Psyllid ID: psy16913

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-
Protein Sequence
MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY
Secondary Structure (PSIPRED)
cccccccEEEEEEEEEccccccccccccccccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEEEEccccccHHcccEEEEEEEccccccEEEcccHHHHHHHHHHHccccEccEEEEEEEcccccccccc
Coil and Loop (DISEMBL)
mflpfgnvissKVFIDratnqskcfgecnrkvsvnqkcfgfvsfdnpasAHTAIQAMNGFQIGMKRLKVQlkrpkdaarpy
Flexible Loop (DISEMBL)
mflpfgnvisskvfidRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKvqlkrpkdaarpy
Low Complexity Region (SEG)
MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY
Disordered region (IsUnstruct)
**LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRL**************
Disordered Region (DISOPRED)
MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK*************
Disordered Region (DISEMBL)
MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ***********
Disordered Region (DISPRO)
*FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY
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	81	2.2.26 [Sep-21-2011]
Q9IBD1	452	CUGBP Elav-like family me	no	N/A	0.827	0.148	0.765	2e-28
Q91579	462	CUGBP Elav-like family me	N/A	N/A	0.827	0.145	0.753	6e-28
A0JM51	486	CUGBP Elav-like family me	yes	N/A	0.827	0.137	0.740	6e-28
Q6DGV1	520	CUGBP Elav-like family me	no	N/A	0.827	0.128	0.753	1e-27
Q8N6W0	485	CUGBP Elav-like family me	yes	N/A	0.827	0.138	0.740	2e-27
Q7ZWM3	462	CUGBP Elav-like family me	N/A	N/A	0.827	0.145	0.740	2e-27
Q8CIN6	465	CUGBP Elav-like family me	no	N/A	0.827	0.144	0.740	2e-27
Q5SZQ8	465	CUGBP Elav-like family me	no	N/A	0.827	0.144	0.740	2e-27
Q08E07	461	CUGBP Elav-like family me	no	N/A	0.827	0.145	0.740	2e-27
Q7TN33	460	CUGBP Elav-like family me	no	N/A	0.814	0.143	0.737	2e-26

>sp|Q9IBD1|CELF3_DANRE CUGBP Elav-like family member 3 OS=Danio rerio GN=celf3 PE=2 SV=2

 Score =  124 bits (311), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 62/81 (76%), Positives = 64/81 (79%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 386 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 431

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 432 QIGMKRLKVQLKRPKDANRPY 452

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.
Danio rerio (taxid: 7955)

>sp|Q91579|CEL3A_XENLA CUGBP Elav-like family member 3-A OS=Xenopus laevis GN=tnrc4-a PE=2 SV=2

 Score =  122 bits (306), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 61/81 (75%), Positives = 63/81 (77%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNP SA  AIQAMNGF
Sbjct: 396 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPGSAQAAIQAMNGF 441

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 442 QIGMKRLKVQLKRPKDANRPY 462

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.

Xenopus laevis (taxid: 8355)

>sp|A0JM51|CELF5_XENTR CUGBP Elav-like family member 5 OS=Xenopus tropicalis GN=celf5 PE=2 SV=1

 Score =  122 bits (306), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 60/81 (74%), Positives = 64/81 (79%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGN+ISSKVF+DRATNQSKCFG              FVSFDNP+SA TAIQAMNGF
Sbjct: 420 MFLPFGNIISSKVFMDRATNQSKCFG--------------FVSFDNPSSAQTAIQAMNGF 465

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKD  +PY
Sbjct: 466 QIGMKRLKVQLKRPKDTTQPY 486

RNA-binding protein that may be implicated in the regulation of pre-mRNA alternative splicing.

Xenopus tropicalis (taxid: 8364)

>sp|Q6DGV1|CELF4_DANRE CUGBP Elav-like family member 4 OS=Danio rerio GN=celf4 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 61/81 (75%), Positives = 63/81 (77%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVISSKVF+DRATNQSKCFG              FVSFDNP SA  AIQ+MNGF
Sbjct: 454 MFLPFGNVISSKVFVDRATNQSKCFG--------------FVSFDNPGSAQAAIQSMNGF 499

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 500 QIGMKRLKVQLKRPKDANRPY 520

RNA-binding protein that may be implicated in the regulation of pre-mRNA alternative splicing.

