        106 QVSFKTNKGKT  116 (117)
Q Consensus       106 ~v~~a~~~~~~  116 (117)
                      +|.+++.++.+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.3e-22  Score=116.85  Aligned_cols=88  Identities=24%  Similarity=0.432  Sum_probs=82.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE-EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE---
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQ-SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI---  104 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~---  104 (117)
                      ...+.++|||+|||.++++++|+++|..||.|. .+.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            346788999999999999999999999999999 9999999889999999999999999999999999999999999   


Q ss_pred             -EEEEEecCCCCC
Q psy13319        105 -LQVSFKTNKGKT  116 (117)
Q Consensus       105 -l~v~~a~~~~~~  116 (117)
                       |+|.|+++.+..
T Consensus        85 ~l~v~~a~~~~~~   97 (99)
T 2div_A           85 RFKLNYATYSGPS   97 (99)
T ss_dssp             ECCEEETTCCSSS
T ss_pred             eEEEeecCCCCCC
Confidence             999999887654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=4.4e-22  Score=113.57  Aligned_cols=83  Identities=25%  Similarity=0.434  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34667889999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            975

>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=99.89  E-value=3.8e-22  Score=117.06  Aligned_cols=88  Identities=24%  Similarity=0.417  Sum_probs=81.9

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CcEeC
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN------GYALG  101 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------~~~~~  101 (117)
                      ....+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..++      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            345678899999999999999999999999999999999998899999999999999999999999999      99999


Q ss_pred             CeEEEEEEecCCCC
Q psy13319        102 NRILQVSFKTNKGK  115 (117)
Q Consensus       102 g~~l~v~~a~~~~~  115 (117)
                      |+.|+|.++.++.+
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999987654

>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=3.6e-22  Score=116.94  Aligned_cols=87  Identities=29%  Similarity=0.550  Sum_probs=81.5

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...++.++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..++|..+.|+.|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33567789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q psy13319        108 SFKTNKG  114 (117)
Q Consensus       108 ~~a~~~~  114 (117)
                      ++++++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998765

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=3.7e-22  Score=114.10  Aligned_cols=85  Identities=28%  Similarity=0.553  Sum_probs=80.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +++++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      +++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=3e-22  Score=116.65  Aligned_cols=87  Identities=26%  Similarity=0.481  Sum_probs=81.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...++++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ++.+++.
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9987653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.89  E-value=4.6e-22  Score=114.64  Aligned_cols=84  Identities=24%  Similarity=0.338  Sum_probs=78.9

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE--------EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA   99 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~   99 (117)
                      ......++|||+|||.++++++|+++|+.||.|..        +.++.++.+|.++|||||+|.+.++|++|++.|+|..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567789999999999999999999999999999        9999998899999999999999999999999999999


Q ss_pred             eCCeEEEEEEec
Q psy13319        100 LGNRILQVSFKT  111 (117)
Q Consensus       100 ~~g~~l~v~~a~  111 (117)
                      +.|+.|+|.+|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999974

>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=3.7e-22  Score=114.45  Aligned_cols=83  Identities=25%  Similarity=0.557  Sum_probs=78.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ++++|||+|||.++++++|+++|+.||.|..+.+..++.+|.++|||||+|.+.++|++|+..++|..+.|+.|+|.+++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            36789999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      +++
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.88  E-value=6.5e-22  Score=117.29  Aligned_cols=83  Identities=41%  Similarity=0.630  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.|+|..+.|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34577899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.88  E-value=1.7e-21  Score=112.93  Aligned_cols=85  Identities=27%  Similarity=0.453  Sum_probs=79.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..|| |..+.++.++.++.++|||||+|.+.++|++|+ .|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345678999999999999999999999997 999999999989999999999999999999999 799999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ++++++.
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9987654

>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=4.4e-22  Score=116.71  Aligned_cols=87  Identities=25%  Similarity=0.457  Sum_probs=81.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...++++|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|+|..+.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34577899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ++.+++.
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9987654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=2.1e-22  Score=116.77  Aligned_cols=86  Identities=26%  Similarity=0.337  Sum_probs=80.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++..+.
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            986543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=1.4e-22  Score=116.14  Aligned_cols=82  Identities=24%  Similarity=0.448  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCC--eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----EeCCeE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGA--VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY----ALGNRI  104 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~--i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~----~~~g~~  104 (117)
                      ..=.+|||+|||+.+++++|+++|++||.  +..++++.++.+|.++|||||+|.+.++|++|++.|+|.    .++|+.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34467999999999999999999999995  578999999999999999999999999999999999986    589999


Q ss_pred             EEEEEecC
Q psy13319        105 LQVSFKTN  112 (117)
Q Consensus       105 l~v~~a~~  112 (117)
                      |.|+||++
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2e-22  Score=116.63  Aligned_cols=88  Identities=32%  Similarity=0.519  Sum_probs=81.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34567889999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            99887554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=1.2e-21  Score=113.59  Aligned_cols=86  Identities=29%  Similarity=0.497  Sum_probs=79.5

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....+.++|||+|||+.+++++|+++|..||.|..+.+..+  ++.++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34557889999999999999999999999999999999887  7899999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++.+
T Consensus        88 ~~a~~~~~   95 (103)
T 2d9p_A           88 ALAQRKEE   95 (103)
T ss_dssp             EECSSCCC
T ss_pred             EEeccccc
Confidence            99987654

>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=7.1e-22  Score=115.17  Aligned_cols=87  Identities=23%  Similarity=0.381  Sum_probs=80.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCcEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRD-LQTNKCKGFGFVTMTNYDEAVVAIQSL-NGYALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l-~~~~~~g~~l~  106 (117)
                      ...+.++|||+|||..+++++|+++|..||.|..+.++.+ +.++.++|||||+|.+.++|++|+..| ++..+.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3567789999999999999999999999999999999888 678999999999999999999999999 99999999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.+++++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999987553

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.88  E-value=9.8e-22  Score=119.54  Aligned_cols=88  Identities=28%  Similarity=0.468  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+..++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      +++.+.++
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3.3e-22  Score=114.50  Aligned_cols=85  Identities=34%  Similarity=0.637  Sum_probs=79.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEE-EEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++++|||+|||..+++++|+++|..||.|..+ .++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 9999888899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            886554

>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=99.88  E-value=1.5e-21  Score=113.37  Aligned_cols=84  Identities=24%  Similarity=0.466  Sum_probs=78.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT-NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+.++|||+|||..+++++|+++|..|| |..+.++.++.+ +.++|||||+|.+.++|++|+ .+++..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            45678999999999999999999999999 999999999887 899999999999999999999 899999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++..
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987654

>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=99.88  E-value=4.3e-22  Score=120.00  Aligned_cols=88  Identities=30%  Similarity=0.515  Sum_probs=82.2

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ....++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33456788999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q psy13319        107 VSFKTNKG  114 (117)
Q Consensus       107 v~~a~~~~  114 (117)
                      |.++++++
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998765

>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=115.88  Aligned_cols=87  Identities=24%  Similarity=0.332  Sum_probs=80.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe---CCeEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL---GNRIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~---~g~~l  105 (117)
                      ...+.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            356778999999999999999999999999999999999988899999999999999999999999999887   88999


Q ss_pred             EEEEecCCCC
Q psy13319        106 QVSFKTNKGK  115 (117)
Q Consensus       106 ~v~~a~~~~~  115 (117)
                      +|.+++++.+
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999987654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=7.9e-22  Score=113.35  Aligned_cols=85  Identities=26%  Similarity=0.388  Sum_probs=78.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQ---TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ++.++|||+|||.++++++|+++|..||.|..+.+..++.   ++.++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4567899999999999999999999999999999988765   5688999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++.+
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99887554

>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=1.3e-21  Score=115.17  Aligned_cols=87  Identities=23%  Similarity=0.271  Sum_probs=80.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE--------EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQ--------SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ...+.++|||+|||.++++++|+++|..||.|.        .+.++.++.++.++|||||+|.+.++|++|+..|++..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            346788999999999999999999999999998        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEEEecCCCC
Q psy13319        101 GNRILQVSFKTNKGK  115 (117)
Q Consensus       101 ~g~~l~v~~a~~~~~  115 (117)
                      .|+.|+|.+++.+..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999887654

>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=99.88  E-value=2.8e-21  Score=112.70  Aligned_cols=82  Identities=23%  Similarity=0.327  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||..+++++|+++|..||.|..+.++.++ ++.++|+|||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45678999999999999999999999999999999999997 89999999999999999999999999999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      +++
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=1.3e-21  Score=112.19  Aligned_cols=85  Identities=26%  Similarity=0.339  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHH----HhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLW----QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      ...++++|||+|||.++++++|+    ++|..||.|..+.++.++.+   +|||||+|.+.++|++|+..|+|..+.|+.
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567899999999999999999    99999999999999888654   789999999999999999999999999999


Q ss_pred             EEEEEecCCCCC
Q psy13319        105 LQVSFKTNKGKT  116 (117)
Q Consensus       105 l~v~~a~~~~~~  116 (117)
                      |+|.++++....
T Consensus        82 l~V~~a~~~~~~   93 (96)
T 2dgx_A           82 ILVSLATGASGP   93 (96)
T ss_dssp             EEEEECCCSSCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999877654

>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=99.87  E-value=1.5e-21  Score=115.43  Aligned_cols=80  Identities=33%  Similarity=0.513  Sum_probs=74.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      ..+|||+|||+++++++|+++|..||.|..++++.++  +.++|||||+|.+.++|++|+..|+|..+.|+.|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999885  45789999999999999999999999999999999999876


Q ss_pred             CC
Q psy13319        113 KG  114 (117)
Q Consensus       113 ~~  114 (117)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.87  E-value=1.1e-21  Score=112.76  Aligned_cols=86  Identities=16%  Similarity=0.197  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+..++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34567899999999999999999999999999888788888889999999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ++....
T Consensus        91 ~a~~~~   96 (98)
T 2cqp_A           91 LGSGPS   96 (98)
T ss_dssp             ESSCSS
T ss_pred             EcCCCC
Confidence            987543

>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=99.87  E-value=7.1e-21  Score=110.31  Aligned_cols=87  Identities=29%  Similarity=0.410  Sum_probs=78.7

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .....+.++|||+|||.++++++|+++|..||.|..+.++.++.  .++|||||+|.+.++|++|+..|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456778999999999999999999999999999999988753  3789999999999999999999999999999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.+++++..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cq3_A           87 VNNATARVM   95 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEcccCCC
Confidence            999987654

>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=5.4e-21  Score=108.52  Aligned_cols=84  Identities=15%  Similarity=0.284  Sum_probs=78.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||.++++++|+++|..| .|..+.++.+ .+|.++|+|||+|.+.++|++|+. +++..+.|+.|+|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4567899999999999999999999999 8999999998 789999999999999999999999 999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      +++++++
T Consensus        84 a~~~~~s   90 (91)
T 2dgw_A           84 EKSGPSS   90 (91)
T ss_dssp             ESSCCCC
T ss_pred             CCcCCCC
Confidence            9887653

>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=99.87  E-value=1.1e-22  Score=115.48  Aligned_cols=82  Identities=16%  Similarity=0.180  Sum_probs=72.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCC--CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .+|||+|||.++++++|+++|..||  .|..+.++.++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4699999999999999999999999  99999999999999999999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy13319        112 NKGK  115 (117)
Q Consensus       112 ~~~~  115 (117)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>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=5e-21  Score=110.96  Aligned_cols=86  Identities=23%  Similarity=0.409  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....+.++|||+|||..+++++|+++|..||.|..+.++.++.  .++|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3456778999999999999999999999999999999988754  35899999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99987543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.87  E-value=1.6e-21  Score=114.30  Aligned_cols=89  Identities=26%  Similarity=0.416  Sum_probs=76.4

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .....++.++|||+|||.++++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|++|+..+ +..+.|+.|
T Consensus        18 ~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l   96 (109)
T 2rs2_A           18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTI   96 (109)
T ss_dssp             --------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEE
Confidence            3344567889999999999999999999999999999999999888999999999999999999999975 688999999


Q ss_pred             EEEEecCCCC
Q psy13319        106 QVSFKTNKGK  115 (117)
Q Consensus       106 ~v~~a~~~~~  115 (117)
                      +|.++.++..
T Consensus        97 ~V~~a~~~~~  106 (109)
T 2rs2_A           97 DPKVAFPRRA  106 (109)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999987654

>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=1.7e-21  Score=109.82  Aligned_cols=84  Identities=14%  Similarity=0.277  Sum_probs=77.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK-CKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..++|||+|||.++++++|+++|..||.|..+.++.++.++. ++|+|||+|.+.++|++|+..|+|..+.|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            467899999999999999999999999999999988877665 7999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      .+.+.
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=2.1e-21  Score=110.94  Aligned_cols=83  Identities=31%  Similarity=0.452  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||+.+++++|+++|..||.|..+.++.++. +.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            346778999999999999999999999999999999999875 8899999999999999999999999999999999999


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>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=99.87  E-value=5.3e-21  Score=118.41  Aligned_cols=86  Identities=23%  Similarity=0.349  Sum_probs=80.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45778999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +++.+.
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            986543

>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=99.87  E-value=4.6e-21  Score=107.93  Aligned_cols=81  Identities=21%  Similarity=0.314  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+. +++..+.|+.|+|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            35677899999999999999999999999999999999999899999999999999999999997 48889999999998


Q ss_pred             Ee
Q psy13319        109 FK  110 (117)
Q Consensus       109 ~a  110 (117)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=1.1e-21  Score=121.73  Aligned_cols=81  Identities=19%  Similarity=0.232  Sum_probs=76.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCC--CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..++|||+|||+++++++|+++|..||  .|..+.++.++.+|.++|||||+|.+.++|++|+..|+|..+.|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=1.3e-21  Score=115.82  Aligned_cols=85  Identities=29%  Similarity=0.454  Sum_probs=79.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||.++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|++|+..|+|..+.|+.|+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999987 899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++....
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            886543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=3.9e-21  Score=113.65  Aligned_cols=86  Identities=30%  Similarity=0.378  Sum_probs=79.4

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .....+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..+++ .+.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            33456778999999999999999999999999999999999988899999999999999999999999998 89999999


Q ss_pred             EEEecCC
Q psy13319        107 VSFKTNK  113 (117)
Q Consensus       107 v~~a~~~  113 (117)
                      |.++...
T Consensus        90 V~~a~~~   96 (116)
T 2cqd_A           90 VNLAYLG   96 (116)
T ss_dssp             EEESTTT
T ss_pred             EEEcccC
Confidence            9998653

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.87  E-value=1.1e-21  Score=117.44  Aligned_cols=87  Identities=26%  Similarity=0.483  Sum_probs=80.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....++++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            34456889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q psy13319        108 SFKTNKG  114 (117)
Q Consensus       108 ~~a~~~~  114 (117)
                      .++.++.
T Consensus        97 ~~a~~~~  103 (126)
T 3ex7_B           97 DWCFVRG  103 (126)
T ss_dssp             EESEESS
T ss_pred             EEecCCC
Confidence            9987544

>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=1.2e-20  Score=111.13  Aligned_cols=84  Identities=30%  Similarity=0.359  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||.++++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|+.|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34567899999999999999999999999999999999886 58899999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      +++..
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98743

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.87  E-value=2.7e-22  Score=115.95  Aligned_cols=83  Identities=28%  Similarity=0.274  Sum_probs=78.4

Q ss_pred             CCCcEEEEeCCCC------CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC-e
Q psy13319         31 GSGWCIFVYNLAP------ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-R  103 (117)
Q Consensus        31 ~~~~~l~v~~Lp~------~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g-~  103 (117)
                      ..+++|||+|||.      .+++++|+++|+.||.|..+.++.++.||.++|||||+|.+.++|++|+..|+|..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4578999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             EEEEEEecCC
Q psy13319        104 ILQVSFKTNK  113 (117)
Q Consensus       104 ~l~v~~a~~~  113 (117)
                      .|+|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998753

>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=99.87  E-value=2.7e-21  Score=109.19  Aligned_cols=82  Identities=20%  Similarity=0.301  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|||+|||.++++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|++|+ .+++..+.|+.|+|.+++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4578999999999999999999999999999999999889999999999999999999999 899999999999999988


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ++.
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            753

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.87  E-value=2.9e-21  Score=109.73  Aligned_cols=84  Identities=26%  Similarity=0.323  Sum_probs=77.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||.++++++|+++|..||.|..+.+..+  ++.++|||||+|.+.++|+.|+..|++..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457789999999999999999999999999999998874  688999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            987654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=2e-21  Score=112.98  Aligned_cols=86  Identities=24%  Similarity=0.321  Sum_probs=80.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||+.+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            356788999999999999999999999999999999999988999999999999999999999998 9999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9886553

>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=1.6e-20  Score=112.24  Aligned_cols=85  Identities=20%  Similarity=0.286  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+.+++|||+|||..+++++|+++|..||.|..+.+..++ +|.++|||||+|.+.++|+.|+..++|..+.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45677899999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ++....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            988654

>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=8.8e-21  Score=110.98  Aligned_cols=85  Identities=21%  Similarity=0.350  Sum_probs=76.7

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....+.++|||+|||.++++++|+++|..||.|..+.+..+   +.++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            33457789999999999999999999999999999988544   567899999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .+++++++
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4a_A           94 EFPRSGRG  101 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EEcccCCC
Confidence            99987654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=1.5e-21  Score=113.30  Aligned_cols=85  Identities=28%  Similarity=0.535  Sum_probs=79.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcC-CCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE-eCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGP-FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA-LGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~-~~g~~l~v  107 (117)
                      .++.++|||+|||.++++++|+++|.. ||.|..+.++.++ ++.++|||||+|.+.++|..|+..+++.. +.|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456788999999999999999999999 9999999999998 89999999999999999999999999999 99999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99876543

>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=1.9e-20  Score=108.44  Aligned_cols=84  Identities=30%  Similarity=0.430  Sum_probs=77.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.  ++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            4567889999999999999999999999999999999998899999999999999999999999  47889999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +.++.+
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            887543

>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=99.86  E-value=1.6e-21  Score=111.49  Aligned_cols=83  Identities=18%  Similarity=0.211  Sum_probs=75.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+..++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34568999999999999999999999999998888888888899999999999999999999999999999999999998


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +++
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            764

>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=99.86  E-value=6.8e-22  Score=114.21  Aligned_cols=85  Identities=25%  Similarity=0.453  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ......++|||+|||.++++++|+++|..|| |..+.++.++ .+|.++|||||+|.+.++|.+|+ .++|..+.|+.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            3456789999999999999999999999999 9999999887 58999999999999999999999 7999999999999


Q ss_pred             EEEecCCC
Q psy13319        107 VSFKTNKG  114 (117)
Q Consensus       107 v~~a~~~~  114 (117)
                      |.+++++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99998764

>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=99.86  E-value=7.2e-22  Score=114.61  Aligned_cols=84  Identities=31%  Similarity=0.473  Sum_probs=79.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|++|+..++|..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            45678999999999999999999999999999999999888999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      +++.
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8754

>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=99.86  E-value=1.2e-20  Score=110.86  Aligned_cols=85  Identities=24%  Similarity=0.318  Sum_probs=77.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH---HhhcCCCCeEEEEEEecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         31 GSGWCIFVYNLAPETEESVLW---QLFGPFGAVQSVKVIRDLQTN---KCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~---~~f~~~g~i~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      ...++|||+|||+++++++|+   ++|..||.|..+.++.++.++   .++|||||+|.+.++|++|+..|+|..+.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            456789999999999999999   999999999999998887643   45699999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy13319        105 LQVSFKTNKGK  115 (117)
Q Consensus       105 l~v~~a~~~~~  115 (117)
                      |+|.++.++..
T Consensus        93 l~V~~a~~k~~  103 (111)
T 2cpi_A           93 LKASLGTTKYC  103 (111)
T ss_dssp             EEEESCCCCSC
T ss_pred             EEEEecccccc
Confidence            99999987653

>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=9.1e-21  Score=118.41  Aligned_cols=86  Identities=26%  Similarity=0.465  Sum_probs=79.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...++++|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.+.|+.|+..|+|..+.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      |+..+.
T Consensus       148 ~a~~~~  153 (165)
T 1rk8_A          148 WCFVKG  153 (165)
T ss_dssp             ESEECC
T ss_pred             EecCCC
Confidence            987544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.9e-21  Score=114.17  Aligned_cols=84  Identities=23%  Similarity=0.400  Sum_probs=78.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4568999999999999999999999999999999999988999999999999999999999997 999999999999999


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      .++..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            87654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.86  E-value=1.1e-20  Score=114.81  Aligned_cols=84  Identities=29%  Similarity=0.484  Sum_probs=77.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .....+.++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33456788999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEe
Q psy13319        107 VSFK  110 (117)
Q Consensus       107 v~~a  110 (117)
                      |.+|
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9885

>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=6.8e-21  Score=117.99  Aligned_cols=86  Identities=27%  Similarity=0.364  Sum_probs=80.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|+|..+.|+.|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +++++.
T Consensus       147 a~~~~~  152 (158)
T 2kn4_A          147 ARYGRP  152 (158)
T ss_dssp             ECCSSC
T ss_pred             CCCCCC
Confidence            987543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.86  E-value=5.7e-22  Score=119.68  Aligned_cols=85  Identities=25%  Similarity=0.481  Sum_probs=79.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE--EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----EeCCe
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS--VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY----ALGNR  103 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~--~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~----~~~g~  103 (117)
                      ....++|||+|||+++++++|+++|..||.|..  ++++.++.+|.++|||||+|.+. +|.+|+..|+|.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            356789999999999999999999999999966  99999998999999999999999 999999999999    99999


Q ss_pred             EEEEEEecCCCC
Q psy13319        104 ILQVSFKTNKGK  115 (117)
Q Consensus       104 ~l~v~~a~~~~~  115 (117)
                      .|+|.++++..+
T Consensus        99 ~l~V~~a~~~~~  110 (131)
T 2m2b_A           99 TINVEFAKGSKR  110 (131)
T ss_dssp             CCCCEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.4e-20  Score=107.72  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|   .++.+ .++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45678899999999999999999999999977   45555 578899999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++++
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.85  E-value=2.8e-21  Score=113.97  Aligned_cols=82  Identities=23%  Similarity=0.371  Sum_probs=77.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+ .+++..+.|+.|+|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            35679999999999999999999999999999999999888999999999999999999999 89999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      +++
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            753

>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=99.85  E-value=4e-20  Score=106.98  Aligned_cols=81  Identities=17%  Similarity=0.288  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCcEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL--NGYALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~~~~~~g~~l~  106 (117)
                      ..+++++|||+|||+.+++++|+++|..||.|..+.++.+      +|||||+|.+.++|+.|+..+  ++..+.|+.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3467789999999999999999999999999999988754      789999999999999999977  46789999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |+|++.+..
T Consensus        85 V~~a~~~~~   93 (101)
T 2cq1_A           85 IQYSNHKEL   93 (101)
T ss_dssp             EEECSCSSC
T ss_pred             EEEcCcccC
Confidence            999987553

>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=1e-21  Score=110.20  Aligned_cols=81  Identities=30%  Similarity=0.485  Sum_probs=76.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +++++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|+.|+..|+|..+.|+.|+++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            56789999999999999999999999999999999999888999999999999999999999999999999999988775


Q ss_pred             c
Q psy13319        111 T  111 (117)
Q Consensus       111 ~  111 (117)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.5e-21  Score=111.84  Aligned_cols=81  Identities=19%  Similarity=0.272  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l~  106 (117)
                      ...+.++|||+|||+++++++|+++|..||.|..+.++.+      +|||||+|.+.++|+.|+..+++  ..+.|+.|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3567889999999999999999999999999999998865      78999999999999999998864  789999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.|++.+..
T Consensus        86 V~~A~~~~~   94 (105)
T 1sjq_A           86 IQFSNHKEL   94 (105)
T ss_dssp             BCCCSSSSC
T ss_pred             EEEcCCCCC
Confidence            999987654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.85  E-value=1.3e-20  Score=108.58  Aligned_cols=83  Identities=16%  Similarity=0.161  Sum_probs=72.2

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE--eCCe
Q psy13319         26 ANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA--LGNR  103 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~--~~g~  103 (117)
                      .....+++++|||+|||..+++++|+++|.+||.|..+.++..      +|+|||+|.+.++|.+|+..+++..  +.|+
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            3344567899999999999999999999999999999988743      6899999999999999999998864  7899


Q ss_pred             EEEEEEecCCC
Q psy13319        104 ILQVSFKTNKG  114 (117)
Q Consensus       104 ~l~v~~a~~~~  114 (117)
                      +|.|+|++.+.
T Consensus        88 ~i~V~~S~~k~   98 (100)
T 3r27_A           88 PAFVNYSTSQK   98 (100)
T ss_dssp             EEEEEECSCSC
T ss_pred             EEEEEeccccc
Confidence            99999998754

>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=99.85  E-value=3.9e-20  Score=108.97  Aligned_cols=84  Identities=24%  Similarity=0.424  Sum_probs=77.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe--------C
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL--------G  101 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~--------~  101 (117)
                      ..+.++|||+|||.++++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|+.|+..|+|..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4567899999999999999999999999999999999997 899999999999999999999999999988        5


Q ss_pred             CeEEEEEEecCCC
Q psy13319        102 NRILQVSFKTNKG  114 (117)
Q Consensus       102 g~~l~v~~a~~~~  114 (117)
                      ++.|.|.|+++..
T Consensus       101 ~~~l~v~~a~p~~  113 (114)
T 1x5o_A          101 TEPLLCKFSGPSS  113 (114)
T ss_dssp             SSCBEEEECCCSC
T ss_pred             CCceeEEccCCCC
Confidence            7889999998653

>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=1.5e-20  Score=112.22  Aligned_cols=82  Identities=15%  Similarity=0.284  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|+.|+ .++|..+.|+.|+|.+++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999999999999999889999999999999999999999 799999999999999988


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=8.3e-21  Score=109.96  Aligned_cols=80  Identities=14%  Similarity=0.231  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEE
Q psy13319         29 MNGSGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l  105 (117)
                      ..+++++|||+|||+ .+++++|+++|..||.|..+.++.+      +|+|||+|.+.++|..|+..|++  ..+.|+.|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            345788999999999 9999999999999999999998765      57999999999999999998875  56999999


Q ss_pred             EEEEecCCC
Q psy13319        106 QVSFKTNKG  114 (117)
Q Consensus       106 ~v~~a~~~~  114 (117)
                      +|++++..+
T Consensus        85 ~V~~a~~~~   93 (102)
T 1x4d_A           85 RVHLSQKYK   93 (102)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCCC
Confidence            999998543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=4e-20  Score=106.90  Aligned_cols=84  Identities=23%  Similarity=0.389  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..|+   .+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            346778899999999999999999999874   56777888889999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++.+
T Consensus        88 ~a~~~~~   94 (102)
T 2fc8_A           88 WAKPKGE   94 (102)
T ss_dssp             ECCCCCS
T ss_pred             EecCCCC
Confidence            9987654

>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=1.3e-20  Score=110.38  Aligned_cols=85  Identities=29%  Similarity=0.409  Sum_probs=77.4

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ......++|||+|||.++++++|+++|..||.|..+.+..++  +.++|||||+|.+.++|++|+..|+|..+.|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678899999999999999999999999999999998874  447899999999999999999999999999999999


Q ss_pred             EEecCCC
Q psy13319        108 SFKTNKG  114 (117)
Q Consensus       108 ~~a~~~~  114 (117)
                      .+++++.
T Consensus       102 ~~a~~~~  108 (109)
T 2err_A          102 NNATARV  108 (109)
T ss_dssp             EECCCSC
T ss_pred             EECCCCc
Confidence            9988753

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5.1e-21  Score=111.17  Aligned_cols=81  Identities=16%  Similarity=0.252  Sum_probs=75.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++. +.++|||||+|.+.++|..|+. +++..+.|+.|.|.+
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34568899999999999999999999999999999999877 9999999999999999999999 899999999999998


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +.+
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=3.3e-20  Score=105.09  Aligned_cols=80  Identities=30%  Similarity=0.433  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||.++++++|+++|..||.|..+.++        ++||||+|.+.++|++|+..+++..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            34677899999999999999999999999999999886        5699999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      +++++.+.
T Consensus        76 ~a~~~~~~   83 (90)
T 2dnq_A           76 ASKNKSKA   83 (90)
T ss_dssp             CSSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876653

>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=99.84  E-value=1e-20  Score=111.63  Aligned_cols=82  Identities=20%  Similarity=0.185  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCe-EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...+.++|||+|||+++++++|+++|..||.| ..+.++.++ ++.++|||||+|.+.++|++|+.. ++..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999887 899999999999999999999997 999999999999


Q ss_pred             EEecC
Q psy13319        108 SFKTN  112 (117)
Q Consensus       108 ~~a~~  112 (117)
                      .++..
T Consensus        89 ~~a~~   93 (114)
T 2cpy_A           89 HVVTL   93 (114)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99864

>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=99.84  E-value=1.2e-20  Score=110.36  Aligned_cols=85  Identities=16%  Similarity=0.195  Sum_probs=77.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCC-eEEEEEE-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CcEeCCeEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGA-VQSVKVI-RDLQTNKCKGFGFVTMTNYDEAVVAIQSLN--GYALGNRILQ  106 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~-i~~~~~~-~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--~~~~~g~~l~  106 (117)
                      .+.++|||+|||.++++++|+++|..||. |..+.++ .++.++.++|||||+|.+.++|..|+..|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            46789999999999999999999999998 9999888 777888999999999999999999999996  5899999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.|++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.84  E-value=2.5e-21  Score=117.47  Aligned_cols=86  Identities=27%  Similarity=0.364  Sum_probs=80.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45678899999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +++.+.
T Consensus       124 a~~~~~  129 (135)
T 2lea_A          124 ARYGRP  129 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            986543

>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=99.84  E-value=3.6e-20  Score=106.65  Aligned_cols=81  Identities=28%  Similarity=0.458  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||..+++++|+++|..||.|..+.+..+      +|||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3467789999999999999999999999999999988754      6899999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpj_A           85 FACHSAS   91 (99)
T ss_dssp             ESSCCSC
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.84  E-value=4.1e-20  Score=107.42  Aligned_cols=83  Identities=14%  Similarity=0.194  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE-EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS-VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      .....++|||+|||+++++++|+++|..||.|.. +.++.+ .+++++|||||+|.+.++|++|+.. ++..++|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999987 778777 7899999999999999999999997 999999999999


Q ss_pred             EEecCC
Q psy13319        108 SFKTNK  113 (117)
Q Consensus       108 ~~a~~~  113 (117)
                      .++..+
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            988754

>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=1.7e-20  Score=109.20  Aligned_cols=83  Identities=24%  Similarity=0.376  Sum_probs=75.2

Q ss_pred             CCCCcEEEEeCCCCCC------CHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe
Q psy13319         30 NGSGWCIFVYNLAPET------EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR  103 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~  103 (117)
                      ...+++|||+|||..+      ++++|+++|+.||.|..+.++  +.+|.++|||||+|.+.++|+.|+..|+|..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3457899999999999      779999999999999999887  46789999999999999999999999999999998


Q ss_pred             -EEEEEEecCCC
Q psy13319        104 -ILQVSFKTNKG  114 (117)
Q Consensus       104 -~l~v~~a~~~~  114 (117)
                       .|+|.++.+..
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             99999987643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.84  E-value=3.7e-20  Score=109.91  Aligned_cols=81  Identities=17%  Similarity=0.272  Sum_probs=75.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCC---eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGA---VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ..+.++|||+|||+++++++|+++|..||.   |..+.++.++. |+++|||||+|.+.++|++|+. +++..+.|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            456789999999999999999999999998   88999998876 9999999999999999999999 899999999999


Q ss_pred             EEEecC
Q psy13319        107 VSFKTN  112 (117)
Q Consensus       107 v~~a~~  112 (117)
                      |.++..
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            998753

>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=99.84  E-value=5.9e-20  Score=105.53  Aligned_cols=82  Identities=17%  Similarity=0.310  Sum_probs=72.0

Q ss_pred             CCCCCCCCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         26 ANTMNGSGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        26 ~~~~~~~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      .....+++++|||+|||. ++++++|+++|..||.|..+.+.        +|||||+|.+.++|.+|+..++|..+.|+.
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             ----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             ccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            334456788999999998 99999999999999999998872        689999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy13319        105 LQVSFKTNKGK  115 (117)
Q Consensus       105 l~v~~a~~~~~  115 (117)
                      |+|++++.+++
T Consensus        87 l~V~~a~~~~r   97 (97)
T 2xnq_A           87 LILEVSSSNAR   97 (97)
T ss_dssp             CEEEECCCCC-
T ss_pred             EEEEecCCCCC
Confidence            99999987653

>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=99.84  E-value=4.2e-20  Score=107.43  Aligned_cols=80  Identities=18%  Similarity=0.156  Sum_probs=71.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l~v  107 (117)
                      .+++++|||+|||..+++++|+++|..||.|..+.++.+      +|||||+|.+.++|..|+..+++  ..+.|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999988653      78999999999999999998865  4589999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      +|++.+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99987543

>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=99.84  E-value=3.1e-20  Score=110.18  Aligned_cols=81  Identities=19%  Similarity=0.275  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l~  106 (117)
                      ..+++++|||+|||+++++++|+++|..||.|..+.++.+      +|||||+|.+.++|++|+..+++  ..+.|+.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3456789999999999999999999999999999998865      78999999999999999998874  689999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.|++.+..
T Consensus       101 V~~a~~k~~  109 (119)
T 2ad9_A          101 IQFSNHKEL  109 (119)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCCCC
Confidence            999987553

>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=99.84  E-value=1.1e-19  Score=106.29  Aligned_cols=79  Identities=20%  Similarity=0.248  Sum_probs=72.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC-----eE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-----RI  104 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g-----~~  104 (117)
                      ....++|||+|||+++++++|+++|..||.|..+.++.+       |||||+|.+.++|+.|++.|++..+.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            456789999999999999999999999999999988765       799999999999999999999999999     99


Q ss_pred             EEEEEecCCCC
Q psy13319        105 LQVSFKTNKGK  115 (117)
Q Consensus       105 l~v~~a~~~~~  115 (117)
                      |+|.+++++..
T Consensus        85 i~V~~a~~~~~   95 (108)
T 1x4c_A           85 IRVKVDGPRSP   95 (108)
T ss_dssp             EEEEESSCCSC
T ss_pred             EEEEeCCCCCC
Confidence            99999887543

>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=99.84  E-value=5.5e-20  Score=106.60  Aligned_cols=83  Identities=17%  Similarity=0.359  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .....++|||+|||+++++++|+++|..||. ..+.++.++ +++++|||||+|.+.++|++|+. +++..+.++.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3456789999999999999999999999995 499999987 89999999999999999999996 79999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      .+....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987654

>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=99.83  E-value=5.9e-20  Score=105.37  Aligned_cols=82  Identities=23%  Similarity=0.474  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC--CeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG--NRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~--g~~l~  106 (117)
                      ..++.++|||+|||.++++++|+++|..||.|..+.+..+      +|||||+|.+.++|++|+..|++..+.  |+.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3456788999999999999999999999999999988643      679999999999999999999999999  99999


Q ss_pred             EEEecCCCCC
Q psy13319        107 VSFKTNKGKT  116 (117)
Q Consensus       107 v~~a~~~~~~  116 (117)
                      |.|+++++.+
T Consensus        87 V~~a~~~~~~   96 (97)
T 1why_A           87 VDFAKSGPSS   96 (97)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999987653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.83  E-value=2.2e-20  Score=112.14  Aligned_cols=83  Identities=16%  Similarity=0.326  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHH----HhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLW----QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      ..+++++|||+|||+.+++++|+    ++|+.||.|..+.+.   .++.++|||||+|.+.++|..|+..|+|..+.|+.
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34567899999999999998865    699999999988764   35788999999999999999999999999999999


Q ss_pred             EEEEEecCCC
Q psy13319        105 LQVSFKTNKG  114 (117)
Q Consensus       105 l~v~~a~~~~  114 (117)
                      |+|.|++.+.
T Consensus       102 l~V~~a~~~~  111 (127)
T 2a3j_A          102 LVITFSETPQ  111 (127)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCcc
Confidence            9999998654

>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=99.83  E-value=2e-21  Score=110.02  Aligned_cols=80  Identities=35%  Similarity=0.451  Sum_probs=73.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK  113 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  113 (117)
                      ++|||+|||.++++++|+++|+.||.|..+.+..++.++.++|||||+|.+.+ |..|+..++|..+.|+.|+|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999888999999999999999 99999999999999999999998865


Q ss_pred             C
Q psy13319        114 G  114 (117)
Q Consensus       114 ~  114 (117)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.83  E-value=5e-21  Score=104.99  Aligned_cols=75  Identities=27%  Similarity=0.388  Sum_probs=71.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|+. +++..+.|+.|+|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998889999999999999999999998 8999999999999875

>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=99.83  E-value=1.9e-20  Score=107.26  Aligned_cols=83  Identities=20%  Similarity=0.442  Sum_probs=75.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLW----QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .+++++|||+|||.++++++|+    ++|..||.|..+.+..   ++.++|||||+|.+.++|+.|+..|+|..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4567899999999999999999    9999999999988763   46778999999999999999999999999999999


Q ss_pred             EEEEecCCCC
Q psy13319        106 QVSFKTNKGK  115 (117)
Q Consensus       106 ~v~~a~~~~~  115 (117)
                      +|+++++++.
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987654

>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=99.83  E-value=8.5e-21  Score=111.92  Aligned_cols=83  Identities=29%  Similarity=0.473  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCe----EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAV----QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      ..+++++|||+|||..+++++|+++|..||.|    ..+.+.    ++.++|||||+|.+.++|+.|+..|++..+.|+.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   96 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI   96 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            34567899999999999999999999999998    444443    6888999999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy13319        105 LQVSFKTNKGK  115 (117)
Q Consensus       105 l~v~~a~~~~~  115 (117)
                      |+|.+++++..
T Consensus        97 l~v~~a~~~~~  107 (115)
T 2cpx_A           97 LVIEFGKNKKQ  107 (115)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEEccCCCC
Confidence            99999987654

>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=8.7e-20  Score=102.17  Aligned_cols=76  Identities=21%  Similarity=0.336  Sum_probs=70.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL-NGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~  108 (117)
                      ....++|||+|||..+++++|+++|..||.|..+.+..+      +|+|||+|.+.++|+.|+..| ++..+.|+.|+|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            456788999999999999999999999999999988764      789999999999999999988 9999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            975

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.83  E-value=5.7e-20  Score=107.53  Aligned_cols=80  Identities=31%  Similarity=0.538  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|..+.+.        +|||||+|.+.++|+.|+..|+|..+.|+.|+|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34577899999999999999999999999999999886        6799999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      ++++++++
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99876653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=8.4e-21  Score=104.47  Aligned_cols=76  Identities=26%  Similarity=0.435  Sum_probs=72.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ++|||+|||.++++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|++|+..++ ..+.|+.|+|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            469999999999999999999999999999999998889999999999999999999999988 8899999999986

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.83  E-value=4.8e-20  Score=105.48  Aligned_cols=82  Identities=20%  Similarity=0.293  Sum_probs=73.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||..+++++|+++|..||.|..+     ..++.++|||||+|.+.++|+.|+..++|..+.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4567899999999999999999999999987655     24588899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      +.++++.
T Consensus        88 a~~~~~~   94 (96)
T 1fjc_A           88 TGEKGGT   94 (96)
T ss_dssp             CSSSCCC
T ss_pred             cCCCCCC
Confidence            9877653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=2.2e-19  Score=102.06  Aligned_cols=78  Identities=23%  Similarity=0.411  Sum_probs=71.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||..+++++|+++|..||.|..+.++        ++||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4677899999999999999999999999999999886        33999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++++.+
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            987654

>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=99.83  E-value=9.9e-21  Score=113.19  Aligned_cols=83  Identities=25%  Similarity=0.365  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||+++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|++|+. +++..+.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34567899999999999999999999999999876566666789999999999999999999999 99999999999999


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      ++..
T Consensus       100 ~a~~  103 (124)
T 1wel_A          100 PITK  103 (124)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9864

>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=1.3e-19  Score=117.15  Aligned_cols=83  Identities=22%  Similarity=0.446  Sum_probs=77.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||+++++++|+++|+.||.|..++++.++.++.++|||||+|.+.++|..|+..+++..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>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=2.4e-20  Score=113.23  Aligned_cols=82  Identities=16%  Similarity=0.243  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCC---eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGA---VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ...+.++|||+|||+++++++|+++|..||.   |..+.++.++. |+++|||||+|.+.++|++|+. +++..+.|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   88999999876 9999999999999999999999 99999999999


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      +|.++..
T Consensus       118 ~V~~a~~  124 (136)
T 2hgl_A          118 EVFKSHR  124 (136)
T ss_dssp             EEEECCH
T ss_pred             EEEECCh
Confidence            9998764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=5.9e-20  Score=105.40  Aligned_cols=84  Identities=19%  Similarity=0.255  Sum_probs=73.8

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         27 NTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        27 ~~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ....+..++|||+|||.++++++|+++|..||.|. +.++.    +.++|||||+|.+.++|+.|+..|+|..+.|+.|+
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            33455678999999999999999999999999986 55554    35688999999999999999999999999999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.+++++++
T Consensus        88 V~~a~~~~~   96 (97)
T 2e5j_A           88 VALARQQRD   96 (97)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCCC
Confidence            999998764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.6e-19  Score=101.96  Aligned_cols=79  Identities=32%  Similarity=0.458  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCC--CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPF--GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ...+.++|||+|||..+++++|+++|..|  |.|..+.+.        +|||||+|.+.++|+.|+..|++..+.|+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34567899999999999999999999999  889888653        56999999999999999999999999999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |.+++++.+
T Consensus        83 v~~a~~~~~   91 (99)
T 2cpd_A           83 VTLAKPVDK   91 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EEECCCCCC
Confidence            999987654