Danio rerio (taxid: 7955)

>sp|Q8N6W0|CELF5_HUMAN CUGBP Elav-like family member 5 OS=Homo sapiens GN=CELF5 PE=1 SV=1

 Score =  121 bits (303), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/81 (74%), Positives = 62/81 (76%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGN+ISSKVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 419 MFLPFGNIISSKVFMDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 464

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKD   PY
Sbjct: 465 QIGMKRLKVQLKRPKDPGHPY 485

RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Homo sapiens (taxid: 9606)

>sp|Q7ZWM3|CEL3B_XENLA CUGBP Elav-like family member 3-B OS=Xenopus laevis GN=tnrc4-b PE=2 SV=1

 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/81 (74%), Positives = 63/81 (77%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNP SA  AIQ+MNGF
Sbjct: 396 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPGSAQAAIQSMNGF 441

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 442 QIGMKRLKVQLKRPKDANRPY 462

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.

Xenopus laevis (taxid: 8355)

>sp|Q8CIN6|CELF3_MOUSE CUGBP Elav-like family member 3 OS=Mus musculus GN=Celf3 PE=2 SV=1

 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/81 (74%), Positives = 64/81 (79%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFG+VIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 399 MFVPFGHVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 444

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 445 QIGMKRLKVQLKRPKDANRPY 465

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Mus musculus (taxid: 10090)

>sp|Q5SZQ8|CELF3_HUMAN CUGBP Elav-like family member 3 OS=Homo sapiens GN=CELF3 PE=1 SV=1

 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/81 (74%), Positives = 64/81 (79%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFG+VIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 399 MFVPFGHVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 444

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 445 QIGMKRLKVQLKRPKDANRPY 465

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Homo sapiens (taxid: 9606)

>sp|Q08E07|CELF3_BOVIN CUGBP Elav-like family member 3 OS=Bos taurus GN=CELF3 PE=2 SV=1

 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/81 (74%), Positives = 64/81 (79%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFG+VIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 395 MFVPFGHVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 440

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 441 QIGMKRLKVQLKRPKDANRPY 461

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Bos taurus (taxid: 9913)

>sp|Q7TN33|CELF6_MOUSE CUGBP Elav-like family member 6 OS=Mus musculus GN=Celf6 PE=2 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/80 (73%), Positives = 62/80 (77%), Gaps = 14/80 (17%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           FLPFG V+S+KVF+DRATNQSKCFG              FVSFDNP SA TAIQAMNGFQ
Sbjct: 395 FLPFGAVVSAKVFVDRATNQSKCFG--------------FVSFDNPTSAQTAIQAMNGFQ 440

Query: 62  IGMKRLKVQLKRPKDAARPY 81
           IGMKRLKVQLKRPKDA RPY
Sbjct: 441 IGMKRLKVQLKRPKDANRPY 460

RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of TNNT2 in a muscle-specific splicing enhancer (MSE)-dependent manner. Promotes also exon exclusion of INSR pre-mRNA.

Mus musculus (taxid: 10090)

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	81
307175839	278	CUG-BP- and ETR-3-like factor 4 [Campono	0.827	0.241	0.802	4e-28
340725302	360	PREDICTED: CUGBP Elav-like family member	0.827	0.186	0.790	1e-27
340725300	384	PREDICTED: CUGBP Elav-like family member	0.827	0.174	0.790	1e-27
340725298	374	PREDICTED: CUGBP Elav-like family member	0.827	0.179	0.790	1e-27
340725296	373	PREDICTED: CUGBP Elav-like family member	0.827	0.179	0.790	1e-27
328776307	525	PREDICTED: CUGBP Elav-like family member	0.827	0.127	0.790	2e-27
226371663	495	CUGBP Elav-like family member 4 isoform	0.827	0.135	0.790	2e-27
307192008	278	CUG-BP- and ETR-3-like factor 4 [Harpegn	0.827	0.241	0.790	2e-27
350403945	522	PREDICTED: LOW QUALITY PROTEIN: CUGBP El	0.827	0.128	0.790	2e-27
226371659	504	CUGBP Elav-like family member 4 isoform	0.827	0.132	0.790	2e-27

>gi|307175839|gb|EFN65654.1| CUG-BP- and ETR-3-like factor 4 [Camponotus floridanus]

 Score =  128 bits (321), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 65/81 (80%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 212 MFLPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 257

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 258 QIGMKRLKVQLKRPKDASRPY 278

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725302|ref|XP_003401011.1| PREDICTED: CUGBP Elav-like family member 4-like isoform 4 [Bombus terrestris]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 294 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 339

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 340 QIGMKRLKVQLKRPKDASRPY 360

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725300|ref|XP_003401010.1| PREDICTED: CUGBP Elav-like family member 4-like isoform 3 [Bombus terrestris]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 318 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 363

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 364 QIGMKRLKVQLKRPKDASRPY 384

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725298|ref|XP_003401009.1| PREDICTED: CUGBP Elav-like family member 4-like isoform 2 [Bombus terrestris]

 Score =  126 bits (317), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 308 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 353

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 354 QIGMKRLKVQLKRPKDASRPY 374

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725296|ref|XP_003401008.1| PREDICTED: CUGBP Elav-like family member 4-like isoform 1 [Bombus terrestris]

 Score =  126 bits (317), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 307 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 352

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 353 QIGMKRLKVQLKRPKDASRPY 373

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328776307|ref|XP_393833.4| PREDICTED: CUGBP Elav-like family member 4-like [Apis mellifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 459 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 504

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 505 QIGMKRLKVQLKRPKDASRPY 525

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|226371663|ref|NP_001139766.1| CUGBP Elav-like family member 4 isoform C [Mus musculus] gi|27753638|gb|AAO22167.1| bruno-like 4 protein [Mus musculus]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 65/81 (80%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 429 MFLPFGNVISSKVFVDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 474

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 475 QIGMKRLKVQLKRPKDANRPY 495

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|307192008|gb|EFN75398.1| CUG-BP- and ETR-3-like factor 4 [Harpegnathos saltator]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 65/81 (80%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 212 MFLPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 257

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 258 QIGMKRLKVQLKRPKDASRPY 278

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350403945|ref|XP_003486959.1| PREDICTED: LOW QUALITY PROTEIN: CUGBP Elav-like family member 4-like [Bombus impatiens]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 66/81 (81%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 456 MFIPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 501

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA+RPY
Sbjct: 502 QIGMKRLKVQLKRPKDASRPY 522

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|226371659|ref|NP_001139764.1| CUGBP Elav-like family member 4 isoform A [Mus musculus] gi|29387384|gb|AAH48405.1| Brunol4 protein [Mus musculus]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 65/81 (80%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MFLPFGNVISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct: 438 MFLPFGNVISSKVFVDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 483

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
           QIGMKRLKVQLKRPKDA RPY
Sbjct: 484 QIGMKRLKVQLKRPKDANRPY 504

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

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	81
RGD|1307630	355	Celf4 "CUGBP, Elav-like family	0.827	0.188	0.790	2.5e-26
FB|FBgn0264001	422	bru-3 "bruno-3" [Drosophila me	0.827	0.158	0.790	3.2e-26
ZFIN|ZDB-GENE-110408-50	442	celf3b "cugbp, Elav-like famil	0.827	0.151	0.777	6.7e-26
UNIPROTKB|F1NYP4	361	CELF4 "Uncharacterized protein	0.827	0.185	0.777	8.4e-26
ZFIN|ZDB-GENE-000501-2	452	celf3a "cugbp, Elav-like famil	0.827	0.148	0.765	3.2e-25
UNIPROTKB|F1S8E8	420	CELF5 "Uncharacterized protein	0.827	0.159	0.753	3.6e-25
UNIPROTKB|F1P5J4	354	BRUNOL6 "Uncharacterized prote	0.827	0.189	0.753	4.6e-25
UNIPROTKB|Q91579	462	tnrc4-a "CUGBP Elav-like famil	0.827	0.145	0.753	1e-24
UNIPROTKB|F1PXQ8	485	CELF5 "Uncharacterized protein	0.827	0.138	0.753	1.1e-24
UNIPROTKB|F1MD42	489	F1MD42 "Uncharacterized protei	0.827	0.137	0.753	1.1e-24