>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=99.82  E-value=7.4e-20  Score=107.92  Aligned_cols=80  Identities=20%  Similarity=0.446  Sum_probs=74.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+.+++|||+|||..+++++|+++|..||.|..+.++.+   +.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999865   45589999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +.+
T Consensus        82 a~~   84 (115)
T 3lqv_A           82 YNA   84 (115)
T ss_dssp             CCH
T ss_pred             ecC
Confidence            875

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=2.9e-21  Score=111.61  Aligned_cols=85  Identities=18%  Similarity=0.290  Sum_probs=75.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||.++++++|+++|..||.+.. .++.+..++.++|||||+|.+.++|++|+. +++..+.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            456789999999999999999999999998866 555666678889999999999999999999 999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      ++++..+
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9876543

>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=99.82  E-value=1.2e-19  Score=106.13  Aligned_cols=80  Identities=21%  Similarity=0.478  Sum_probs=73.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||..+++++|+++|..||.|..+.++.+      +|||||+|.+.++|++|+..|+|..+.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            346789999999999999999999999999999998765      78999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++++..
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987653

>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=1.8e-19  Score=105.81  Aligned_cols=80  Identities=20%  Similarity=0.344  Sum_probs=71.1

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CcEeCCeEEE
Q psy13319         30 NGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN--GYALGNRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--~~~~~g~~l~  106 (117)
                      ..++++|||+|||++ +++++|+++|..||.|..+.++..      +|||||+|.+.++|+.|+..|+  +..+.|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457889999999998 999999999999999999988643      7899999999999999999885  4568999999


Q ss_pred             EEEecCCCC
Q psy13319        107 VSFKTNKGK  115 (117)
Q Consensus       107 v~~a~~~~~  115 (117)
                      |++++.+.+
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999986543

>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=6.5e-19  Score=109.00  Aligned_cols=83  Identities=29%  Similarity=0.512  Sum_probs=78.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||..+++++|+++|+.||.|..+.+..++.+|.++|+|||+|.+.++|.+|+..|+|..+.|+.|+|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      ||+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            986

>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=99.82  E-value=4.8e-20  Score=120.65  Aligned_cols=81  Identities=16%  Similarity=0.180  Sum_probs=76.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCC--CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFG--AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..++|||+|||+++++++|+++|..||  .|..+.++.++.+++++|||||+|.+.++|++|+..|++..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      ++.
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            764

>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=99.82  E-value=2.6e-19  Score=104.86  Aligned_cols=78  Identities=24%  Similarity=0.375  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         29 MNGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      .....++|||+|||.. +++++|+++|..||.|..+.+        .+|||||+|.+.++|+.|+..|++..+.|+.|+|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3445689999999999 999999999999999999887        3789999999999999999999999999999999


Q ss_pred             EEecCCC
Q psy13319        108 SFKTNKG  114 (117)
Q Consensus       108 ~~a~~~~  114 (117)
                      .+++..+
T Consensus        95 ~~a~~~~  101 (110)
T 1wf1_A           95 NMAGEPK  101 (110)
T ss_dssp             EESCCCC
T ss_pred             EECCCCC
Confidence            9988533

>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=99.82  E-value=3.7e-19  Score=110.21  Aligned_cols=82  Identities=29%  Similarity=0.500  Sum_probs=77.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +++|||+|||+++++++|+++|..||.|..+.++.++.+|.++|+|||+|.+.++|..|+..++|..+.|+.|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57899999999999999999999999999999999988899999999999999999999999999999999999999876


Q ss_pred             CC
Q psy13319        113 KG  114 (117)
Q Consensus       113 ~~  114 (117)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.9e-19  Score=101.93  Aligned_cols=80  Identities=31%  Similarity=0.477  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.|..+.++        ++||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34667889999999999999999999999999999886        3399999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      ++++..++
T Consensus        77 ~a~~~~~~   84 (90)
T 2dnp_A           77 LSTKGQKK   84 (90)
T ss_dssp             ESCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.7e-19  Score=105.72  Aligned_cols=80  Identities=20%  Similarity=0.267  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||+++++++|+++|..| .|..+.++.++. |+++|+|||+|.+.++|++|+ .+++..++|+.|+|..
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            4456899999999999999999999999 899999998865 999999999999999999999 5899999999999987


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +..
T Consensus        90 a~~   92 (109)
T 2dnn_A           90 ATE   92 (109)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            653

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=1e-19  Score=105.07  Aligned_cols=77  Identities=22%  Similarity=0.323  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +.+++|||+|||.++++++|+++|..||.|..+.+..      .+|||||+|.+.++|..|+..|+|..+.|+.|+|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            4578999999999999999999999999999998863      3789999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=5e-19  Score=112.57  Aligned_cols=87  Identities=24%  Similarity=0.399  Sum_probs=82.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||..+++++|+++|..||.|..+.+..++.++.++|+|||+|.+.++|.+|+..|+|..+.|+.|+|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35778999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      ++++.++
T Consensus       191 a~~~~~~  197 (198)
T 2yh0_A          191 ASVGAKN  197 (198)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9987765

>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=99.81  E-value=3e-19  Score=103.47  Aligned_cols=78  Identities=28%  Similarity=0.471  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||.++++++|+++|..||.|..+.++        ++||||+|.+.++|++|+..|++..+.|+.|+|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            4567889999999999999999999999999998875        45999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++++..
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            886543

>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=99.81  E-value=2.5e-19  Score=111.28  Aligned_cols=83  Identities=29%  Similarity=0.508  Sum_probs=78.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ++++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|+|||+|.+.++|+.|+..++|..+.|+.|+|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46789999999999999999999999999999999998889999999999999999999999999999999999999988


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.81  E-value=1.4e-19  Score=101.35  Aligned_cols=73  Identities=21%  Similarity=0.230  Sum_probs=68.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.-|||+||++.+++++|+++|..||+|..+.+..      ++|||||+|.+.++|..|++.||+..+.|+.|+|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45699999999999999999999999999998865      48999999999999999999999999999999999985

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=2.9e-20  Score=103.41  Aligned_cols=73  Identities=25%  Similarity=0.390  Sum_probs=67.0

Q ss_pred             CcEEEEeCCCCCC------CHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe-EE
Q psy13319         33 GWCIFVYNLAPET------EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR-IL  105 (117)
Q Consensus        33 ~~~l~v~~Lp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~-~l  105 (117)
                      +++|||+|||..+      ++++|+++|+.||.|..+.+.  +.+|.++|||||+|.+.++|++|+..|+|..+.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4689999999999      679999999999999999876  46789999999999999999999999999999998 87


Q ss_pred             EE
Q psy13319        106 QV  107 (117)
Q Consensus       106 ~v  107 (117)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=1.1e-19  Score=106.81  Aligned_cols=80  Identities=18%  Similarity=0.142  Sum_probs=71.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....++|||+|||+++++++|+++|..|| .|..+.+..    +.++|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            45678999999999999999999999999 898887742    3468999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      +++..
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98754

>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=99.81  E-value=3.1e-20  Score=108.44  Aligned_cols=82  Identities=13%  Similarity=0.148  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCC---eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGA---VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      .....++|||+|||+++++++|+++|..||.   |..+.++.++. |.++|+|||+|.+.++|++|+. +++..++|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3567889999999999999999999999888   88999988876 9999999999999999999999 89999999999


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      +|.++..
T Consensus        85 ~V~~a~~   91 (107)
T 2lmi_A           85 EVYEINN   91 (107)
T ss_dssp             CCEECCH
T ss_pred             EEEECCH
Confidence            9998764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=1.9e-21  Score=115.03  Aligned_cols=86  Identities=24%  Similarity=0.362  Sum_probs=79.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE--------EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      ..+.++|||+|||..+++++|+++|..||.|..        +.++.++.++.++|||||+|.+.++|++|+..|++..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            356788999999999999999999999999988        888888888999999999999999999999999999999


Q ss_pred             CeEEEEEEecCCCC
Q psy13319        102 NRILQVSFKTNKGK  115 (117)
Q Consensus       102 g~~l~v~~a~~~~~  115 (117)
                      |+.|+|.+++++..
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999887654

>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=99.81  E-value=1.5e-19  Score=102.84  Aligned_cols=80  Identities=25%  Similarity=0.411  Sum_probs=70.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCC-eEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-cEeCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG-YALGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~-~~~~g~~l~v  107 (117)
                      .+..++|||+|||.++++++|+++|..||. +..+.+.       .+|||||+|.+.++|+.|+..|+| ..+.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456788999999999999999999999999 5555442       378999999999999999999999 9999999999


Q ss_pred             EEecCCCCC
Q psy13319        108 SFKTNKGKT  116 (117)
Q Consensus       108 ~~a~~~~~~  116 (117)
                      .+++++..+
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999876543

>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=99.81  E-value=2.1e-19  Score=110.56  Aligned_cols=82  Identities=26%  Similarity=0.391  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .....++|||+|||+.+++++|+++|..||.|..+.++.+     ++|||||+|.+.++|..|+..|+|..+.|+.|+|.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3457789999999999999999999999999999998765     47899999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++++++
T Consensus       144 ~a~~~~r  150 (150)
T 2i2y_A          144 LSNGEKR  150 (150)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9988753

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.9e-19  Score=103.07  Aligned_cols=78  Identities=18%  Similarity=0.333  Sum_probs=70.4

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .++.++|||+|||. .+++++|+++|..||.|..+.+.        +|||||+|.+.++|+.|+..|+|..+.|+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            46788999999998 99999999999999999998873        6799999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      +++.+.+
T Consensus        79 ~a~~~~~   85 (96)
T 2kvi_A           79 VSSSNAR   85 (96)
T ss_dssp             EEECCCC
T ss_pred             EcCcCCC
Confidence            9876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.80  E-value=1.1e-19  Score=105.12  Aligned_cols=80  Identities=24%  Similarity=0.383  Sum_probs=74.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|..||.|..+.++.++ +|.++|||||+|.+.++|++|+.  ++..+.|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            456889999999999999999999999999999999997 89999999999999999999998  899999999999987


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ..+
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            644

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.80  E-value=2e-19  Score=113.54  Aligned_cols=84  Identities=20%  Similarity=0.307  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....+++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|+.|+..|++..+.|+.|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999887 89999999999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      ++...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            98754

>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=2.4e-18  Score=98.63  Aligned_cols=80  Identities=23%  Similarity=0.375  Sum_probs=71.5

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....+.++|||+||  ++++++|+++|..||.|..+.+.      ..+|||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34557789999996  89999999999999999999884      34789999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .++++++.
T Consensus        82 ~~a~~~~~   89 (97)
T 1x5p_A           82 NIARKQPM   89 (97)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=9.5e-20  Score=105.17  Aligned_cols=77  Identities=23%  Similarity=0.394  Sum_probs=71.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK  113 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  113 (117)
                      ++|||+|||.++++++|+++|+.||.|..+.+..+     ++|||||+|.+.++|++|+..|++..+.|+.|+|.+++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999988766     5789999999999999999999999999999999999875


Q ss_pred             CC
Q psy13319        114 GK  115 (117)
Q Consensus       114 ~~  115 (117)
                      .+
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.80  E-value=1e-18  Score=110.99  Aligned_cols=84  Identities=24%  Similarity=0.390  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..++.++|||+|||+++++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|+.|+.. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            346788999999999999999999999999999999999998999999999999999999999986 8999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      ++...
T Consensus        88 ~~~~~   92 (196)
T 1l3k_A           88 RAVSR   92 (196)
T ss_dssp             ECCC-
T ss_pred             cccCc
Confidence            97654

>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=99.80  E-value=6.6e-19  Score=107.50  Aligned_cols=83  Identities=27%  Similarity=0.426  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEE--------EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQS--------VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ...++++|||+|||+.+++++|+++|..||.|..        +.+.   .++.++|||||+|.+.++|.+|+..|+|..+
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            3567789999999999999999999999998865        3333   3588899999999999999999999999999


Q ss_pred             CCeEEEEEEecCCC
Q psy13319        101 GNRILQVSFKTNKG  114 (117)
Q Consensus       101 ~g~~l~v~~a~~~~  114 (117)
                      .|+.|+|.+++...
T Consensus       118 ~g~~l~V~~a~~~~  131 (143)
T 3egn_A          118 FGKPMVVQFARSAR  131 (143)
T ss_dssp             TTEECEEEECCCSC
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999997643

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.80  E-value=1.2e-18  Score=112.07  Aligned_cols=84  Identities=25%  Similarity=0.406  Sum_probs=79.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||..+++++|+++|..||.|..+.+..++.+|.++|+|||+|.+.++|.+|+..|+|..++|+.|+|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .+..
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

>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=9.6e-19  Score=123.68  Aligned_cols=83  Identities=18%  Similarity=0.343  Sum_probs=78.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||..+++++|.++|..||.|..|.++.++.++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            764

>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=99.79  E-value=1.5e-18  Score=108.20  Aligned_cols=82  Identities=23%  Similarity=0.397  Sum_probs=77.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||..+++++|+++|..||.|..+.+..++.+|.++|+|||+|.+.++|.+|+..|+|..+.|+.|+|+|
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            34578899999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ec
Q psy13319        110 KT  111 (117)
Q Consensus       110 a~  111 (117)
                      |.
T Consensus       171 As  172 (172)
T 2g4b_A          171 AS  172 (172)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>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=99.79  E-value=2.1e-19  Score=105.62  Aligned_cols=77  Identities=19%  Similarity=0.109  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+|||..+++++|+++|..||.|..+.+..      .+|+|||+|.+.++|+.|+..|+|..+.|+.|+|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3567999999999999999999999999999988753      3679999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            753

>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=99.79  E-value=3e-20  Score=101.77  Aligned_cols=75  Identities=29%  Similarity=0.469  Sum_probs=70.7

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +|||+|||.++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|+|.+|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            489999999999999999999999999999999988899999999999999999999995 889999999999875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.7e-19  Score=101.31  Aligned_cols=80  Identities=29%  Similarity=0.358  Sum_probs=71.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEE-EEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....++|||+|||+++++++|+++|..||.|..+ .++.++.++    .|||+|.+.++|+.|+..|+|..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456889999999999999999999999999999 477665433    39999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99876

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.7e-18  Score=98.76  Aligned_cols=78  Identities=23%  Similarity=0.325  Sum_probs=69.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|..||.|..+  +.++.++.   ||||+|.+.++|++|+. +++..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            456789999999999999999999999999987  55555554   99999999999999999 9999999999999987


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .++.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.2e-18  Score=103.74  Aligned_cols=79  Identities=14%  Similarity=0.221  Sum_probs=71.3

Q ss_pred             cEEEEeCC----CCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCC----H-HH---HHHHHH--HhCCcE
Q psy13319         34 WCIFVYNL----APETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN----Y-DE---AVVAIQ--SLNGYA   99 (117)
Q Consensus        34 ~~l~v~~L----p~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~----~-~~---a~~a~~--~l~~~~   99 (117)
                      ..|||+||    |+.+++.+|+++|+.||.|.++.+..|+.||.++|||||+|.+    . .+   |.+|+.  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999995    3 22   788888  789999


Q ss_pred             eCCeEEEEEEecC
Q psy13319        100 LGNRILQVSFKTN  112 (117)
Q Consensus       100 ~~g~~l~v~~a~~  112 (117)
                      +.|+.|+|.+.+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998664

>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=99.78  E-value=2.4e-18  Score=97.00  Aligned_cols=75  Identities=24%  Similarity=0.308  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||+++++++|+++|..| .|..+.+.      .++|||||+|.+.++|++|+..++|..+.|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 89888774      458999999999999999999999999999999999987


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      .+
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=3.7e-19  Score=106.24  Aligned_cols=80  Identities=15%  Similarity=0.179  Sum_probs=72.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCe----EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAV----QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      ++.++|||+|||+++++++|+++|..||.|    ..+.++.+ .+|+++|||||+|.+.++|++|+.. ++..++++.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            567899999999999999999999999875    68888888 4799999999999999999999996 99999999999


Q ss_pred             EEEecC
Q psy13319        107 VSFKTN  112 (117)
Q Consensus       107 v~~a~~  112 (117)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            988753

>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=99.78  E-value=4.4e-19  Score=106.25  Aligned_cols=81  Identities=16%  Similarity=0.203  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE--EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQ--SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      .....++|||+|||+++++++|+++|..| .|.  .+.++.++. |+++|||||+|.+.++|++|+.. ++..++|+.|+
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            34567889999999999999999999999 576  899988876 99999999999999999999995 78899999999


Q ss_pred             EEEecC
Q psy13319        107 VSFKTN  112 (117)
Q Consensus       107 v~~a~~  112 (117)
                      |..+..
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            988764

>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=99.77  E-value=5.4e-18  Score=107.61  Aligned_cols=83  Identities=23%  Similarity=0.314  Sum_probs=75.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            4568999999999999999999999999999999999988899999999999999999999986 799999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .++.
T Consensus       181 ~~k~  184 (196)
T 1l3k_A          181 LSKQ  184 (196)
T ss_dssp             C---
T ss_pred             CChh
Confidence            8654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.8e-18  Score=97.75  Aligned_cols=75  Identities=23%  Similarity=0.290  Sum_probs=66.0

Q ss_pred             CCCcE-EEEeCCCCCCCHHH----HHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         31 GSGWC-IFVYNLAPETEESV----LWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        31 ~~~~~-l~v~~Lp~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      +++.+ |||+|||..+++++    |+++|..|| .|..+       ++   |+|||.|.+.++|++|++.|+|..+.|+.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34555 99999999999887    558999995 98877       33   89999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy13319        105 LQVSFKTNKGK  115 (117)
Q Consensus       105 l~v~~a~~~~~  115 (117)
                      |+|+||+.+++
T Consensus        76 i~v~~A~~~sd   86 (96)
T 2diu_A           76 IIVSFTPKNRE   86 (96)
T ss_dssp             CEEESSCCSCC
T ss_pred             EEEEecCCCcc
Confidence            99999987764

>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=99.77  E-value=1e-17  Score=103.95  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=76.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v  107 (117)
                      ....++|||+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|.+|+..|+|..+.|  ++|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            4567899999999999999999999999999999999998889999999999999999999999999999977  99999


Q ss_pred             EEe
Q psy13319        108 SFK  110 (117)
Q Consensus       108 ~~a  110 (117)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            886

>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=5.7e-18  Score=104.74  Aligned_cols=80  Identities=28%  Similarity=0.454  Sum_probs=73.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK  113 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  113 (117)
                      ++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|+|||+|.+.++|..|+..++|..+.|+.|+|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            579999999999999999999999999999998886 4778999999999999999999999999999999999998754


Q ss_pred             C
Q psy13319        114 G  114 (117)
Q Consensus       114 ~  114 (117)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.77  E-value=1e-18  Score=108.42  Aligned_cols=81  Identities=21%  Similarity=0.357  Sum_probs=76.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||..+++++|+++|+.||.|..+.+..++.+|.++|+|||+|.+.++|.+|+. +++..+.|+.|+|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            46789999999999999999999999999999999988889999999999999999999998 79999999999999998


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=1.4e-17  Score=99.96  Aligned_cols=77  Identities=26%  Similarity=0.285  Sum_probs=68.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEEE
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGF-GFVTMTNYDEAVVAIQSLNGYALGN--RILQVSF  109 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~  109 (117)
                      --.|||+||++.+++++|+++|+.||.|..+.+....     +|+ |||+|.+.++|+.|++.|+|..+.|  ..|+|+|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            3468899999999999999999999999999876542     567 9999999999999999999999987  8999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      ++.+.
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98653

>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=99.76  E-value=1.9e-19  Score=109.56  Aligned_cols=82  Identities=20%  Similarity=0.384  Sum_probs=73.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+++++++|+++|..|| +..+.++.++. ++++|||||+|.+.++|++|+ .+++..+.++.|+|..
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            45678899999999999999999999999 67999998875 999999999999999999999 6899999999999998


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      +....
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            77643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=5.8e-18  Score=109.41  Aligned_cols=80  Identities=33%  Similarity=0.504  Sum_probs=74.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ...+|||+|||..+++++|+++|..||.|..+.++.+.  +.++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999998874  4579999999999999999999999999999999999987


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.76  E-value=6.8e-18  Score=108.75  Aligned_cols=77  Identities=21%  Similarity=0.309  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCC-CCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         31 GSGWCIFVYNLA-PETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++++|||+||| ..+++++|+++|..||.|..++++.+     .+|+|||+|.+.++|+.|++.|||..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            357899999999 79999999999999999999998754     278999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      ++.
T Consensus        77 s~~   79 (205)
T 3tyt_A           77 SKQ   79 (205)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            864

>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=7e-18  Score=95.41  Aligned_cols=77  Identities=23%  Similarity=0.302  Sum_probs=62.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE--eCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA--LGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~--~~g~~l~v  107 (117)
                      ..+..+|||+|||+++++++|+++|+.||.|..+.++.+     ++|||||+|.+.++|++    +++..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            456788999999999999999999999999999988764     58999999999999884    45544  56999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .++.++..
T Consensus        79 ~~a~~k~~   86 (89)
T 3d2w_A           79 SNAEPKHN   86 (89)
T ss_dssp             EECC----
T ss_pred             EEcCCCCc
Confidence            99987654