RGD|1307630 Celf4 "CUGBP, Elav-like family member 4" [Rattus norvegicus (taxid:10116)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 64/81 (79%), Positives = 65/81 (80%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct:   289 MFLPFGNVISSKVFVDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 334

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   335 QIGMKRLKVQLKRPKDANRPY 355

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0264001 bru-3 "bruno-3" [Drosophila melanogaster (taxid:7227)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 64/81 (79%), Positives = 65/81 (80%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVISSKVFIDRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct:   356 MFLPFGNVISSKVFIDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 401

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA+RPY
Sbjct:   402 QIGMKRLKVQLKRPKDASRPY 422

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=ISA

GO:0043234 "protein complex" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

ZFIN|ZDB-GENE-110408-50 celf3b "cugbp, Elav-like family member 3b" [Danio rerio (taxid:7955)]

 Score = 294 (108.6 bits), Expect = 6.7e-26, P = 6.7e-26
 Identities = 63/81 (77%), Positives = 65/81 (80%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct:   376 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 421

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   422 QIGMKRLKVQLKRPKDANRPY 442

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NYP4 CELF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 63/81 (77%), Positives = 64/81 (79%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVISSKVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct:   295 MFLPFGNVISSKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 340

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   341 QIGMKRLKVQLKRPKDANRPY 361

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-000501-2 celf3a "cugbp, Elav-like family member 3a" [Danio rerio (taxid:7955)]

 Score = 289 (106.8 bits), Expect = 3.2e-25, P = 3.2e-25
 Identities = 62/81 (76%), Positives = 64/81 (79%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct:   386 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 431

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   432 QIGMKRLKVQLKRPKDANRPY 452

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1S8E8 CELF5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 61/81 (75%), Positives = 63/81 (77%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGN+ISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct:   354 MFLPFGNIISSKVFMDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 399

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKD   PY
Sbjct:   400 QIGMKRLKVQLKRPKDPGHPY 420

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P5J4 BRUNOL6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 61/81 (75%), Positives = 63/81 (77%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNP SA  AIQAMNGF
Sbjct:   288 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPTSAQAAIQAMNGF 333

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   334 QIGMKRLKVQLKRPKDANRPY 354

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q91579 tnrc4-a "CUGBP Elav-like family member 3-A" [Xenopus laevis (taxid:8355)]

 Score = 285 (105.4 bits), Expect = 1.0e-24, P = 1.0e-24
 Identities = 61/81 (75%), Positives = 63/81 (77%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNP SA  AIQAMNGF
Sbjct:   396 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPGSAQAAIQAMNGF 441

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKDA RPY
Sbjct:   442 QIGMKRLKVQLKRPKDANRPY 462

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISS

UNIPROTKB|F1PXQ8 CELF5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 286 (105.7 bits), Expect = 1.1e-24, P = 1.1e-24
 Identities = 61/81 (75%), Positives = 63/81 (77%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGN+ISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct:   419 MFLPFGNIISSKVFMDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 464

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKD   PY
Sbjct:   465 QIGMKRLKVQLKRPKDPGHPY 485

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1MD42 F1MD42 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 286 (105.7 bits), Expect = 1.1e-24, P = 1.1e-24
 Identities = 61/81 (75%), Positives = 63/81 (77%)

Query:     1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
             MFLPFGN+ISSKVF+DRATNQSKCFG              FVSFDNPASA TAIQAMNGF
Sbjct:   423 MFLPFGNIISSKVFMDRATNQSKCFG--------------FVSFDNPASAQTAIQAMNGF 468

Query:    61 QIGMKRLKVQLKRPKDAARPY 81
             QIGMKRLKVQLKRPKD   PY
Sbjct:   469 QIGMKRLKVQLKRPKDPGHPY 489

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8N6W0	CELF5_HUMAN	No assigned EC number	0.7407	0.8271	0.1381	yes	N/A
Q7TSY6	CELF4_MOUSE	No assigned EC number	0.9534	0.5308	0.0884	no	N/A
Q9BZC1	CELF4_HUMAN	No assigned EC number	0.9534	0.5308	0.0884	no	N/A
A0JM51	CELF5_XENTR	No assigned EC number	0.7407	0.8271	0.1378	yes	N/A
Q4R535	CELF4_MACFA	No assigned EC number	0.9534	0.5308	0.0907	N/A	N/A
Q0V9L3	CELF4_XENTR	No assigned EC number	0.9302	0.5308	0.1014	no	N/A
Q5NVC8	CELF4_PONAB	No assigned EC number	0.9534	0.5308	0.0884	no	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	81
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-32
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-30
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-29
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-24
smart00360	73	smart00360, RRM, RNA recognition motif	7e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-11
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-10
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-08
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-07
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-07
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	6e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	3e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	9e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-05
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	5e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	7e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-04
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	4e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	6e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	6e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	9e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.001
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.001
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.001
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.003
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.003
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.003
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.003
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.004
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.004

>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 =  106 bits (266), Expect = 3e-32
 Identities = 52/70 (74%), Positives = 54/70 (77%), Gaps = 14/70 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          MFLPFGNVIS+KVF+DRATNQSKCFG              FVSFDNPASA  AIQAMNGF
Sbjct: 24 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 69

Query: 61 QIGMKRLKVQ 70
          QIGMKRLKVQ
Sbjct: 70 QIGMKRLKVQ 79

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

 Score =  102 bits (254), Expect = 2e-30
 Identities = 51/80 (63%), Positives = 59/80 (73%), Gaps = 14/80 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          MF+PFGNV+S+KVFID+ TN SKCFG              FVS+DNP SA  AIQAMNGF
Sbjct: 27 MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQAMNGF 72

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          QIGMKRLKVQLKR K+ ++P
Sbjct: 73 QIGMKRLKVQLKRSKNDSKP 92

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|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 = 99.2 bits (248), Expect = 2e-29
 Identities = 42/70 (60%), Positives = 49/70 (70%), Gaps = 14/70 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F PFGNVIS+KVF+D+ T QSKCFG              FVS+DNP SA  AI+AMNGF
Sbjct: 18 LFAPFGNVISAKVFVDKNTGQSKCFG--------------FVSYDNPESAQAAIKAMNGF 63

Query: 61 QIGMKRLKVQ 70
          Q+G KRLKVQ
Sbjct: 64 QVGGKRLKVQ 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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 86.6 bits (214), Expect = 3e-24
 Identities = 46/69 (66%), Positives = 49/69 (71%), Gaps = 14/69 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          FLPFGNVIS+KVFID+ TN SKCFG              FVS+DNP SA  AIQAMNGFQ
Sbjct: 25 FLPFGNVISAKVFIDKQTNLSKCFG--------------FVSYDNPDSAQAAIQAMNGFQ 70

Query: 62 IGMKRLKVQ 70
          IG KRLKVQ
Sbjct: 71 IGTKRLKVQ 79

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

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

 Score = 54.5 bits (132), Expect = 7e-12
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG V S ++  D+ T +SK F               FV F++   A  A++A+NG 
Sbjct: 19 LFSKFGKVESVRLVRDKETGKSKGFA--------------FVEFESEEDAEKALEALNGK 64

Query: 61 QIGMKRLKV 69
          ++  + LKV
Sbjct: 65 ELDGRPLKV 73

Length = 73

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

 Score = 54.3 bits (131), Expect = 1e-11
 Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  DR T QS  +G              FV + +   A  AI  +NGF
Sbjct: 20 LFEAIGPIESCKIVRDRITGQSLGYG--------------FVDYVDENDAQKAINTLNGF 65