>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=99.75  E-value=1.1e-17  Score=103.89  Aligned_cols=79  Identities=24%  Similarity=0.233  Sum_probs=70.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~  109 (117)
                      ...+|||+||++.+++++|+++|++||.|..+.+...    ..+|+|||+|.+.++|+.|++.|+|..+.|  +.|+|+|
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            3457899999999999999999999999999988543    247899999999999999999999999965  9999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      ++++.
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            98753

>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=1.3e-17  Score=104.06  Aligned_cols=83  Identities=27%  Similarity=0.349  Sum_probs=74.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCcEeC---CeEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN--KCKGFGFVTMTNYDEAVVAIQSLNGYALG---NRILQ  106 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~~~~~~---g~~l~  106 (117)
                      +.++|||+|||+++++++|+++|..||.|..+.++.++.++  .++|||||+|.+.++|++|+..+++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            57899999999999999999999999999999999998776  78999999999999999999999997765   66788


Q ss_pred             EEEecCCC
Q psy13319        107 VSFKTNKG  114 (117)
Q Consensus       107 v~~a~~~~  114 (117)
                      +.++....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88766543

>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=5.5e-18  Score=109.03  Aligned_cols=82  Identities=30%  Similarity=0.426  Sum_probs=74.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|.+|+..+++..+.|+.|+|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            56789999999999999999999999999999999988889999999999999999999999999999999999998876


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ..
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.75  E-value=1.4e-17  Score=103.04  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=75.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE--EEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI--LQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~--l~v  107 (117)
                      ....++|||+|||..+++++|+++|..||.|..+.+..++.+|.++|+|||+|.+.++|.+|+..|+|..+.|+.  |+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            345688999999999999999999999999999999999888999999999999999999999999999999865  888


Q ss_pred             EEe
Q psy13319        108 SFK  110 (117)
Q Consensus       108 ~~a  110 (117)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>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=99.75  E-value=3.2e-18  Score=101.07  Aligned_cols=75  Identities=21%  Similarity=0.245  Sum_probs=65.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE-----E
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI-----L  105 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~-----l  105 (117)
                      ...++|||+|||.++++++|+++|..||.|..+.++.+       |||||+|.+.++|+.|++.|++..+.|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45688999999999999999999999999999988654       79999999999999999999999999988     7


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      +|..+.+
T Consensus        87 ~v~~~~~   93 (115)
T 3beg_B           87 RVKVDGP   93 (115)
T ss_dssp             EEEECC-
T ss_pred             EeccCCC
Confidence            7777554

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.5e-18  Score=100.22  Aligned_cols=74  Identities=18%  Similarity=0.276  Sum_probs=62.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQT---NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ...++|||+|||+++++++|+++|..||.|. +.++.+..+   |.++|||||+|.+.++|++|+..++  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568899999999999999999999999998 777777666   7889999999999999999999882  244444443

>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=99.75  E-value=6.2e-18  Score=99.45  Aligned_cols=78  Identities=18%  Similarity=0.212  Sum_probs=68.9

Q ss_pred             CCCCcEEEE--eCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe-----CC
Q psy13319         30 NGSGWCIFV--YNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL-----GN  102 (117)
Q Consensus        30 ~~~~~~l~v--~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~-----~g  102 (117)
                      .++.++|||  +||+.++++++|+++|..||.|..+.+..      .+|||||+|.+.++|++|++.|||..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345788999  77999999999999999999999887643      278999999999999999999999988     68


Q ss_pred             eEEEEEEecCC
Q psy13319        103 RILQVSFKTNK  113 (117)
Q Consensus       103 ~~l~v~~a~~~  113 (117)
                      +.|.|.|+...
T Consensus        96 ~~l~v~~a~~~  106 (114)
T 2cq2_A           96 ITLYLNFVEKV  106 (114)
T ss_dssp             EECEEEEESCC
T ss_pred             cEEEEEecccC
Confidence            89999998753

>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=99.75  E-value=2.2e-17  Score=103.22  Aligned_cols=80  Identities=19%  Similarity=0.295  Sum_probs=72.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||..+++++|+++|+.||.|..+     ..++.++|+|||+|.+.++|.+|+..|+|..+.|+.|+|.|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            4567899999999999999999999999987665     45688899999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      +.+++
T Consensus       171 a~~k~  175 (175)
T 1fje_B          171 TGEKG  175 (175)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98763

>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=2.6e-17  Score=109.99  Aligned_cols=82  Identities=21%  Similarity=0.449  Sum_probs=74.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLW----QLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ..+.++|||+|||.++++++|+    ++|..||.|..+.+..   ++.++|||||+|.+.++|++|+..++|..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4668899999999999999966    8999999999998875   57889999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q psy13319        106 QVSFKTNKG  114 (117)
Q Consensus       106 ~v~~a~~~~  114 (117)
                      +|.|++...
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999987654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=7e-17  Score=96.38  Aligned_cols=74  Identities=20%  Similarity=0.284  Sum_probs=66.1

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEEEec
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGF-GFVTMTNYDEAVVAIQSLNGYALGN--RILQVSFKT  111 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~a~  111 (117)
                      .|||+||++.+++++|+++|+.||.|..+.+...      .|+ |||+|.+.++|..|+..|+|..+.|  +.|+|.+++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4689999999999999999999999999988542      265 9999999999999999999999987  589999998


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ++.
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            654

>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=99.73  E-value=1.4e-17  Score=93.46  Aligned_cols=72  Identities=25%  Similarity=0.461  Sum_probs=65.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCC----C-------CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPF----G-------AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA   99 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~   99 (117)
                      .+.++|||+|||.++++++|+++|..|    |       .+..+.+..+      +|||||+|.+.++|++|+ .++|..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8988887644      789999999999999999 899999


Q ss_pred             eCCeEEEEEE
Q psy13319        100 LGNRILQVSF  109 (117)
Q Consensus       100 ~~g~~l~v~~  109 (117)
                      +.|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999874

>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=99.73  E-value=3.2e-17  Score=102.20  Aligned_cols=81  Identities=20%  Similarity=0.332  Sum_probs=73.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC---CeEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG---NRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~---g~~l~  106 (117)
                      ....++|||+|||..+++++|+++|+.||.|..+.++.++ +|.++|+|||+|.+.++|.+|+..|+|..+.   +++|+
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            3467899999999999999999999999999999998885 5889999999999999999999999998765   48999


Q ss_pred             EEEec
Q psy13319        107 VSFKT  111 (117)
Q Consensus       107 v~~a~  111 (117)
                      |.||.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>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=99.73  E-value=6.8e-18  Score=95.07  Aligned_cols=78  Identities=19%  Similarity=0.261  Sum_probs=65.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|..||.|..+.++.+     ++|||||+|.+.++|+++...  ...+.|+.|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35689999999999999999999999999999988654     588999999999999764321  34568999999998


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.73  E-value=1.6e-17  Score=103.03  Aligned_cols=79  Identities=22%  Similarity=0.439  Sum_probs=72.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ++++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..  +..+.|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999988999999999999999999999994  678899999888865


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.73  E-value=7.1e-17  Score=103.11  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=72.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||.++++++|+++|..||.|..+++..+. ++.++|+|||+|.+.++|+.|+..+ +..+.|+.|.|.+++
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999998875 4889999999999999999999865 568999999999876


Q ss_pred             C
Q psy13319        112 N  112 (117)
Q Consensus       112 ~  112 (117)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.72  E-value=9.4e-17  Score=107.39  Aligned_cols=84  Identities=27%  Similarity=0.413  Sum_probs=78.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +.+++|||+|||..+++++|.++|..||.|..+.++.++.+|.++|+|||+|.+.++|.+|+..++|..+.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35678999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .+..
T Consensus       173 ~~~~  176 (284)
T 3smz_A          173 DAGQ  176 (284)
T ss_dssp             CGGG
T ss_pred             CCCC
Confidence            7643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.72  E-value=1.4e-16  Score=92.63  Aligned_cols=82  Identities=17%  Similarity=0.203  Sum_probs=71.8

Q ss_pred             CCCcEEEEeCCCC-----CCCHHHHHHhhcCCCCeEEEEEEecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         31 GSGWCIFVYNLAP-----ETEESVLWQLFGPFGAVQSVKVIRDLQT-NKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        31 ~~~~~l~v~~Lp~-----~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      .++++|+|.|+..     +-.+++|++.|++||.|..+.++.++.+ +.++|++||+|.+.++|.+|+..|||..+.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4577899999963     2367899999999999999999987644 578999999999999999999999999999999


Q ss_pred             EEEEEecC
Q psy13319        105 LQVSFKTN  112 (117)
Q Consensus       105 l~v~~a~~  112 (117)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>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=99.72  E-value=3.6e-17  Score=109.80  Aligned_cols=83  Identities=28%  Similarity=0.416  Sum_probs=76.0

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCC-CCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQ-TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ....++|||+|||.. +++++|+++|..||.|..+.++.+.. ||.++|+|||+|.+.++|.+|+ .|+|..+.|+.|+|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            456789999999999 99999999999999999999988765 5889999999999999999999 99999999999999


Q ss_pred             EEecCC
Q psy13319        108 SFKTNK  113 (117)
Q Consensus       108 ~~a~~~  113 (117)
                      .|+.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999876

>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=99.72  E-value=1.4e-16  Score=106.61  Aligned_cols=84  Identities=21%  Similarity=0.262  Sum_probs=77.8

Q ss_pred             CCCCcEEEEeCCCCCC-CHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPET-EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....++|||+|||..+ ++++|+++|..||.|..+.++.+. +|.++|+|||+|.+.++|.+|+..|+|..++|+.|+|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            3567889999999995 999999999999999999998885 68899999999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      |+.++.
T Consensus       260 ~a~~~~  265 (284)
T 3smz_A          260 FCAPGP  265 (284)
T ss_dssp             ECCSSS
T ss_pred             EecCCC
Confidence            998764

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.71  E-value=3.3e-17  Score=107.53  Aligned_cols=79  Identities=18%  Similarity=0.280  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCC---------CHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         30 NGSGWCIFVYNLAPET---------EESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ....++|||+||+..+         ++++|+++|..||.|..+.++.+      +|||||+|.+.++|+.|++.|+|..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4578899999999998         69999999999999999998754      78999999999999999999999998


Q ss_pred             ------------CCeEEEEEEecCCC
Q psy13319        101 ------------GNRILQVSFKTNKG  114 (117)
Q Consensus       101 ------------~g~~l~v~~a~~~~  114 (117)
                                  .|+.|.|.||+..+
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999998654

>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=99.70  E-value=4.4e-17  Score=106.28  Aligned_cols=79  Identities=28%  Similarity=0.488  Sum_probs=73.1

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .+++++|||+|||. .+++++|+++|..||.|..+.++.++     +|||||+|.+.++|++|++.++|..+.|+.|+|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            46788999999999 99999999999999999999998764     7899999999999999999999999999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      +++..
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            98754

>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=99.70  E-value=2.6e-16  Score=105.19  Aligned_cols=77  Identities=29%  Similarity=0.467  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~  108 (117)
                      ..++++|||+|||..+++++|+++|..||.|..+.++.++     +|+|||+|.+.++|.+|+..|+|..+. |+.|+|+
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            4467899999999999999999999999999999988553     589999999999999999999999999 9999999


Q ss_pred             Eec
Q psy13319        109 FKT  111 (117)
Q Consensus       109 ~a~  111 (117)
                      |++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            986

>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=99.69  E-value=2.9e-16  Score=104.25  Aligned_cols=80  Identities=30%  Similarity=0.468  Sum_probs=72.4

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         28 TMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ......++|||+|||+++++++|.++|..||.|..+.+..+      +|||||+|.+.++|..|+..++|..+.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            33466789999999999999999999999999999988543      789999999999999999999999999999999


Q ss_pred             EEecCC
Q psy13319        108 SFKTNK  113 (117)
Q Consensus       108 ~~a~~~  113 (117)
                      .++.+.
T Consensus        91 ~~a~~~   96 (261)
T 3sde_A           91 RFATHG   96 (261)
T ss_dssp             EECCCS
T ss_pred             eecccC
Confidence            998753

>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=99.68  E-value=1.2e-15  Score=89.55  Aligned_cols=82  Identities=18%  Similarity=0.218  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEeCCCCCCC-----------HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         29 MNGSGWCIFVYNLAPETE-----------ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~-----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      ...++++|+|.||.....           +++|+++|.+||.|..+.+ .++   .++|+|||+|.+.++|++|+..|+|
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345688999999955432           5799999999999999955 443   3689999999999999999999999


Q ss_pred             cEeCCeEEEEEEecCCC
Q psy13319         98 YALGNRILQVSFKTNKG  114 (117)
Q Consensus        98 ~~~~g~~l~v~~a~~~~  114 (117)
                      ..+.|+.|+|.++.++.
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999987643

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.67  E-value=2.2e-17  Score=103.27  Aligned_cols=84  Identities=17%  Similarity=0.280  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ...+.++|||+|||.++++++|+++|..||.+.. ..+.+..++.++|||||+|.+.++|.+|++ ++|..+.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3567889999999999999999999999987654 223334567889999999999999999995 99999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ++....
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            987643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.66  E-value=1.3e-16  Score=101.62  Aligned_cols=77  Identities=29%  Similarity=0.497  Sum_probs=71.0

Q ss_pred             CCcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ++++|||+|||+ .+++++|+++|..||.|..+.++.++     +|||||+|.+.++|..|+..++|..+.|+.|+|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            367899999999 99999999999999999999887663     689999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      +..
T Consensus        77 ~~~   79 (198)
T 1qm9_A           77 KHQ   79 (198)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.64  E-value=6.7e-16  Score=103.59  Aligned_cols=82  Identities=15%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..++|||+|||..+++++|.++|..|| .|..+.++.++. +.++|||||+|.+.++|..|+..++|..+.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 999999988765 778999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .+..
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            7654

>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=99.64  E-value=9.3e-16  Score=100.00  Aligned_cols=78  Identities=28%  Similarity=0.419  Sum_probs=71.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~  108 (117)
                      +++++|||+|||..+++++|+++|..|| .|..+.+...     .+|+|||+|.+.++|.+|+..|+|..+. |+.|+|+
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999988543     2679999999999999999999999999 9999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      |++++
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            98864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=7.3e-16  Score=98.13  Aligned_cols=78  Identities=28%  Similarity=0.416  Sum_probs=71.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCC-CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFG-AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~  108 (117)
                      +++++|||+|||..+++++|+++|..|| .|..+.++.+.     +|+|||+|.+.++|.+|+..|+|..+. |+.|+|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4688999999999999999999999999 99999886532     689999999999999999999999999 9999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      |++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98764

>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=99.63  E-value=3e-15  Score=99.31  Aligned_cols=81  Identities=28%  Similarity=0.347  Sum_probs=72.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CcEeC---CeEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN-GYALG---NRILQV  107 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~-~~~~~---g~~l~v  107 (117)
                      ++.+|||+|||..+++++|+++|..||.|..+.++.+ .+|.++|+|||+|.+.++|.+|+..++ +..+.   ++.|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4678999999999999999999999999999999988 579999999999999999999999994 45554   899999


Q ss_pred             EEecCC
Q psy13319        108 SFKTNK  113 (117)
Q Consensus       108 ~~a~~~  113 (117)
                      .++...
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            987653

>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=99.63  E-value=2.2e-15  Score=93.75  Aligned_cols=75  Identities=21%  Similarity=0.375  Sum_probs=66.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCC----C-------CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPF----G-------AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      +.++|||+|||+++++++|+++|..|    |       .+..+.+..      .+|||||+|.+.++|++|+ .+++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            56899999999999999999999999    6       666665543      3789999999999999999 7999999


Q ss_pred             CCeEEEEEEecCC
Q psy13319        101 GNRILQVSFKTNK  113 (117)
Q Consensus       101 ~g~~l~v~~a~~~  113 (117)
                      .|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987754

>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=99.62  E-value=1.1e-15  Score=98.40  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=68.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCe--EEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCe----E
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAV--QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNR----I  104 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i--~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~----~  104 (117)
                      +++++|||+|||+.+++++|+++|+.||.|  ..+++..+.  +..+|+|||+|.+.++|..|+..|||..+.|+    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            467899999999999999999999999998  888887664  55579999999999999999999999999876    4


Q ss_pred             EEEEEe
Q psy13319        105 LQVSFK  110 (117)
Q Consensus       105 l~v~~a  110 (117)
                      +.|.+|
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            666554

>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=99.60  E-value=6.7e-15  Score=85.49  Aligned_cols=81  Identities=20%  Similarity=0.244  Sum_probs=69.0

Q ss_pred             CCcEEEEeCC--CCCCC--------HHHHHHhhcCCCCeEEEEEEecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCcE
Q psy13319         32 SGWCIFVYNL--APETE--------ESVLWQLFGPFGAVQSVKVIRDLQT--NKCKGFGFVTMTNYDEAVVAIQSLNGYA   99 (117)
Q Consensus        32 ~~~~l~v~~L--p~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~~~~   99 (117)
                      +++.|.+.|+  |....        +++|++.|++||.|..+.++.++.+  +.++|++||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5677889988  33333        2689999999999999999887654  3578999999999999999999999999


Q ss_pred             eCCeEEEEEEecC
Q psy13319        100 LGNRILQVSFKTN  112 (117)
Q Consensus       100 ~~g~~l~v~~a~~  112 (117)
                      +.|+.|++.++..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999763

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.60  E-value=3.9e-15  Score=94.48  Aligned_cols=75  Identities=21%  Similarity=0.388  Sum_probs=65.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCC----C-------CeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPF----G-------AVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ..++|||+|||+++++++|+++|..|    |       .+..+.+      +..+|||||+|.+.++|++|+ .++|..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       5555544      344889999999999999999 7999999


Q ss_pred             CCeEEEEEEecCC
Q psy13319        101 GNRILQVSFKTNK  113 (117)
Q Consensus       101 ~g~~l~v~~a~~~  113 (117)
                      .|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999997653

>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=99.60  E-value=1.6e-14  Score=85.46  Aligned_cols=80  Identities=24%  Similarity=0.227  Sum_probs=69.2

Q ss_pred             CCcEEEEeCCCCC--C---CHHHHHHhhcCCCCeEEEEEEecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC
Q psy13319         32 SGWCIFVYNLAPE--T---EESVLWQLFGPFGAVQSVKVIRDLQ----TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN  102 (117)
Q Consensus        32 ~~~~l~v~~Lp~~--~---~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g  102 (117)
                      ++++|++.|+-..  +   -+++|++.|.+||.|..+.+..++.    ++..+|++||+|.+.++|.+|+..|||..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            5678999998422  2   2589999999999999999988754    35678999999999999999999999999999


Q ss_pred             eEEEEEEec
Q psy13319        103 RILQVSFKT  111 (117)
Q Consensus       103 ~~l~v~~a~  111 (117)
                      +.|++.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>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=99.59  E-value=7.8e-16  Score=89.31  Aligned_cols=72  Identities=15%  Similarity=0.272  Sum_probs=62.5

Q ss_pred             EeCCCCCCCHHHHHHhh------------cCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         38 VYNLAPETEESVLWQLF------------GPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        38 v~~Lp~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      +.|||..+++++|.+.|            ++||.|..+.++.+.. +.++|++||+|.+.++|.+|+..|||..+.|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            55677777777666665            9999999999988754 7889999999999999999999999999999999


Q ss_pred             EEEEe
Q psy13319        106 QVSFK  110 (117)
Q Consensus       106 ~v~~a  110 (117)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.8e-13  Score=78.73  Aligned_cols=76  Identities=20%  Similarity=0.215  Sum_probs=62.0

Q ss_pred             CcEEEEeCCC-------CCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         33 GWCIFVYNLA-------PETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        33 ~~~l~v~~Lp-------~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ..++-|.-..       ..+++++|+++|..||.|..+.++     +.++|||||+|.+.++|+.|+..+++  +.++.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4455555433       457899999999999999999887     35689999999999999999997544  679999


Q ss_pred             EEEEecCCCC
Q psy13319        106 QVSFKTNKGK  115 (117)
Q Consensus       106 ~v~~a~~~~~  115 (117)
                      +|.|++.++.
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999886553

>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=99.49  E-value=1.1e-13  Score=95.05  Aligned_cols=76  Identities=20%  Similarity=0.249  Sum_probs=63.9

Q ss_pred             CCCCcEEEEeC--CCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC---Ce-
Q psy13319         30 NGSGWCIFVYN--LAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG---NR-  103 (117)
Q Consensus        30 ~~~~~~l~v~~--Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~---g~-  103 (117)
                      ..++.+|||+|  |+..+++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|++.|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45678899999  578899999999999999998876642      3789999999999999999999998773   45 


Q ss_pred             -EEEEEEec
Q psy13319        104 -ILQVSFKT  111 (117)
Q Consensus       104 -~l~v~~a~  111 (117)
                       .|.++|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             56667753

>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=99.45  E-value=1.3e-12  Score=76.84  Aligned_cols=76  Identities=14%  Similarity=0.278  Sum_probs=63.3

Q ss_pred             CCcEEEEeCCCCCCC----------HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC
Q psy13319         32 SGWCIFVYNLAPETE----------ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG  101 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~  101 (117)
                      +++.|.+.|+=..-.          +++|++.|++||.|..+.+..+.    .+|++||+|.+.++|.+|+..|||..++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            456788887733222          25889999999999999886542    4899999999999999999999999999


Q ss_pred             CeEEEEEEec
Q psy13319        102 NRILQVSFKT  111 (117)
Q Consensus       102 g~~l~v~~a~  111 (117)
                      |+.|++.|+.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999975

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=6.1e-12  Score=70.45  Aligned_cols=79  Identities=27%  Similarity=0.379  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEeCCCC----CCCH----HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         29 MNGSGWCIFVYNLAP----ETEE----SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~----~~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ..+++.+|+|.-.+.    .+..    .+|.+.|..||.+..+++..++        +||+|.+.+.|.+|+. |+|..+
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v   73 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKEL   73 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEe
Confidence            346777888887762    3333    5788999999999999998762        8999999999999999 999999


Q ss_pred             CCeEEEEEEecCCCCC
Q psy13319        101 GNRILQVSFKTNKGKT  116 (117)
Q Consensus       101 ~g~~l~v~~a~~~~~~  116 (117)
                      .|+.|+|+++++.+-.
T Consensus        74 ~Gr~LkV~lkt~dW~~   89 (91)
T 2dnr_A           74 LNRTITIALKSPSGPS   89 (91)
T ss_dssp             TTEEEEEEECCCSSCS
T ss_pred             CCeEEEEEeCCCCccc
Confidence            9999999999987654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=1.4e-11  Score=72.91  Aligned_cols=76  Identities=17%  Similarity=0.191  Sum_probs=66.0

Q ss_pred             CCCCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCC-HHHHHHHHHHhC--CcEeCCe
Q psy13319         28 TMNGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN-YDEAVVAIQSLN--GYALGNR  103 (117)
Q Consensus        28 ~~~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~-~~~a~~a~~~l~--~~~~~g~  103 (117)
                      ..-+.++.|||+||+.. +++++|+++|+.||.|..|.+..+..      .|||.|.+ ..+|..++..++  +..+.|.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            34578899999999999 99999999999999999999977743      59999999 899999999985  5778888


Q ss_pred             EEEEEE
Q psy13319        104 ILQVSF  109 (117)
Q Consensus       104 ~l~v~~  109 (117)
                      .+++..
T Consensus        87 ~~~~ev   92 (121)
T 1owx_A           87 EVTWEV   92 (121)
T ss_dssp             SEEEEE
T ss_pred             EEEEEE
Confidence            777765

>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=99.14  E-value=2.1e-10  Score=74.23  Aligned_cols=66  Identities=27%  Similarity=0.251  Sum_probs=58.9

Q ss_pred             CHHHHHHhhcCCCCeEEEEEEecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         46 EESVLWQLFGPFGAVQSVKVIRDLQ----TNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        46 ~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      .++++.+.|.+||.|..+.+..+..    ++.++|++||+|.+.++|.+|+..|+|..+.|+.|++.+..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            4578999999999999999875543    34889999999999999999999999999999999999865

>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=99.09  E-value=3.6e-10  Score=63.60  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=62.6

Q ss_pred             CCCCCcEEEEeCCCCC------CCH---HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Q psy13319         29 MNGSGWCIFVYNLAPE------TEE---SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA   99 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~------~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~   99 (117)
                      ..+++.+|+|.-++..      ..+   .+|.+.|..||.+..+++..++        +||+|.+.+.|.+|+. |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            4577888999888743      222   4688999999999999998772        9999999999999999 99999


Q ss_pred             eCCeEEEEEEec
Q psy13319        100 LGNRILQVSFKT  111 (117)
Q Consensus       100 ~~g~~l~v~~a~  111 (117)
                      +.|+.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.78  E-value=7.9e-08  Score=55.34  Aligned_cols=73  Identities=12%  Similarity=0.207  Sum_probs=65.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCC-----CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPF-----GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI  104 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~  104 (117)
                      .+..+++-+-+||..++...|+.++.++     |.+..+.+..+      .+.|+|+|.+...|-+|.-.|+|..+.|+.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3557889999999999999999999999     99999988776      448999999999999988889999999999


Q ss_pred             EEEE
Q psy13319        105 LQVS  108 (117)
Q Consensus       105 l~v~  108 (117)
                      |++.
T Consensus        92 Lr~g   95 (117)
T 2l9w_A           92 IRSG   95 (117)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            9986

>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=98.09  E-value=2.9e-05  Score=43.77  Aligned_cols=57  Identities=25%  Similarity=0.416  Sum_probs=48.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL   95 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   95 (117)
                      ....+.+++ ++|+.+...||.++|+.||. ..|+++.+.       .|||.|.+++.|..++..+
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            345566777 99999999999999999994 457787763       6999999999999998865

>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=0.00021  Score=39.91  Aligned_cols=79  Identities=11%  Similarity=0.199  Sum_probs=61.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCcEeCC---e--EEE
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK--CKGFGFVTMTNYDEAVVAIQSLNGYALGN---R--ILQ  106 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~~~~~~g---~--~l~  106 (117)
                      .+|-|++||+..+++++.+.++....+.-..++..+.+.+  ..+-||+.|.+.++...-...++|..+.+   .  +..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            3688999999999999999999988776666665543332  25789999999999999999999987642   2  345


Q ss_pred             EEEecC
Q psy13319        107 VSFKTN  112 (117)
Q Consensus       107 v~~a~~  112 (117)
                      |++|--
T Consensus        82 VE~AP~   87 (91)
T 1uw4_A           82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCC
Confidence            666543

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.89  E-value=3.9e-05  Score=43.36  Aligned_cols=55  Identities=25%  Similarity=0.436  Sum_probs=46.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN   96 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   96 (117)
                      .+.+++ ++|+.+...||.++|+.|| -..|+|+.+.       .|||.|.+++.|..++..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            355667 9999999999999999999 5567888763       69999999999999999763

>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=5.1e-05  Score=43.31  Aligned_cols=74  Identities=9%  Similarity=0.059  Sum_probs=60.4

Q ss_pred             CcEEEEeCCCCCCCH-----HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         33 GWCIFVYNLAPETEE-----SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~-----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ..+|+|.||+.++-.     ..++++|..|+......+...-      .-..|.|.+.++|.+|-..|++..+.|+.++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            456999999887522     4778999999988776665442      24789999999999999999999999999999


Q ss_pred             EEecC
Q psy13319        108 SFKTN  112 (117)
Q Consensus       108 ~~a~~  112 (117)
                      -|+.+
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            98763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.64  E-value=0.0014  Score=37.33  Aligned_cols=70  Identities=20%  Similarity=0.183  Sum_probs=54.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcC----C-CCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGP----F-GAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~----~-g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ..+.+|.|.|||..+.++.|+-.|.+    . |.+..+....        +-|+|+|.+...+++.++. ....+.+..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            45678999999999999999999987    2 4566664432        3699999999999999884 3567778887


Q ss_pred             EEEE
Q psy13319        106 QVSF  109 (117)
Q Consensus       106 ~v~~  109 (117)
                      .|.-
T Consensus        77 sV~P   80 (104)
T 2dhx_A           77 SLRP   80 (104)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            7754

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.62  E-value=0.00058  Score=39.92  Aligned_cols=73  Identities=12%  Similarity=0.185  Sum_probs=57.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC-eEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN-RILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g-~~l~v~  108 (117)
                      ....+-|.|-+.|... ...+.+.|..||.|.+....      ....+-+|.|.++.+|++|+.. ||..+.+ -.|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEE
Confidence            3456778899999984 67788999999999876551      1234899999999999999995 9999874 556665


Q ss_pred             Ee
Q psy13319        109 FK  110 (117)
Q Consensus       109 ~a  110 (117)
                      ..
T Consensus        93 p~   94 (119)
T 1wwh_A           93 PC   94 (119)
T ss_dssp             EC
T ss_pred             EC
Confidence            53

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.41  E-value=0.001  Score=37.45  Aligned_cols=80  Identities=14%  Similarity=0.179  Sum_probs=56.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCcEeCC-----eEE
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK--CKGFGFVTMTNYDEAVVAIQSLNGYALGN-----RIL  105 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~~~~~~g-----~~l  105 (117)
                      +-+|-|+.||+..+|+++.+.+..+-.+....++....+.+  ..+-|||.|.+.++...-...++|..+-+     .+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            34588999999999999999998865543333322222211  24579999999999999999999987642     245


Q ss_pred             EEEEecC
Q psy13319        106 QVSFKTN  112 (117)
Q Consensus       106 ~v~~a~~  112 (117)
                      .|++|--
T Consensus        89 ~VE~APy   95 (97)
T 2l08_A           89 VVEFAPF   95 (97)
T ss_dssp             EEEECCC
T ss_pred             EEEecCC
Confidence            5666643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.80  E-value=0.0017  Score=38.49  Aligned_cols=77  Identities=22%  Similarity=0.286  Sum_probs=53.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEE-EEEEe------------cCCCC-CcceEEEEEeCCHHHHHHHHHHhCCc
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQS-VKVIR------------DLQTN-KCKGFGFVTMTNYDEAVVAIQSLNGY   98 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~-~~~~~------------~~~~~-~~~g~~fv~f~~~~~a~~a~~~l~~~   98 (117)
                      ..-|.|-+.|+.. ...+.+.|++||.|.+ .....            .+..+ ....+..|.|.+..+|.+|+. .||.
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            3457788997775 4568889999999855 11100            00001 135688999999999999999 4999


Q ss_pred             EeCCeEEEEEEec
Q psy13319         99 ALGNRILQVSFKT  111 (117)
Q Consensus        99 ~~~g~~l~v~~a~  111 (117)
                      .+.|..|-|...+
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999888877654

>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=96.05  E-value=0.0093  Score=35.95  Aligned_cols=34  Identities=15%  Similarity=0.063  Sum_probs=27.1

Q ss_pred             EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q psy13319         62 SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNG   97 (117)
Q Consensus        62 ~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~   97 (117)
                      ++++.++.  +..+||+||+|.+.++|++|+..+++
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcc
Confidence            34566664  35799999999999999999987764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.50  E-value=0.0099  Score=42.48  Aligned_cols=56  Identities=7%  Similarity=0.151  Sum_probs=40.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHH
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ   93 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~   93 (117)
                      ..+.|+|. .|...++.+|.+.|+.||.|..+.+-.+.     .-|+.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            34789997 79999999999999999999887654432     3599999999988887654

>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=94.96  E-value=0.0075  Score=36.14  Aligned_cols=40  Identities=13%  Similarity=0.020  Sum_probs=35.2

Q ss_pred             CCcceEEEEEeCCHHHHHHHHHHh-CCcEeCCeEEEEEEecC
Q psy13319         72 NKCKGFGFVTMTNYDEAVVAIQSL-NGYALGNRILQVSFKTN  112 (117)
Q Consensus        72 ~~~~g~~fv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~a~~  112 (117)
                      +..+|+++++|.+.+.|++|+..+ +|..+.| .+.+.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            455899999999999999999999 9999999 888887654

>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=94.17  E-value=0.25  Score=35.73  Aligned_cols=56  Identities=25%  Similarity=0.427  Sum_probs=45.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN   96 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   96 (117)
                      ....++|+ +|..+...+|.+.|+.||. ..++++.+       ..+||.|.+.+.|..++..+.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            34566665 9999999999999999995 45666544       269999999999999999874

---

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	117
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-15
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
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:) 2e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-13
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-13
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-11
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-11
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-11
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	6e-10
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	8e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-04

>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 = 72.6 bits (178), Expect = 6e-19
 Identities = 18/74 (24%), Positives = 43/74 (58%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V +L P+  E++L++ F P G + S++V RD+ T +  G+ +V      +A  A+ ++
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 96  NGYALGNRILQVSF 109
           N   +  + +++ +
Sbjct: 63  NFDVIKGKPVRIMW 76

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.7 bits (173), Expect = 5e-18
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQS 94
           I V N+  +  +  + +LF  FG +++V++ + +  T   +GFGFV      +A  A  +
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 70

Query: 95  L-NGYALGNRILQVSFKTNKGKT 116
           L +   L  R L + +  ++   
Sbjct: 71  LCHSTHLYGRRLVLEWADSEVTV 93

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 1e-17
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +++ NL  +     ++ +FG +G    ++ IR   T + +G  +V   +  +A  A   
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYG---PIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 95  LNGYALGNRILQVSFKTNK 113
           L+G+ + NR L V +    
Sbjct: 66  LSGFNVCNRYLVVLYYNAN 84

>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 = 67.6 bits (165), Expect = 1e-16
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 35  CIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
            +F+ NL     ++S +  +F  +G +    V         KGF FV   N   A  A+ 
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVA 68

Query: 94  SLNGYALGNRILQVSFKTNK 113
             +G  +  ++L ++     
Sbjct: 69  GEDGRMIAGQVLDINLAAEP 88

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 1e-16
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L     +  + +L   FG +++  +++D  T   KG+ F    + +    AI  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NG  LG++ L V   +   K +
Sbjct: 64  NGMQLGDKKLLVQRASVGAKNA 85

>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 = 67.3 bits (164), Expect = 1e-16
 Identities = 20/74 (27%), Positives = 39/74 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL+  T E  +++LF   G ++ + +  D       GF FV   +  +A  A++ +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 96  NGYALGNRILQVSF 109
           NG  L +RI++  +
Sbjct: 70  NGTRLDDRIIRTDW 83

>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 = 66.6 bits (162), Expect = 2e-16
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVI---RDLQTNKCKGFGFVTMTNYDEAVVAI 92
           +F+ NL   T E  L  +F   GA++S  +             GFGFV     ++A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 93  QSLNGYALGNRILQVSFKTNKGKTS 117
           + L G+ +    L+V       K +
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 64.6 bits (157), Expect = 9e-16
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL     ++ + +LF  FG ++   V  D ++ +  G   V      +A+ A++  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 61

Query: 96  NGYALGNRILQVSFKT 111
           NG  L  R + +   T
Sbjct: 62  NGVPLDGRPMNIQLVT 77

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 64.6 bits (157), Expect = 1e-15
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL     +  L  +FG +G++    ++RD  T + +G  FV     +EA  AI +L
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 96  NGYAL--GNRILQVSF 109
           N      G++ L V  
Sbjct: 69  NNVIPEGGSQPLSVRL 84

>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 = 64.3 bits (156), Expect = 2e-15
 Identities = 25/81 (30%), Positives = 43/81 (53%)

Query: 29  MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
           M  +   ++V  LA E ++ VL   F PFG +  +++  D +T K +GF FV     ++A
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 89  VVAIQSLNGYALGNRILQVSF 109
             AI ++N   L  R ++V+ 
Sbjct: 61  AAAIDNMNESELFGRTIRVNL 81

>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 = 64.0 bits (155), Expect = 2e-15
 Identities = 22/82 (26%), Positives = 45/82 (54%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           GW +FV ++  E +E  + + F  +G ++++ +  D +T   KG+  V    + +A+ A 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 93  QSLNGYALGNRILQVSFKTNKG 114
           ++LNG  +  + +QV +   KG
Sbjct: 67  EALNGAEIMGQTIQVDWCFVKG 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 = 64.2 bits (156), Expect = 2e-15
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++   +A    + ++ Q F PFG +  ++V         KG+ FV  + ++ A  AI S+
Sbjct: 21  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHESAAHAIVSV 74

Query: 96  NGYALGNRILQVSFKTNK 113
           NG  +   +++  +    
Sbjct: 75  NGTTIEGHVVKCYWGKES 92

>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 = 63.9 bits (155), Expect = 2e-15
 Identities = 21/80 (26%), Positives = 43/80 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L  +  E +LW+LF   G V +  + +D  T + +G+GFV   + ++A  AI+ +
Sbjct: 12  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 71

Query: 96  NGYALGNRILQVSFKTNKGK 115
           +   L  + ++V+  +   K
Sbjct: 72  DMIKLYGKPIRVNKASAHNK 91

>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 = 63.6 bits (154), Expect = 2e-15
 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 4/83 (4%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAV-QSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           IF+ NL PE +E +L+  F  FG + Q+ K++RD  T   KG+ F+   ++D +  AI++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 95  LNGYALGNRILQVSF---KTNKG 114
           +NG  L NR + VS+   K +KG
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSKG 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 9e-15
 Identities = 24/73 (32%), Positives = 40/73 (54%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           C+ V+ L+  T E  L ++F  +G +  V ++ D Q+ + +GF FV   N D+A  A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 95  LNGYALGNRILQV 107
            NG  L  R ++V
Sbjct: 71  ANGMELDGRRIRV 83

>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 = 62.0 bits (150), Expect = 1e-14
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL   T E ++ + F         +V       K + + FV  +N ++AV A+++L
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NG  L    ++V+      K S
Sbjct: 65  NGKVLDGSPIEVTLAKPVDKDS 86

>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 = 62.0 bits (150), Expect = 1e-14
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ ET E  L   +  +G +    V+RD  + + +GFGFVT ++  E   A+   
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-A 81

Query: 96  NGYALGNRILQVSFKTNK 113
             +++  R+++      +
Sbjct: 82  RPHSIDGRVVEPKRAVAR 99

>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 = 61.6 bits (149), Expect = 2e-14
 Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 25  PANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN 84
           P+   +G G  IF+ NL    +   L+  F  FG + S KV+ D   +K   +GFV    
Sbjct: 1   PSLRKSGVGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFET 57

Query: 85  YDEAVVAIQSLNGYALGNRILQVSFKTNK 113
            + A  AI+ +NG  L +R + V    ++
Sbjct: 58  QEAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.2 bits (148), Expect = 2e-14
 Identities = 22/74 (29%), Positives = 41/74 (55%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L  +  +  L+ LF   G + + +++RD +T    G+ FV  T+  ++  AI+ L
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 96  NGYALGNRILQVSF 109
           NG  + N+ L+VS+
Sbjct: 65  NGITVRNKRLKVSY 78

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-14
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + +     E  E V  ++   +G V+ + V  +   +   G  +V     ++A  A+  L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 96  NGYALGNRILQVSF 109
           N      + +    
Sbjct: 89  NNRWFNGQPIHAEL 102

>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 = 61.1 bits (148), Expect = 2e-14
 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L  +T E  L + F  FG V  V+V +DL+T   KGFGFV  T Y+  V  +   
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 96  NGYALGNRILQVSFKTNK 113
           +   +  R        +K
Sbjct: 71  HM--IDGRWCDCKLPNSK 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 = 61.2 bits (148), Expect = 3e-14
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +   NL+    E  L ++F     ++ V         K KG  ++   +  +A   ++  
Sbjct: 19  LLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
            G  +  R + + +   KG T 
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTR 95

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 4e-14
 Identities = 37/81 (45%), Positives = 49/81 (60%)

Query: 33  GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAI 92
           G  +F+Y+L  E  +  L Q+F PFG V S KV  D QTN  K FGFV+  N   A  AI
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 93  QSLNGYALGNRILQVSFKTNK 113
           QS+NG+ +G + L+V  K +K
Sbjct: 78  QSMNGFQIGMKRLKVQLKRSK 98

>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 = 60.4 bits (146), Expect = 4e-14
 Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I V NL+ +T E+ L +LF PFG++  + + +D  T + KGF F++    ++A  AI  +
Sbjct: 11  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 70

Query: 96  NGYALGNRILQVSF---KTN 112
           +G+   + IL V +    TN
Sbjct: 71  SGFGYDHLILNVEWAKPSTN 90

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 6e-14
 Identities = 17/78 (21%), Positives = 26/78 (33%), Gaps = 1/78 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F   LA       L   F   G V+ V++I D  + + KG  +V              L
Sbjct: 21  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV-PLAIGL 79

Query: 96  NGYALGNRILQVSFKTNK 113
            G  L    + V     +
Sbjct: 80  TGQRLLGVPIIVQASQAE 97

>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 = 60.1 bits (145), Expect = 7e-14
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V NL+ +  E ++ QLF   G  +S K+I +        + FV    + +A  A+ ++
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 96  NGYALGNRILQVSFKTNKGK 115
           NG  +  + ++V++ T    
Sbjct: 69  NGRKILGKEVKVNWATTPSS 88

>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 = 59.8 bits (144), Expect = 1e-13
 Identities = 21/91 (23%), Positives = 31/91 (34%), Gaps = 8/91 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVI--------RDLQTNKCKGFGFVTMTNYD 86
            I+V  L        L   F   G V+  K           D +T K KG   V+  +  
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 87  EAVVAIQSLNGYALGNRILQVSFKTNKGKTS 117
            A  A++  +G       L+VS    K   +
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>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 = 59.4 bits (143), Expect = 1e-13
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKV-----IRDLQTNKCKGFGFVTMTNYDEAVV 90
           ++V N+     E  +   F     +  +       +  +Q N+ K F F+   + DE   
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 91  AIQSLNGYALGNRILQVS 108
           A+   +G     + L++ 
Sbjct: 64  AMA-FDGIIFQGQSLKIR 80