Query: 61 QIGMKRLKV 69
          +I  KRLKV
Sbjct: 66 EIRNKRLKV 74

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

 Score = 51.9 bits (125), Expect = 1e-10
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 16/63 (25%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN--GFQ 61
          PFG +IS+K  +D+ TN  KC            K +GFV FD+P +A  AI+ +N  G Q
Sbjct: 23 PFGKIISTKAILDKKTN--KC------------KGYGFVDFDSPEAALKAIEGLNGRGVQ 68

Query: 62 IGM 64
             
Sbjct: 69 AQF 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 51.8 bits (125), Expect = 1e-10
 Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 14/73 (19%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V S++V  DR T +S+  G            FGFV  +    A+ AI+ +NG  
Sbjct: 20 FGQFGEVTSARVITDRETGRSR--G------------FGFVEMETAEEANAAIEKLNGTD 65

Query: 62 IGMKRLKVQLKRP 74
           G + L V   RP
Sbjct: 66 FGGRTLTVNEARP 78

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

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

 Score = 50.9 bits (122), Expect = 3e-10
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +FL  G V + K+  D+ T  S  +G            FGFV + +   A  AI+ +NG 
Sbjct: 20 LFLAVGPVKNCKIVRDKRTGYS--YG------------FGFVDYQSAEDAQRAIRTLNGL 65

Query: 61 QIGMKRLKVQLKRP 74
          Q+  KR+KV   RP
Sbjct: 66 QLQNKRIKVAYARP 79

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

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

 Score = 50.2 bits (121), Expect = 4e-10
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 15/69 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F  FGN++S KV  D     SK  G            +GFV F+   +A  AI+ +NG 
Sbjct: 22 TFSAFGNILSCKVATD-ENGGSK--G------------YGFVHFETEEAAVRAIEKVNGM 66

Query: 61 QIGMKRLKV 69
           +  K++ V
Sbjct: 67 LLNDKKVFV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 52.9 bits (127), Expect = 8e-10
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 15/79 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F   G + S+KV +D     S+ FG              FV F NP  A+ A+  M+G 
Sbjct: 305 LFSECGEITSAKVMLD-EKGVSRGFG--------------FVCFSNPEEANRAVTEMHGR 349

Query: 61  QIGMKRLKVQLKRPKDAAR 79
            +G K L V L + K+  R
Sbjct: 350 MLGGKPLYVALAQRKEQRR 368

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

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

 Score = 46.1 bits (110), Expect = 2e-08
 Identities = 27/71 (38%), Positives = 32/71 (45%), Gaps = 15/71 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F PFG + S+KV  D    +SK FG              FV F +P  A  A+  MNG 
Sbjct: 21 EFSPFGTITSAKVMTD-EKGRSKGFG--------------FVCFSSPEEATKAVTEMNGR 65

Query: 61 QIGMKRLKVQL 71
           IG K L V L
Sbjct: 66 IIGGKPLYVAL 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 45.4 bits (108), Expect = 3e-08
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 15/70 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG + S ++  D+                   K F FV F++P  A  A++A+NG 
Sbjct: 18 LFSKFGEIESVRIVRDK---------------DGKSKGFAFVEFESPEDAEKALEALNGK 62

Query: 61 QIGMKRLKVQ 70
          ++  ++LKV 
Sbjct: 63 ELDGRKLKVS 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 45.5 bits (108), Expect = 3e-08
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 14/70 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V+ ++V  DR T +S+ FG              +V F++P  A  AI+AM+G +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFG--------------YVDFESPEDAKKAIEAMDGKE 65

Query: 62 IGMKRLKVQL 71
          +  + + V  
Sbjct: 66 LDGRPINVDF 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 45.0 bits (107), Expect = 5e-08
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 14/72 (19%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F PFG V + KV  D  TN  KC            K +GFV+  N   A++AI ++NG+
Sbjct: 21 LFSPFGAVTNVKVIRDLTTN--KC------------KGYGFVTMTNYEEAYSAIASLNGY 66