>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 = 59.3 bits (143), Expect = 1e-13
 Identities = 14/78 (17%), Positives = 28/78 (35%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
               I V N+        +   F  +  +     ++  +     G   V   + DEA  A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 92  IQSLNGYALGNRILQVSF 109
           +  LN   +G+R +++  
Sbjct: 68  VIDLNDRPIGSRKVKLVL 85

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 2e-13
 Identities = 24/74 (32%), Positives = 39/74 (52%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L     +     LFG  G ++S K++RD  T +  G+GFV   +  +A  AI +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 96  NGYALGNRILQVSF 109
           NG  L  + ++VS+
Sbjct: 65  NGLRLQTKTIKVSY 78

>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 = 58.9 bits (142), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V N+     +  L Q+FG FG +  V++I + + +K   FGFVT  N  +A  A + L
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADADRAREKL 71

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G  +  R ++V+  T +  T+
Sbjct: 72  HGTVVEGRKIEVNNATARVMTN 93

>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 = 58.1 bits (140), Expect = 3e-13
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ +T +  L + FG FG V+   V+RD  T + +GFGFVT  +       +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 96  NGYALGNRILQVSF 109
           + + L ++ +    
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 58.1 bits (140), Expect = 4e-13
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL P+  E  + +LF  +G    V        +K KGFGF+ +     A +A   L
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEV------FIHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +   L  + L+V F  +    +
Sbjct: 65  DNMPLRGKQLRVRFACHSASLT 86

>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 = 57.7 bits (139), Expect = 4e-13
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ +T +  L   F  FG V    +  D  T + +GFGFV     +     +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 96  NGYALGNRILQV 107
             + L  +++  
Sbjct: 61  KEHKLNGKVIDP 72

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (140), Expect = 5e-13
 Identities = 25/82 (30%), Positives = 41/82 (50%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL+P   E  L  LF  F   +   +   + T + +G  F+T  N + A  A+  +
Sbjct: 21  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           NGY L  +IL + F  NK + S
Sbjct: 81  NGYKLYGKILVIEFGKNKKQRS 102

>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 = 57.8 bits (139), Expect = 6e-13
 Identities = 28/82 (34%), Positives = 40/82 (48%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV NL+  + E  L +LF  +G +  +    D  T K KGF FVT    + AV A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           +G     R+L V   T K + S
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEAS 92

>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 = 57.4 bits (138), Expect = 6e-13
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           ++V  L     +  L QLF  +G + + +++ D  T   +G GF+      EA  AI+ L
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 96  NGYALG--NRILQVSF 109
           NG         + V F
Sbjct: 69  NGQKPSGATEPITVKF 84

>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 = 58.0 bits (140), Expect = 6e-13
 Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 40  NLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYA 99
            +  E  E  L      FG ++ + +          G   V+  + +EA   IQ+L+G  
Sbjct: 27  LVLNEIRED-LRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW 81

Query: 100 LGNRILQVSFKTNKGKT 116
            G R +        G T
Sbjct: 82  FGGRQITAQAW--DGTT 96

>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 = 57.4 bits (138), Expect = 8e-13
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I+V NL P+     +  +F  +GA++ + +           F FV   +  +A  A+   
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 96  NGYALGNRILQVSFKTNKGKT 116
           +GY      L+V F  +   T
Sbjct: 74  DGYDYDGYRLRVEFPRSGRGT 94

>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 = 56.5 bits (136), Expect = 1e-12
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+P+T E  + + FG FG V+S+++  D +TNK +GF F+T    +     ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 96  NGYALGNRILQV 107
             + +G    ++
Sbjct: 61  KYHNVGLSKCEI 72

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 1e-12
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            I V NL       VL Q+F  FG V  +           +    +   +   A  A  S
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHAKLS 64

Query: 95  LNGYAL--GNRILQVSFKTNK 113
           L+G  +      L++ F    
Sbjct: 65  LDGQNIYNACCTLRIDFSKLT 85

>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 = 56.7 bits (136), Expect = 2e-12
 Identities = 27/78 (34%), Positives = 46/78 (58%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV  L+ +T E  L Q+F  +G +  V V++D +T + +GFGFVT  N D+A  A+ ++
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 96  NGYALGNRILQVSFKTNK 113
           NG ++  R ++V      
Sbjct: 68  NGKSVDGRQIRVDQAGKS 85

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-12
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL+P      L QLFG         +    Q     G+ FV   + + A+ AI++L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 96  NG-YALGNRILQVSFKTNKGKTS 117
           +G   L  +I++V +  +K   S
Sbjct: 58  SGKVELHGKIMEVDYSVSKKLRS 80

>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 = 55.8 bits (134), Expect = 2e-12
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +F+  L+ ET +  L   F  +G +    V+RD  T + +GFGFVT    +E   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-A 67

Query: 96  NGYALGNRILQV 107
             + +  R+++ 
Sbjct: 68  RPHKVDGRVVEP 79

>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 = 55.4 bits (133), Expect = 5e-12
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGP-FGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           I++ NL  + ++  L +     F     +  I   ++ K +G  FV       A  A++S
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 95  LNGYALGNRILQVSFKTNKGK 115
           + G+   ++ +++ +      
Sbjct: 66  MQGFPFYDKPMRIQYAKTDSD 86

>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 = 55.1 bits (132), Expect = 8e-12
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L   T ++ L + F  FG ++   VI D QT K +G+GFVTM +   A  A +  
Sbjct: 13  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 72

Query: 96  NGYALGNRILQVSFKTNKGK 115
           N   +  R   V+      K
Sbjct: 73  NPI-IDGRKANVNLAYLGAK 91

>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 = 54.4 bits (130), Expect = 9e-12
 Identities = 13/74 (17%), Positives = 30/74 (40%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ N  P   +  +  L      V     +  L+ N  + F ++ +T+ ++A   ++ L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 96  NGYALGNRILQVSF 109
           NG  +    L    
Sbjct: 64  NGLKIEGYTLVTKV 77

>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 = 56.5 bits (135), Expect = 9e-12
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 29  MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
            + +   IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  ++D  
Sbjct: 93  AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152

Query: 89  VVAIQSLNGYALGNRILQVSFKTNK 113
              +     + +     +V    +K
Sbjct: 153 DKIVI-QKYHTVNGHNCEVRKALSK 176

>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 = 51.9 bits (123), Expect = 6e-10
 Identities = 19/63 (30%), Positives = 31/63 (49%)

Query: 36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
          +F+  L+ ET +  L   F  +G +    V+RD  T + +GFGFVT    +E   A+ + 
Sbjct: 9  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 96 NGY 98
             
Sbjct: 69 PHK 71

>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 = 54.0 bits (129), Expect = 1e-11
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  L+  T    +   F  FG V    ++ D  TN+ +GFGFVT  + D      + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 96  NGYALGNRILQVSF 109
           + + + N++++   
Sbjct: 61  HFHEINNKMVECKK 74

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.8 bits (131), Expect = 1e-11
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 8/100 (8%)

Query: 24  LPANTMNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMT 83
           LP++   G    +F+ NL+ ++EE  L ++   FG ++ V+V+    T   KG  F    
Sbjct: 1   LPSDVTEG--KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFM 58

Query: 84  NYDEAVVAIQSLN------GYALGNRILQVSFKTNKGKTS 117
             + A   + + +      G  L  R L+V     + + +
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 54.7 bits (131), Expect = 1e-11
 Identities = 11/78 (14%), Positives = 25/78 (32%), Gaps = 4/78 (5%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQS--VKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
           +F+  +    +   + +            +         K +GF FV   ++  A +A +
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 94  SLNG--YALGNRILQVSF 109
            L      L    + V +
Sbjct: 64  KLMPGRIQLWGHQIAVDW 81

>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 = 52.8 bits (126), Expect = 5e-11
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I V NL  ++    +  L   +        ++    ++ K   FVT+ N ++A  AIQ  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 96  NGYALGNRILQVSFKTNKGKTS 117
           + Y+   + L V  +       
Sbjct: 61  HQYSFRGKDLIVQLQPTDALLC 82

>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 = 52.7 bits (126), Expect = 5e-11
 Identities = 15/83 (18%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            +FV     +  E  L + F  +G V  V           + F FVT  +   A      
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLCG- 60

Query: 95  LNGYALGNRILQVSFKTNKGKTS 117
                +    + +S    K  ++
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSN 82

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 5e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +FV N+  E  E  L  +F   G V S +++ D +T K KG+GF    + + A+ A+++L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 96  NGYALGNRILQVSFKTNK 113
           NG     R L+V    ++
Sbjct: 71  NGREFSGRALRVDNAASE 88

>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 = 52.3 bits (125), Expect = 5e-11
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
            G  ++VY    +   ++L   F PFG +  + +         +   FVT    + A  A
Sbjct: 4   KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 55

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           +  LNG  + +  L+V+    +
Sbjct: 56  VAELNGTQVESVQLKVNIARKQ 77

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 5e-11
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 36  IFVYNLAPETEESVLWQLF---GPFGAVQSVKVIRDLQTNKC---KGFGFVTMTNYDEAV 89
           +FV  L+    +  + +     G FG +  V +                +VT    ++A+
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 90  VAIQSLNGYALGNRILQVS 108
            AIQ +N   +  R L+ S
Sbjct: 71  RAIQCVNNVVVDGRTLKAS 89

>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 = 53.0 bits (126), Expect = 9e-11
 Identities = 25/80 (31%), Positives = 45/80 (56%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  +    +E  L QLF  +G ++SVK++ D +T + +G+GFV   +   A  AI  L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 96  NGYALGNRILQVSFKTNKGK 115
           NG+ + N+ L+V+   +  +
Sbjct: 105 NGFNILNKRLKVALAASGHQ 124

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (124), Expect = 1e-10
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 29  MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEA 88
           +N +  C  + N+     +  + Q        ++   +      +  G   V   N D+A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 89  VVAIQSLNGYALGNRILQVSFKTNK 113
             + + L+   L  R   V   T +
Sbjct: 64  RKSER-LHRKKLNGREAFVHVVTLE 87

>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 = 50.9 bits (121), Expect = 3e-10
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
            F+ NL  +  E  + + F                  + KGFG+    + D   ++  SL
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSALSL 76

Query: 96  NGYALGNRILQVSFKTNK 113
           N  +LGN+ ++V      
Sbjct: 77  NEESLGNKRIRVDVADQA 94

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 3e-10
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           IFV  +  +TEE  L   F  +G ++ ++++ D  + K +GF FVT  +  ++V  I   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 63

Query: 96  NGYALGNRILQV 107
             + +     +V
Sbjct: 64  KYHTVNGHNCEV 75

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.5 bits (120), Expect = 3e-10
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 33  GWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVV 90
           G  I + NL+ E  +E++L + F  FG+++ + +     + +      F+   N D A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 91  AIQSLNGYALGNRILQVSFKTNK 113
           A+Q +N   LGNR + VS    K
Sbjct: 64  ALQ-MNRSLLGNREISVSLADKK 85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 6e-10
 Identities = 23/71 (32%), Positives = 38/71 (53%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++  L P T +  L +L  P+G + S K I D  TNKCKG+GFV   +   A  A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 96  NGYALGNRILQ 106
               +  ++ +
Sbjct: 61  KASGVQAQMAK 71

>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 = 49.4 bits (117), Expect = 1e-09
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 36  IFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
           + V NL PE      L+ LFG +G VQ VK++        K    V M + ++A +A+  
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMSH 59

Query: 95  LNGYALGNRILQVSFKTNK 113
           LNG+ L  + ++++   ++
Sbjct: 60  LNGHKLHGKPIRITLSKHQ 78

>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 = 49.2 bits (117), Expect = 2e-09
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 40  NLAPETEESVLWQLFGPFGAVQSVKVIRDLQT--NKCKGFGFVTMTNYDEAVVAIQSLNG 97
           +   E     +      +G V+S+++ R +        G  FV  T+  +   A+Q L G
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 98  YALGNRILQVSF 109
               NR++   +
Sbjct: 81  RKFANRVVVTKY 92

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.6 bits (113), Expect = 4e-09
 Identities = 10/79 (12%), Positives = 26/79 (32%), Gaps = 9/79 (11%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V+     +   +L   F  +G +    +           +  +   +  +A  A+   
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-K 58

Query: 96  NGYALGNR-ILQVSFKTNK 113
           +G   G   ++ V    +K
Sbjct: 59  DGRIFGESIMIGVKPCIDK 77

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 5e-09
 Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +G C+ +  L     E+ ++  F P   ++    I      +  G   V    +++AV A
Sbjct: 14  TGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIG--PDGRVTGEADVEFATHEDAVAA 71

Query: 92  IQSLNGYALGNRILQVSFKTNKGK 115
           +   +   + +R +++   +  G 
Sbjct: 72  MA-KDKANMQHRYVELFLNSTAGT 94

>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 = 46.3 bits (109), Expect = 2e-08
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 7/78 (8%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S + + V  L P      L       G V            +  G G V     ++   A
Sbjct: 14  SDFRVLVSGLPPSGSWQDLKDHMREAGDVCY-------ADVQKDGMGMVEYLRKEDMEYA 66

Query: 92  IQSLNGYALGNRILQVSF 109
           ++ L+     +   + S+
Sbjct: 67  LRKLDDTKFRSHEGETSY 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTN-YDEAVVAIQS 94
            F  +L  +T    L  LF   G ++ +         +    G +       EA+   + 
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWI------DFVRGAKEGIILFKEKAKEALGKAKD 67

Query: 95  LNGYALGNRILQVSFKTNKGKT 116
            N   L  R  +V+++  +G+ 
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEV 89

>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 = 45.8 bits (108), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            ++V  L P T  + L + F  FG+++++         K   F ++   + D A  A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSFAYIQYESLDAAQAACAK 72

Query: 95  LNGYALG--NRILQVSFKTNK 113
           + G+ LG  +R L+V F  + 
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSG 93

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 7e-08
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +    L      + L  +    G V ++           K + F      +E+  A  +L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRTTEESKRAYVTL 76

Query: 96  NGYAL-GNRILQVSFK 110
           NG  +  +   +++  
Sbjct: 77  NGKEVVDDLGQKITLY 92

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (105), Expect = 8e-08
 Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 1/82 (1%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           +G+C+++  L  E E   +   F     V+    I      K  G GFV   N  +   A
Sbjct: 17  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 76

Query: 92  IQSLNGYALGNRILQVSFKTNK 113
           +   +   +GNR +QV   T K
Sbjct: 77  LC-RHKQYMGNRFIQVHPITKK 97

>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 = 44.8 bits (105), Expect = 8e-08
 Identities = 7/80 (8%), Positives = 20/80 (25%), Gaps = 11/80 (13%)

Query: 35  CIFVYNLAPETEESV-----LWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAV 89
            +       +             LF  +    + +  +            +  +N   A 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAA 60

Query: 90  VAIQSLNGYALGNRILQVSF 109
            A   L+      + +++ F
Sbjct: 61  DARLRLHKTEFLGKEMKLYF 80

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.1 bits (101), Expect = 3e-07
 Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 35  CIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ 93
            + + +    +     L QL  PFG + +  +         + F  +  T   +A V   
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI----LNKINEAFIEMATTEDAQAAVDYY 65

Query: 94  SLNGYALGNRILQVSFKTNKGK 115
           +     +  + ++V       +
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKR 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (98), Expect = 5e-07
 Identities = 11/74 (14%), Positives = 21/74 (28%), Gaps = 7/74 (9%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V  L P      L       G V               G G V     ++   A++ L
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 96  NGYALGNRILQVSF 109
           +     +   + ++
Sbjct: 56  DNTKFRSHEGETAY 69

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 7e-07
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + + N+ P   E  L  LF   G V    V       K +    + M + +EAV A+  
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 95  LNGYALG-NRILQVSFKTNK 113
           L+ + LG N  L+VSF  + 
Sbjct: 68  LHNHDLGENHHLRVSFSKST 87

>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 = 42.1 bits (98), Expect = 8e-07
 Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 8/81 (9%)

Query: 35  CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQS 94
            + V  L     E+ L +    FG +  V +         K    V   N D A   +  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVTF 70

Query: 95  L--NGYALGNRILQVSFKTNK 113
                  +  +    ++ T+K
Sbjct: 71  AADVPVYIAGQQAFFNYSTSK 91

>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 = 41.7 bits (97), Expect = 1e-06
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++ NL    +E  L  +  PFG       I    +   +G GF  M + ++    I   
Sbjct: 21  LYISNLPLSMDEQELENMLKPFG-QVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 96  NGYALGNRILQVS 108
           NG  +       +
Sbjct: 80  NGKFIKTPPGVSA 92

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 2e-06
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           +++     +     + +     G V ++++ R       KG  FV   + + A   ++  
Sbjct: 9   VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-T 66

Query: 96  NGYALGNRILQVSFK 110
            G       L + FK
Sbjct: 67  PGQKYKETDLLILFK 81

>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 = 40.3 bits (93), Expect = 4e-06
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 32  SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVA 91
           S   I   NL   T  + + + F  FG++  V         +      V      EA  A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKA 62

Query: 92  IQSLNGYALGNRILQVSF 109
            + L      +  L + +
Sbjct: 63  FRHLAYSKFHHVPLYLEW 80

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.7 bits (89), Expect = 8e-06
 Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 3/76 (3%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           + V NL     ++ +++ F   G +  V V       K   F  +    YD   +A  + 
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDG-ALAAITK 59

Query: 96  NGYALGNRILQVSFKT 111
               +G   + VS  T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>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 = 38.7 bits (89), Expect = 1e-05
 Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 9/90 (10%)

Query: 27  NTMNGS-GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY 85
           + M+G+    + +  L  E  E+ +  L  PF        + ++   K K   F+ +   
Sbjct: 1   DKMDGAPSRVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATE 54

Query: 86  DEAVVAIQ--SLNGYALGNRILQVSFKTNK 113
           + A+  +   S     L N+ + + +  +K
Sbjct: 55  EAAITMVNYYSAVTPHLRNQPIYIQYSNHK 84

>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 = 35.7 bits (81), Expect = 1e-04
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 36  IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL 95
           I +  L  +     +  L   +        ++    +K KG  FVT+ N ++A  AI + 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 96  NGYALGNRILQVSFKTNK 113
           +   L  R L V  +   
Sbjct: 54  HQSRLRERELSVQLQPTD 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	117
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.93
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.92
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.92
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.92
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.92
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.92
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	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	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.91
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.91
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.9
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.9
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.9
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.89
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.87
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.85
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.85
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.85
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.85
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.85
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.85
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.84
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.84
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.84
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.84
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.84
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.83
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.81
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.81
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.8
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.73
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
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	99.66
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.61
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.58
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.56
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.47
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.06
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.98
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.94
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.9

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.93  E-value=7.3e-25  Score=122.77  Aligned_cols=84  Identities=26%  Similarity=0.479  Sum_probs=79.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .++++|||+|||.++++++|.++|+.||.|..++++.++.+|.++|||||+|.+.++|+.|+..|||..+.|+.|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .+++
T Consensus        85 ~~kG   88 (88)
T d1rk8a_          85 FVKG   88 (88)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            8764

>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=2.8e-25  Score=125.65  Aligned_cols=87  Identities=24%  Similarity=0.406  Sum_probs=82.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+..++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|+|..+.|+.|+|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      |+++.++
T Consensus        86 A~~~~~n   92 (93)
T d1x5ua1          86 ASAHNKN   92 (93)
T ss_dssp             TTTTSCC
T ss_pred             cCCCCCC
Confidence            9988764

>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=99.92  E-value=6.5e-25  Score=126.10  Aligned_cols=88  Identities=42%  Similarity=0.607  Sum_probs=82.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ..+++++|||+|||+++++++|+++|+.||.+..+.++.++.+|.++|||||+|.+.++|+.|++.|+|..+.|+.|+|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCC
Q psy13319        109 FKTNKGKT  116 (117)
Q Consensus       109 ~a~~~~~~  116 (117)
                      |++++.++
T Consensus        94 ~a~~k~~~  101 (102)
T d2cpza1          94 LKRSKNDS  101 (102)
T ss_dssp             CCCCSCCC
T ss_pred             EeCCCCCC
Confidence            99887654

>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=2e-24  Score=121.49  Aligned_cols=85  Identities=29%  Similarity=0.527  Sum_probs=80.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .++..+|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|+|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45677899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      |+++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>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=7.4e-25  Score=121.23  Aligned_cols=80  Identities=28%  Similarity=0.495  Sum_probs=77.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +++|||+|||.++++++|+++|+.||.|..+++..++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.||++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            56899999999999999999999999999999999988999999999999999999999999999999999999999976

>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=8.1e-25  Score=122.83  Aligned_cols=86  Identities=28%  Similarity=0.462  Sum_probs=80.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..++|..++|+.|+|.+|
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13319        111 TNKGKT  116 (117)
Q Consensus       111 ~~~~~~  116 (117)
                      ++++.+
T Consensus        83 ~p~~~k   88 (89)
T d2cqba1          83 KPMRIK   88 (89)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=4e-24  Score=120.87  Aligned_cols=83  Identities=24%  Similarity=0.373  Sum_probs=79.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|++.|+|..+.|+.|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>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=99.92  E-value=7.9e-25  Score=121.91  Aligned_cols=84  Identities=24%  Similarity=0.410  Sum_probs=80.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNK  113 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  113 (117)
                      ++|||+|||+++++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|+.|+..++|..+.|+.|+|.+|++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy13319        114 GKTS  117 (117)
Q Consensus       114 ~~~~  117 (117)
                      .+.+
T Consensus        82 ~~~a   85 (85)
T d2u2fa_          82 AKNA   85 (85)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            7654

>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=5e-24  Score=117.81  Aligned_cols=79  Identities=30%  Similarity=0.522  Sum_probs=76.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .+|||+|||+++++++|+++|+.||.|..+++..+..++.++|||||+|.+.++|+.|+..|+|..+.|+.|+|.||++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5699999999999999999999999999999999988999999999999999999999999999999999999999986

>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=99.91  E-value=4e-24  Score=117.75  Aligned_cols=78  Identities=23%  Similarity=0.518  Sum_probs=75.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .|||+|||+.+++++|.++|+.||.|..++++.++.+|.++|||||+|.+.++|..|++.|+|..+.|+.|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999999863

>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=5.9e-24  Score=121.45  Aligned_cols=85  Identities=32%  Similarity=0.393  Sum_probs=79.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|+.|++.|++..+.|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      +.+..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87553

>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=99.91  E-value=1.9e-23  Score=125.89  Aligned_cols=85  Identities=29%  Similarity=0.496  Sum_probs=79.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +..++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|..|++.|||..+.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      +.+.+
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76554

>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=1.3e-23  Score=116.48  Aligned_cols=78  Identities=31%  Similarity=0.545  Sum_probs=74.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ++++++|||+|||.++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|+..|+|..+.|+.|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            456788999999999999999999999999999999999999999999999999999999999999999999999986

>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=99.90  E-value=7.1e-24  Score=119.13  Aligned_cols=85  Identities=32%  Similarity=0.526  Sum_probs=79.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+.++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|+..|+|..+.|+.|+|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45677999999999999999999999999999999988889999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.90  E-value=3.5e-23  Score=115.11  Aligned_cols=80  Identities=26%  Similarity=0.394  Sum_probs=74.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  108 (117)
                      ..+++|||+|||.++++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|.+|++.++|..+.|  ++|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            355679999999999999999999999999999999999999999999999999999999999999998875  789999


Q ss_pred             Ee
Q psy13319        109 FK  110 (117)
Q Consensus       109 ~a  110 (117)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.90  E-value=2.8e-23  Score=115.55  Aligned_cols=79  Identities=27%  Similarity=0.413  Sum_probs=74.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~  109 (117)
                      .+++|||+|||+++++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|+.|++.|||..+.|  ++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35679999999999999999999999999999999999899999999999999999999999999999987  5599988


Q ss_pred             e
Q psy13319        110 K  110 (117)
Q Consensus       110 a  110 (117)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=5.5e-23  Score=115.45  Aligned_cols=85  Identities=25%  Similarity=0.453  Sum_probs=76.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+..++.++  +|||||+|.+.++|+.|+..++|..+.|+.|+|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999998876544  78999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      |++...+
T Consensus        83 a~~~~~~   89 (90)
T d2cqia1          83 ATTPSSQ   89 (90)
T ss_dssp             CCCTTCC
T ss_pred             cCCCCCC
Confidence            9876543

>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=99.90  E-value=2.3e-23  Score=117.89  Aligned_cols=85  Identities=24%  Similarity=0.408  Sum_probs=77.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHh-CCcEeCCeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQSL-NGYALGNRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~  108 (117)
                      ....+|||+|||.++++++|+++|+.||.|..+.++.+. .+|.++|||||+|.+.++|..|+..| ++..+.|++|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            456779999999999999999999999999999998764 47899999999999999999999998 8999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ||+.+..
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.90  E-value=1.1e-23  Score=116.26  Aligned_cols=80  Identities=16%  Similarity=0.316  Sum_probs=69.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+..|||..+.|+.|+|.+++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            46899999999999999999999999998887877778899999999999999999999999999999999999999876

>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=99.90  E-value=5.3e-23  Score=117.12  Aligned_cols=88  Identities=24%  Similarity=0.429  Sum_probs=80.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CcEeCCe
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLN------GYALGNR  103 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------~~~~~g~  103 (117)
                      .+++++|||+|||+++++++|+++|..||.+..+.+..+..++.++|||||+|.+.++|.+|+..++      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            4567899999999999999999999999999999999988889999999999999999999999886      5678899


Q ss_pred             EEEEEEecCCCCCC
Q psy13319        104 ILQVSFKTNKGKTS  117 (117)
Q Consensus       104 ~l~v~~a~~~~~~~  117 (117)
                      .|+|++++++.+.+
T Consensus        85 ~l~v~~a~~k~~aa   98 (98)
T d1x4ha1          85 QLKVDLAVTRDEAA   98 (98)
T ss_dssp             EEEEECCCCCCCCC
T ss_pred             EEEEEECCCCCcCc
Confidence            99999999877653

>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=99.89  E-value=3.1e-24  Score=123.17  Aligned_cols=88  Identities=28%  Similarity=0.439  Sum_probs=81.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+++++|||+|||.++++++|+++|+.||.+..+.+..+..+|.++|||||+|.+.++|+.|++.|+|..+.|+.|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35678999999999999999999999999998888888777899999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q psy13319        110 KTNKGKTS  117 (117)
Q Consensus       110 a~~~~~~~  117 (117)
                      ++++.++|
T Consensus        95 ak~k~~rs  102 (102)
T d2cpxa1          95 GKNKKQRS  102 (102)
T ss_dssp             CCCCSCCC
T ss_pred             CCCcccCC
Confidence            99988765

>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=99.89  E-value=9.4e-23  Score=113.13  Aligned_cols=80  Identities=25%  Similarity=0.397  Sum_probs=75.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +..++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.+.|++|++ +++..+.|+.|+|..|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            445789999999999999999999999999999999999999999999999999999999998 5899999999999887


Q ss_pred             c
Q psy13319        111 T  111 (117)
Q Consensus       111 ~  111 (117)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=1.7e-22  Score=113.35  Aligned_cols=82  Identities=30%  Similarity=0.447  Sum_probs=75.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.  ...++|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4567799999999999999999999999999999999999999999999999999999999984  45799999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8754

>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=99.89  E-value=3.8e-22  Score=112.60  Aligned_cols=84  Identities=30%  Similarity=0.422  Sum_probs=76.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+.+++++|+++|..||.|..+.++.+.  +.++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4456789999999999999999999999999999998875  34689999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      |+++..
T Consensus        86 A~~r~~   91 (93)
T d2cq3a1          86 ATARVM   91 (93)
T ss_dssp             CCSSCC
T ss_pred             cCcCCC
Confidence            998764

>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=99.89  E-value=3.5e-23  Score=114.64  Aligned_cols=80  Identities=36%  Similarity=0.694  Sum_probs=74.4

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEE-EEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCCC
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSV-KVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG  114 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  114 (117)
                      |||+|||+++++++|+++|+.||.+..+ .++.++.+|+++|||||+|.+.++|+.|++.++|..+.|++|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 788888899999999999999999999999999999999999999998765


Q ss_pred             C
Q psy13319        115 K  115 (117)
Q Consensus       115 ~  115 (117)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.89  E-value=1.2e-22  Score=116.75  Aligned_cols=82  Identities=32%  Similarity=0.389  Sum_probs=75.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.+++ .+.|+.|+|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3446799999999999999999999999999999999999999999999999999999999998876 799999999998


Q ss_pred             cCC
Q psy13319        111 TNK  113 (117)
Q Consensus       111 ~~~  113 (117)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            753

>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=1.2e-22  Score=112.93  Aligned_cols=80  Identities=28%  Similarity=0.441  Sum_probs=73.6

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTN---KCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      |||+|||+++++++|+++|+.||.|..+.++.++.++   .++|||||+|.+.++|+.|++.++|..+.|+.|+|.+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999998876655   4689999999999999999999999999999999999876


Q ss_pred             CCC
Q psy13319        113 KGK  115 (117)
Q Consensus       113 ~~~  115 (117)
                      ..+
T Consensus        81 ~~k   83 (85)
T d2cpfa1          81 ATK   83 (85)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            554

>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=99.89  E-value=9e-23  Score=111.73  Aligned_cols=77  Identities=23%  Similarity=0.363  Sum_probs=73.0

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +|||+|||+++++++|+++|+.||.|..+++..++ ++.++|+|||+|.+.++|+.|++.+||..+.|+.|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999998875 789999999999999999999999999999999999999863

>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=99.89  E-value=3.2e-23  Score=119.29  Aligned_cols=83  Identities=31%  Similarity=0.482  Sum_probs=78.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|+|..+.|+.|+|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ++.
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            643

>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=5.9e-23  Score=117.93  Aligned_cols=83  Identities=23%  Similarity=0.398  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||+++++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            45789999999999999999999999999999999999999999999999999999999997 69999999999999988


Q ss_pred             CCCC
Q psy13319        112 NKGK  115 (117)
Q Consensus       112 ~~~~  115 (117)
                      ++.+
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>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=99.88  E-value=3e-23  Score=118.83  Aligned_cols=81  Identities=23%  Similarity=0.374  Sum_probs=76.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +.++|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|++|+. ++|..+.|+.|+|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999999999999999999999999999996 99999999999999986


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.88  E-value=2.8e-22  Score=114.66  Aligned_cols=86  Identities=23%  Similarity=0.277  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeE--------EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQ--------SVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      ...+..+|||+|||..+++++|.++|..||.|.        .+.+..++.+|.++|||||+|.+.++|..|++.|+|..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345678999999999999999999999999873        456667778899999999999999999999999999999


Q ss_pred             CCeEEEEEEecCCC
Q psy13319        101 GNRILQVSFKTNKG  114 (117)
Q Consensus       101 ~g~~l~v~~a~~~~  114 (117)
                      .|+.|+|++++++.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998754

>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=1.4e-22  Score=113.54  Aligned_cols=82  Identities=32%  Similarity=0.489  Sum_probs=75.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      ..+|||+|||+++++++|+++|+.||.|..+.++.+.  +.++|||||+|.+.++|++|+..|+|..+.|+.|+|+++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999998875  34689999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy13319        113 KGKT  116 (117)
Q Consensus       113 ~~~~  116 (117)
                      ++++
T Consensus        86 ~~~R   89 (89)
T d1cvja2          86 RKER   89 (89)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7653

>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=99.88  E-value=7.8e-22  Score=111.69  Aligned_cols=83  Identities=22%  Similarity=0.361  Sum_probs=74.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+++++|||+|||+++++++|+++|..||.|..+.+..+   +..++||||+|.+.++|+.|++.|++..+.|++|+|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            456778999999999999999999999999988877544   55689999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++..+.
T Consensus        88 a~~~r~   93 (95)
T d1x4aa1          88 PRSGRG   93 (95)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987653

>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=99.88  E-value=4e-23  Score=112.88  Aligned_cols=76  Identities=26%  Similarity=0.435  Sum_probs=72.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      |+|||+|||+++++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|++|+. +++..++|+.|+|..|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 6999999999999876

>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=99.88  E-value=9.1e-22  Score=107.86  Aligned_cols=77  Identities=23%  Similarity=0.335  Sum_probs=72.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      -++|||+|||+++++++|+++|+.||.+..+.+..++.++.++|+|||+|.+.+++.+|++ ++|..+.|+.|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999997 7999999999999875

>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=1.9e-22  Score=112.37  Aligned_cols=82  Identities=29%  Similarity=0.417  Sum_probs=71.2

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHhhcCCCCeEEEEEEec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         32 SGWCIFVYNLAPETE-ESVLWQLFGPFGAVQSVKVIRD-LQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~-~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ++++|||+|||.+++ +++|+++|+.||.|..+.+..+ ..++.++|||||+|.+.++|+.|++ +++..+.|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            478999999999875 5679999999999999988654 5678899999999999999999996 999999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      +++++
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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=99.87  E-value=9.8e-22  Score=114.66  Aligned_cols=80  Identities=20%  Similarity=0.418  Sum_probs=73.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ++.+++|||+|||.++++++|+++|+.||.|..+++..+   +.++|||||+|.+.++|..|++.|+|..+.|+.|+|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345789999999999999999999999999999988754   56689999999999999999999999999999999999


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +..
T Consensus        81 a~~   83 (114)
T d2f9da1          81 YNA   83 (114)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            764

>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=1.8e-22  Score=109.70  Aligned_cols=75  Identities=21%  Similarity=0.344  Sum_probs=70.6

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +|||+|||+++++++|.++|+.||.|..+.++.++.+++++|||||+|.+.++|++|+. +++..+.|+.|+|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 6889999999988643

>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=99.87  E-value=2.2e-21  Score=107.97  Aligned_cols=81  Identities=26%  Similarity=0.367  Sum_probs=72.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ...++|||+|||.++++++|+++|+.||.+..+.+..      ++|||||+|.+.++|..|+..|+|..+.|+.|+|+|+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999887766643      3789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy13319        111 TNKGKTS  117 (117)
Q Consensus       111 ~~~~~~~  117 (117)
                      ++..+.|
T Consensus        80 kP~~~~s   86 (86)
T d2cpda1          80 KPVDKDS   86 (86)
T ss_dssp             CCCCCCC
T ss_pred             cCCCCCC
Confidence            9888765

>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=7.5e-22  Score=111.96  Aligned_cols=79  Identities=22%  Similarity=0.481  Sum_probs=73.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +..++|||+|||..+++++|+++|+.||.|..+++..+      +|||||+|.+.++|+.|+..|+|..+.|+.|+|+|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999865      789999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13319        111 TNKGK  115 (117)
Q Consensus       111 ~~~~~  115 (117)
                      ++++.
T Consensus        90 k~~p~   94 (96)
T d1x4ga1          90 KESPD   94 (96)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87664

>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=4e-22  Score=109.59  Aligned_cols=77  Identities=29%  Similarity=0.455  Sum_probs=69.7

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-EeCCeEEEEEEecCC
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY-ALGNRILQVSFKTNK  113 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~-~~~g~~l~v~~a~~~  113 (117)
                      +|||+|||.++++++|+++|..||.+....+...      +|||||+|.+.++|+.|++.|+|. .+.|+.|+|+|+.++
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            5999999999999999999999999876655543      789999999999999999999985 799999999999998


Q ss_pred             CCCC
Q psy13319        114 GKTS  117 (117)
Q Consensus       114 ~~~~  117 (117)
                      +++|
T Consensus        77 ~~rs   80 (80)
T d2cqha1          77 KLRS   80 (80)
T ss_dssp             CCCC
T ss_pred             CcCC
Confidence            8875

>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=99.86  E-value=2.5e-21  Score=107.03  Aligned_cols=78  Identities=23%  Similarity=0.423  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC-CeEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG-NRILQV  107 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~-g~~l~v  107 (117)
                      ..+++++|||+|||.++++++|.++|+.||.|..+++..+     .+|+|||+|.+.++|..|+..|+|..+. |+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            3566789999999999999999999999999999988654     2679999999999999999999998884 789999


Q ss_pred             EEec
Q psy13319        108 SFKT  111 (117)
Q Consensus       108 ~~a~  111 (117)
                      +||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.85  E-value=6.8e-22  Score=107.34  Aligned_cols=75  Identities=27%  Similarity=0.388  Sum_probs=71.5

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +|||+|||+++++++|+++|+.||.+..+.+..++.++.++|+|||+|.+.++|+.|++ ++|..+.|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999998899999999999999999999997 8999999999999875

>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=99.85  E-value=4.7e-21  Score=108.63  Aligned_cols=82  Identities=20%  Similarity=0.302  Sum_probs=73.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||.++++++|+++|..||.+..+.     .++.++|||||+|.+.++|++|+..|+|..+.|+.|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45678999999999999999999999999876543     2577899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13319        110 KTNKGKT  116 (117)
Q Consensus       110 a~~~~~~  116 (117)
                      +.+++..
T Consensus        88 a~~k~~~   94 (96)
T d1fjca_          88 TGEKGGT   94 (96)
T ss_dssp             CSSSCCC
T ss_pred             eCCCCCC
Confidence            9987653

>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=99.85  E-value=2.9e-22  Score=108.84  Aligned_cols=75  Identities=29%  Similarity=0.469  Sum_probs=70.1

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      +|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|++. ++..++|+.|+|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999984 777899999988764

>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=99.85  E-value=3.4e-21  Score=107.15  Aligned_cols=81  Identities=17%  Similarity=0.217  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+...+|||+|||+++++++|+++|..+|.+.....+....++.++|+|||+|.+.++|++|++.+|+..+.|++|+|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34566799999999999999999999999886543344446799999999999999999999999999999999999987


Q ss_pred             e
Q psy13319        110 K  110 (117)
Q Consensus       110 a  110 (117)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.85  E-value=7.3e-21  Score=109.25  Aligned_cols=83  Identities=23%  Similarity=0.461  Sum_probs=72.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .+.++|||+|||+++++++|+++|+.|| +..+.++.+. .++.++|||||+|.+.++|++++. +++..+.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4568999999999999999999999998 7677666554 467889999999999999987775 899999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            886543

>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=9.7e-21  Score=105.07  Aligned_cols=78  Identities=17%  Similarity=0.259  Sum_probs=72.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .++|||+|||.++++++|.++|+.||.|..+.+..+. ++.++|+|||+|.+.++|++|++ +++..+.|+.|.|.++.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            5689999999999999999999999999999987764 78999999999999999999997 699999999999998653

>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=1.1e-20  Score=107.38  Aligned_cols=77  Identities=22%  Similarity=0.384  Sum_probs=68.7

Q ss_pred             CCCCcEEEEeCCC-CCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         30 NGSGWCIFVYNLA-PETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        30 ~~~~~~l~v~~Lp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....++|||+||| ..+++++|+++|++||.|..+.+        .+|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456779999997 46788899999999999999887        26899999999999999999999999999999999


Q ss_pred             EecCCC
Q psy13319        109 FKTNKG  114 (117)
Q Consensus       109 ~a~~~~  114 (117)
                      ++++++
T Consensus        84 ~a~~~~   89 (98)
T d1wf2a_          84 LAAEPK   89 (98)
T ss_dssp             ETTSCC
T ss_pred             ECCCCC
Confidence            997643

>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=99.85  E-value=4.7e-21  Score=109.58  Aligned_cols=82  Identities=22%  Similarity=0.365  Sum_probs=73.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..+.|+++.+.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            345678999999999999999999999999999988877 4688999999999999999999999999999999888776


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +.+
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.84  E-value=3.4e-21  Score=109.19  Aligned_cols=83  Identities=17%  Similarity=0.196  Sum_probs=73.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCC-eEEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHhCC--cEeCCeEEEEE
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGA-VQSVKVIRDL-QTNKCKGFGFVTMTNYDEAVVAIQSLNG--YALGNRILQVS  108 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~-i~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~~--~~~~g~~l~v~  108 (117)
                      +++|||+|||.++++++|+++|+.||. +..+.++.+. .++.++|||||+|.+.++|..|++.|++  ..++|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999995 8889888774 4578899999999999999999999865  56679999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ||+++.+
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987543

>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=99.84  E-value=6.7e-21  Score=105.94  Aligned_cols=77  Identities=30%  Similarity=0.502  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..+      ++||||+|.+.++|+.|++.|+|..+.|+.|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3467999999999999999999999999999988755      6799999999999999999999999999999999998


Q ss_pred             CCC
Q psy13319        112 NKG  114 (117)
Q Consensus       112 ~~~  114 (117)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            764

>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=99.84  E-value=2.8e-22  Score=112.71  Aligned_cols=82  Identities=17%  Similarity=0.291  Sum_probs=73.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+++++++|+++|..||.|..+.++.+ .+|.++|||||+|.+.++|++|++ ++|..+.|+.|+|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            346778999999999999999999999999887777544 578999999999999999999996 899999999999999


Q ss_pred             ecCC
Q psy13319        110 KTNK  113 (117)
Q Consensus       110 a~~~  113 (117)
                      |+.+
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8764

>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=99.84  E-value=3.8e-21  Score=108.04  Aligned_cols=81  Identities=21%  Similarity=0.462  Sum_probs=71.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHH----hhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEE
Q psy13319         32 SGWCIFVYNLAPETEESVLWQ----LFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      ++++|||+|||+.+++++|++    +|+.||.|..+.+..   ++.++|||||+|.+.++|..|+..++|..+.|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            468999999999999988864    579999999987754   4677899999999999999999999999999999999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      .||+.+..
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987653

>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=1.6e-20  Score=105.02  Aligned_cols=77  Identities=23%  Similarity=0.358  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCCCCCHHHH---HHhhcCCCCeEEEEEEecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         32 SGWCIFVYNLAPETEESVL---WQLFGPFGAVQSVKVIRDLQTNKC---KGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~~---~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ...+|||+|||+.+++++|   .++|++||.|..+.++.++.++..   +|||||+|.+.++|..|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3456999999999999999   678999999999999988766543   5999999999999999999999999999999


Q ss_pred             EEE
Q psy13319        106 QVS  108 (117)
Q Consensus       106 ~v~  108 (117)
                      +++
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.84  E-value=5.5e-20  Score=102.60  Aligned_cols=81  Identities=17%  Similarity=0.301  Sum_probs=72.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCcEeCCeEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL--NGYALGNRILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~~~~~~g~~l~v  107 (117)
                      .+++++|||+|||..+++++|+++|+.||.|..+.+..+      +++|||+|.+.++|++|+..+  ++..+.|++|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            567889999999999999999999999999999988754      579999999999999999865  568899999999


Q ss_pred             EEecCCCCC
Q psy13319        108 SFKTNKGKT  116 (117)
Q Consensus       108 ~~a~~~~~~  116 (117)
                      .|++.+.-+
T Consensus        79 ~~sk~~~lk   87 (88)
T d2cq1a1          79 QYSNHKELK   87 (88)
T ss_dssp             EECSCSSCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.84  E-value=1e-20  Score=105.66  Aligned_cols=79  Identities=27%  Similarity=0.316  Sum_probs=69.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe-CCeEEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL-GNRILQVSF  109 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~-~g~~l~v~~  109 (117)
                      +++++|||+|||.++++++|.++|+.||.+..+....    ++.+|+|||+|.+.++|.+|+..|+|..+ .|+.|+|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            4578999999999999999999999999998776543    34478999999999999999999999888 489999999


Q ss_pred             ecCC
Q psy13319        110 KTNK  113 (117)
Q Consensus       110 a~~~  113 (117)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8763

>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=9.4e-21  Score=103.79  Aligned_cols=76  Identities=24%  Similarity=0.405  Sum_probs=69.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+|++  +++++|+++|+.||.|..+.+..+      +++|||+|.+.++|..|+..|+|..+.|+.|+|+|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            467899999996  899999999999999999988644      679999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8765

>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=99.84  E-value=3.3e-20  Score=106.50  Aligned_cols=84  Identities=13%  Similarity=0.139  Sum_probs=74.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ..++..|||+|||+++++++|+++|..+|.+....++....++.++|+|||+|.+.++|++|++ +++..|.|+.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            4456679999999999999999999999988776666777789999999999999999999997 899999999999999


Q ss_pred             ecCCC
Q psy13319        110 KTNKG  114 (117)
Q Consensus       110 a~~~~  114 (117)
                      ++...
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87643

>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=99.84  E-value=3.9e-21  Score=111.50  Aligned_cols=78  Identities=19%  Similarity=0.094  Sum_probs=70.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..+++|||+|||+.+++++|+++|+.||.|..+.+..      .+|||||+|.+.++|.+|++.|||..+.|+.|+|.|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3567899999999999999999999999999987732      3789999999999999999999999999999999998


Q ss_pred             cCCC
Q psy13319        111 TNKG  114 (117)
Q Consensus       111 ~~~~  114 (117)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7543

>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=3e-21  Score=104.01  Aligned_cols=71  Identities=32%  Similarity=0.589  Sum_probs=67.7

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEE
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQ  106 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~  106 (117)
                      |||+|||.++++++|.++|..||.+..+.+..++.++.++|+|||+|.+.++|++|+..|||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999998999999999999999999999999999999988764

>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=99.83  E-value=4.4e-20  Score=104.76  Aligned_cols=80  Identities=24%  Similarity=0.478  Sum_probs=71.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCC--eEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGN--RILQV  107 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g--~~l~v  107 (117)
                      .++.++|||+|||+++++++|+++|+.||.|..+++..+      +++|||+|.+.++|+.|++.|++..+.|  ++|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            345688999999999999999999999999999988654      6799999999999999999999999875  58999


Q ss_pred             EEecCCCC
Q psy13319        108 SFKTNKGK  115 (117)
Q Consensus       108 ~~a~~~~~  115 (117)
                      +|+++.+.
T Consensus        88 ~~ak~~~~   95 (97)
T d1whya_          88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99997664

>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=3.6e-20  Score=106.01  Aligned_cols=84  Identities=17%  Similarity=0.347  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ....+++|||+|||+++++++|+++|..+| +..+.++.+. ++..+|||||+|.+.++|++|++ +++..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            345677899999999999999999999998 4567777664 58889999999999999999987 79999999999999


Q ss_pred             EecCCCC
Q psy13319        109 FKTNKGK  115 (117)
Q Consensus       109 ~a~~~~~  115 (117)
                      ++.....
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9886543

>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=99.82  E-value=6.3e-20  Score=102.36  Aligned_cols=76  Identities=24%  Similarity=0.310  Sum_probs=65.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      .++|||+|||.++++++|+++|+.||. ..+..      +..++||||+|.+.++|++|++.||+..+.|++|+|++++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            467999999999999999999999992 22222      34588999999999999999999999999999999999876


Q ss_pred             CCC
Q psy13319        113 KGK  115 (117)
Q Consensus       113 ~~~  115 (117)
                      +..
T Consensus        78 ~~~   80 (88)
T d1wg1a_          78 DAL   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=6e-20  Score=104.34  Aligned_cols=79  Identities=18%  Similarity=0.207  Sum_probs=70.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+.+++++|+++|+.||.|..+.+..       +|+|||+|.+.++|+.|++.|||..+.|+.|+|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34677899999999999999999999999999988753       47999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13319        110 KTNKGK  115 (117)
Q Consensus       110 a~~~~~  115 (117)
                      ++.+..
T Consensus        85 ~~~~~~   90 (98)
T d1wg4a_          85 IRVYPE   90 (98)
T ss_dssp             EEEECC
T ss_pred             EecCCC
Confidence            875443

>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=99.82  E-value=3.2e-20  Score=107.32  Aligned_cols=76  Identities=29%  Similarity=0.502  Sum_probs=69.4

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         33 GWCIFVYNLAP-ETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        33 ~~~l~v~~Lp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +++|||+|||+ .+++++|+++|+.||.|..+.++.++     +|+|||+|.+.++|.+|++.|+|..+.|+.|+|+|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57899999965 58999999999999999999998763     6899999999999999999999999999999999987


Q ss_pred             CC
Q psy13319        112 NK  113 (117)
Q Consensus       112 ~~  113 (117)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.81  E-value=2.8e-19  Score=102.53  Aligned_cols=80  Identities=18%  Similarity=0.144  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCcEeCCeEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL--NGYALGNRILQ  106 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~~~~~~g~~l~  106 (117)
                      ..+++++|||+|||..+++++|+++|..||.|..+.+.++      +++|||+|.+.++|+.|+..+  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            4467889999999999999999999999999999988654      679999999999999999977  55678899999


Q ss_pred             EEEecCCC
Q psy13319        107 VSFKTNKG  114 (117)
Q Consensus       107 v~~a~~~~  114 (117)
                      |+|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99987643

>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=99.81  E-value=2.2e-19  Score=97.33  Aligned_cols=74  Identities=24%  Similarity=0.347  Sum_probs=67.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      .+|||+|||+++++++|+++|+.||.|..+++..++.  ..+++|||+|.+.++|++|+. +++..++|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            3799999999999999999999999999999988764  345799999999999999986 7999999999999864

>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=99.81  E-value=2.6e-19  Score=96.98  Aligned_cols=72  Identities=25%  Similarity=0.394  Sum_probs=64.1

Q ss_pred             EEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecCCC
Q psy13319         36 IFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTNKG  114 (117)
Q Consensus        36 l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  114 (117)
                      |||+|||+++++++|+++|++|| +..+..      ++.+|+|||+|.+.++|++|+..|||..+.|+.|+|++++.+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444433      4458899999999999999999999999999999999987654

>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=99.80  E-value=1.2e-19  Score=103.88  Aligned_cols=82  Identities=17%  Similarity=0.130  Sum_probs=71.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      .....+|||+|||+++++++|.++|..+|.+.....+....+|.++|+|||+|.+.++|++|+. +++..+.|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3455679999999999999999999999988765455555689999999999999999999996 899999999999998


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            653

>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=99.80  E-value=5.5e-20  Score=102.61  Aligned_cols=77  Identities=19%  Similarity=0.258  Sum_probs=67.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||+.+++++|+++|.+||.|..+++.     ..+++||||+|.+.++|++|+.  ++..+.|+.|+|.+++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            46789999999999999999999999999888654     3457899999999999999985  7888999999999998


Q ss_pred             CCCC
Q psy13319        112 NKGK  115 (117)
Q Consensus       112 ~~~~  115 (117)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6554

>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=99.80  E-value=3.1e-19  Score=101.52  Aligned_cols=79  Identities=19%  Similarity=0.340  Sum_probs=70.3

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHH--HhCCcEeCCeEEE
Q psy13319         30 NGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQ--SLNGYALGNRILQ  106 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~--~l~~~~~~g~~l~  106 (117)
                      ...+++|||+|||.+ +++++|.++|+.||.|..+.++.+      +|+|||+|.+.++|.+|+.  .+++..+.|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            456789999999986 899999999999999999988755      5799999999999999997  4678899999999


Q ss_pred             EEEecCCC
Q psy13319        107 VSFKTNKG  114 (117)
Q Consensus       107 v~~a~~~~  114 (117)
                      |.|++.++
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997654

>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=99.80  E-value=4.9e-19  Score=98.84  Aligned_cols=80  Identities=14%  Similarity=0.221  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEeCCCCC-CCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCcEeCCeEE
Q psy13319         29 MNGSGWCIFVYNLAPE-TEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL--NGYALGNRIL  105 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~~~~~~g~~l  105 (117)
                      ..+.+++|||+|||.. +++++|.++|++||.|..+.+..+      +++|||+|.+.++|..|+..+  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            3567889999999987 789999999999999999988765      458999999999999999966  6788999999


Q ss_pred             EEEEecCCC
Q psy13319        106 QVSFKTNKG  114 (117)
Q Consensus       106 ~v~~a~~~~  114 (117)
                      +|+|++..+
T Consensus        78 ~V~~s~~~~   86 (89)
T d1x4da1          78 RVHLSQKYK   86 (89)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCcc
Confidence            999998654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.8e-20  Score=103.61  Aligned_cols=70  Identities=19%  Similarity=0.233  Sum_probs=64.1

Q ss_pred             EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         35 CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        35 ~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      +|||+|||+.+++++|+++|+.||.|..+.+..       .|||||+|.+.++|+.|+..|+|..+.|+.|+|.+++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            599999999999999999999999999998753       3699999999999999999999999999998887654

>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=99.79  E-value=4.7e-19  Score=102.24  Aligned_cols=79  Identities=23%  Similarity=0.193  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeC--CeEEEEE
Q psy13319         31 GSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALG--NRILQVS  108 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~--g~~l~v~  108 (117)
                      .+..+|||+|||..+++++|+++|.+||.|..+.+..++    .+|+|||+|.+.++|+.|+..|+|..+.  +..|++.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            445679999999999999999999999999999888763    3789999999999999999999998874  7889999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      |++.+
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            98754

>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=99.79  E-value=1.6e-19  Score=104.82  Aligned_cols=82  Identities=26%  Similarity=0.379  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEE
Q psy13319         30 NGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSF  109 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  109 (117)
                      ....++|||+|||+.+++++|.++|..+|.+..+.++.+..+|.++|+|||+|.+.++|++|+. +++..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            4567789999999999999999999999988665556666789999999999999999999997 899999999999988


Q ss_pred             ecC
Q psy13319        110 KTN  112 (117)
Q Consensus       110 a~~  112 (117)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            753

>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=99.76  E-value=6e-18  Score=105.33  Aligned_cols=84  Identities=23%  Similarity=0.309  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         29 MNGSGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        29 ~~~~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      .....++|||+|||..+++++|.++|..||.|..+.+..+..++.++|+|||+|.+.++|.+|++ +++..+.|+.|+|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            34567889999999999999999999999999999999998889999999999999999999997 68889999999999


Q ss_pred             EecCC
Q psy13319        109 FKTNK  113 (117)
Q Consensus       109 ~a~~~  113 (117)
                      +|.++
T Consensus       172 ~A~~k  176 (183)
T d1u1qa_         172 KALSK  176 (183)
T ss_dssp             ECCCH
T ss_pred             ecCCc
Confidence            98764

>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=99.73  E-value=2.2e-18  Score=98.70  Aligned_cols=79  Identities=10%  Similarity=0.045  Sum_probs=68.8

Q ss_pred             CCCcEEEEeCCCCCC-CH----HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEE
Q psy13319         31 GSGWCIFVYNLAPET-EE----SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRIL  105 (117)
Q Consensus        31 ~~~~~l~v~~Lp~~~-~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l  105 (117)
                      ....+|||+||+.++ ++    ++|+++|+.||.|..+.++..      +++|||+|.+.++|.+|+..|||..+.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            346789999999986 33    568999999999999988743      6799999999999999999999999999999


Q ss_pred             EEEEecCCCC
Q psy13319        106 QVSFKTNKGK  115 (117)
Q Consensus       106 ~v~~a~~~~~  115 (117)
                      +|.|++....
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999976543

>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=99.68  E-value=9.4e-20  Score=102.01  Aligned_cols=78  Identities=18%  Similarity=0.296  Sum_probs=66.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEE-----ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEE
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVI-----RDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVS  108 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~-----~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  108 (117)
                      ++|||+|||.++++++|+++|+.+|.+..+.+.     .+..++.++|||||+|.+.++|+.|+. |+|..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            679999999999999999999999876554332     334567789999999999999999986 99999999999997


Q ss_pred             EecC
Q psy13319        109 FKTN  112 (117)
Q Consensus       109 ~a~~  112 (117)
                      .+++
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6553

>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=99.66  E-value=6.8e-18  Score=96.64  Aligned_cols=76  Identities=16%  Similarity=0.171  Sum_probs=70.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEe
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFK  110 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  110 (117)
                      ..++|++++..+.+++++++|++||.|..+.++.+ .++.++|++||+|.+.++|.+|+..|+|..+.|+.|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34788888888999999999999999999999766 57899999999999999999999999999999999999985

>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=99.64  E-value=2.1e-15  Score=93.60  Aligned_cols=79  Identities=25%  Similarity=0.415  Sum_probs=70.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEec
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKT  111 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  111 (117)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|++||+|.+.++|+.|+.. ++..+.++.+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            347999999999999999999999999999999999999999999999999999999999985 6777888777776544

>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=99.61  E-value=1.4e-15  Score=88.08  Aligned_cols=76  Identities=21%  Similarity=0.254  Sum_probs=63.1

Q ss_pred             CCCCc-EEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCH-HHHHHHHHHhCCcEeCCeEEEE
Q psy13319         30 NGSGW-CIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNY-DEAVVAIQSLNGYALGNRILQV  107 (117)
Q Consensus        30 ~~~~~-~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~-~~a~~a~~~l~~~~~~g~~l~v  107 (117)
                      .+.++ .+||+|||..+++++|+++|+.||.|..+.++.+      +|+|||.|.+. ++|..|+..+++..+.++.+.|
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            34455 4599999999999999999999999999999754      78999999985 7899999999998877666666


Q ss_pred             EEec
Q psy13319        108 SFKT  111 (117)
Q Consensus       108 ~~a~  111 (117)
                      .+..
T Consensus        81 ~~~~   84 (113)
T d1owxa_          81 TWEV   84 (113)
T ss_dssp             EEEE
T ss_pred             EEee
Confidence            5543

>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=99.60  E-value=5.7e-15  Score=83.56  Aligned_cols=81  Identities=19%  Similarity=0.248  Sum_probs=68.2

Q ss_pred             CCCCcEEEEeCC--CCCCC---------HHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q psy13319         30 NGSGWCIFVYNL--APETE---------ESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGY   98 (117)
Q Consensus        30 ~~~~~~l~v~~L--p~~~~---------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~   98 (117)
                      ...+++|+|.|+  |.+..         +++|.+.|++||.|..+.+..+    ..+|++||.|.+.++|..|+..|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            456789999999  54321         2578899999999999877544    34789999999999999999999999


Q ss_pred             EeCCeEEEEEEecCCC
Q psy13319         99 ALGNRILQVSFKTNKG  114 (117)
Q Consensus        99 ~~~g~~l~v~~a~~~~  114 (117)
                      .+.|+.|+|.+..++.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987654

>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=99.58  E-value=3e-15  Score=84.99  Aligned_cols=64  Identities=19%  Similarity=0.251  Sum_probs=56.8

Q ss_pred             CCCcEEEEe--CCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         31 GSGWCIFVY--NLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        31 ~~~~~l~v~--~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      .+..+++|.  |||..+++++|+++|++||.|..+.+..+      ++||||+|.+.++|..|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456778885  59999999999999999999999887654      57999999999999999999999876

>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=99.56  E-value=6.7e-15  Score=80.32  Aligned_cols=73  Identities=12%  Similarity=0.201  Sum_probs=60.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeE-EEEEEe
Q psy13319         32 SGWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRI-LQVSFK  110 (117)
Q Consensus        32 ~~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~-l~v~~a  110 (117)
                      +++.|+|+|+|++.+++ +.+.|+.||.|..+.+.      ..++|+||+|.+.++|++|+. +||..++|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            35679999999998865 55689999999998764      337899999999999999996 8999999974 567766


Q ss_pred             cC
Q psy13319        111 TN  112 (117)
Q Consensus       111 ~~  112 (117)
                      .+
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.47  E-value=4.9e-14  Score=80.28  Aligned_cols=82  Identities=20%  Similarity=0.236  Sum_probs=68.6

Q ss_pred             CCCcEEEEeCC--CCCCC--------HHHHHHhhcCCCCeEEEEEEecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCc
Q psy13319         31 GSGWCIFVYNL--APETE--------ESVLWQLFGPFGAVQSVKVIRDLQTN--KCKGFGFVTMTNYDEAVVAIQSLNGY   98 (117)
Q Consensus        31 ~~~~~l~v~~L--p~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~~~   98 (117)
                      ++++.|.+.|+  |....        .++|++.|.+||.|..+.+.+++.+.  ...|++||+|.+.++|.+|+..|+|.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45778999999  55432        25788999999999999988765443  34689999999999999999999999


Q ss_pred             EeCCeEEEEEEecC
Q psy13319         99 ALGNRILQVSFKTN  112 (117)
Q Consensus        99 ~~~g~~l~v~~a~~  112 (117)
                      .++|+.|++.|...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999763

>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=98.06  E-value=6.8e-05  Score=40.53  Aligned_cols=80  Identities=11%  Similarity=0.203  Sum_probs=63.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCcEeCC---e--EEE
Q psy13319         34 WCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNK--CKGFGFVTMTNYDEAVVAIQSLNGYALGN---R--ILQ  106 (117)
Q Consensus        34 ~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~~~~~~g---~--~l~  106 (117)
                      .+|-|+.||+..+++++.+.++..|.+....+...+.+.+  ...-||+.|.+.++.....+.++|..+.+   .  +-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            3688999999999999999999999888777766654443  24789999999999999999999988642   1  345


Q ss_pred             EEEecCC
Q psy13319        107 VSFKTNK  113 (117)
Q Consensus       107 v~~a~~~  113 (117)
                      |++|--+
T Consensus        82 VE~AP~q   88 (91)
T d1uw4a_          82 VEFAPFQ   88 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEcCcc
Confidence            6666443

>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=97.98  E-value=2.9e-05  Score=39.72  Aligned_cols=62  Identities=29%  Similarity=0.442  Sum_probs=52.0

Q ss_pred             HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEeCCeEEEEEEecC
Q psy13319         48 SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYALGNRILQVSFKTN  112 (117)
Q Consensus        48 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  112 (117)
                      +.|...|.+++.|..+.+...   ......|-|...+.++|.-++..|+...+++++|.|+++..
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 QLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSC---CSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEec---cCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            456677889999998877554   23345799999999999999999999999999999999763

>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=97.94  E-value=2.3e-05  Score=42.12  Aligned_cols=72  Identities=19%  Similarity=0.308  Sum_probs=56.6

Q ss_pred             CCCCcEEEEeCCCCCC------CH---HHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEe
Q psy13319         30 NGSGWCIFVYNLAPET------EE---SVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSLNGYAL  100 (117)
Q Consensus        30 ~~~~~~l~v~~Lp~~~------~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~~~~~  100 (117)
                      .+++-+|.|.=..+..      .+   .+|.+.|..||++.-++++.+        -.+|+|.+-+.|.+|+. ++|..+
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEE
Confidence            3455666664443322      22   467788999999999999866        69999999999999999 799999


Q ss_pred             CCeEEEEEEe
Q psy13319        101 GNRILQVSFK  110 (117)
Q Consensus       101 ~g~~l~v~~a  110 (117)
                      .|+.|+|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999864

>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=96.90  E-value=0.0068  Score=32.73  Aligned_cols=55  Identities=24%  Similarity=0.408  Sum_probs=44.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhcCCCCeEEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q psy13319         33 GWCIFVYNLAPETEESVLWQLFGPFGAVQSVKVIRDLQTNKCKGFGFVTMTNYDEAVVAIQSL   95 (117)
Q Consensus        33 ~~~l~v~~Lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   95 (117)
                      -.-+|.-..|..+...+|.++|++||.| .+.++.+.       -|||.....+.+..++..+
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHHHh
Confidence            3347888999999999999999999976 35555542       5999999999999888754