Query: 61 QIGMKRLKVQLK 72
          ++G + L+V  K
Sbjct: 67 RLGGRVLQVSFK 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 44.7 bits (106), Expect = 7e-08
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 14/67 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +  ++V  D  T +SK +G              FVSF     A  AIQ+MNG  
Sbjct: 20 FAPFGEISDARVVKDMQTGKSKGYG--------------FVSFVKKEDAENAIQSMNGQW 65

Query: 62 IGMKRLK 68
          +G + ++
Sbjct: 66 LGGRAIR 72

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

 Score = 44.6 bits (106), Expect = 8e-08
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +   ++  D  T +SK +G              F+ F +   A  A++ +NGF+
Sbjct: 19 FEPFGEIEFVQLQRDPETGRSKGYG--------------FIQFADAEDAKKALEQLNGFE 64

Query: 62 IGMKRLKV 69
          +  + +KV
Sbjct: 65 LAGRPIKV 72

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

>gnl|CDD|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 = 44.5 bits (106), Expect = 9e-08
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 14/72 (19%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V    +  D  T +S+  G            FGFV+F++   A  AI+ +NG +
Sbjct: 22 FSKFGRVEEVLLMKDPETGESR--G------------FGFVTFESVEDADAAIRDLNGKE 67

Query: 62 IGMKRLKVQLKR 73
          +  + +KV+  +
Sbjct: 68 LEGRVIKVEKAK 79

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

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 14/75 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG V + K+  D  TNQ      C        K +GFVS  N   A  AI ++NG+
Sbjct: 289 LFGPFGAVQNVKIIRDLTTNQ------C--------KGYGFVSMTNYDEAAMAILSLNGY 334

Query: 61  QIGMKRLKVQLKRPK 75
            +G + L+V  K  K
Sbjct: 335 TLGNRVLQVSFKTNK 349

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 43.4 bits (103), Expect = 2e-07
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 15/68 (22%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG + S ++  D  T +SK F               FV F++   A  A++A+NG 
Sbjct: 18 LFSKFGPIESIRIVRD-ETGRSKGFA--------------FVEFEDEEDAEKALEALNGK 62

Query: 61 QIGMKRLK 68
          ++G + L+
Sbjct: 63 ELGGRELR 70

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

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

 Score = 42.9 bits (102), Expect = 3e-07
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 15/69 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G + S+KV  D                    K FGFV+F+N  +A  A++ +NG 
Sbjct: 21 LFGKYGKITSAKVMKDD---------------EGKSKGFGFVNFENHEAAQKAVEELNGK 65

Query: 61 QIGMKRLKV 69
          ++  K+L V
Sbjct: 66 EVNGKKLYV 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 43.1 bits (101), Expect = 3e-07
 Identities = 30/75 (40%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          MF PFG V + KV  D  TN  KC G            FGFV+  N   A  AI ++NG+
Sbjct: 21 MFGPFGAVTNVKVIRDFNTN--KCKG------------FGFVTMTNYEEAAMAIASLNGY 66

Query: 61 QIGMKRLKVQLKRPK 75
          ++G K L+V  K  K
Sbjct: 67 RLGDKILQVSFKTSK 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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 43.2 bits (102), Expect = 3e-07
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS   G            +GFV++ +P  A  AI  +NG 
Sbjct: 21 LFSSIGEIESCKLIRDKVTGQS--LG------------YGFVNYVDPEDAEKAINTLNGL 66

Query: 61 QIGMKRLKV 69
          ++  K +KV
Sbjct: 67 RLQNKTIKV 75

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

 Score = 42.6 bits (101), Expect = 4e-07
 Identities = 15/33 (45%), Positives = 24/33 (72%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
          K +GF+ ++NP SA  AI +MN F +G ++L+V
Sbjct: 42 KGYGFIEYENPQSAQDAIASMNLFDLGGQQLRV 74

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

 Score = 42.8 bits (100), Expect = 5e-07
 Identities = 29/75 (38%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          MF PFG V + KV  D  TN  KC G            FGFV+  N   A  AI ++NG+
Sbjct: 23 MFGPFGAVTNVKVIRDFNTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 68

Query: 61 QIGMKRLKVQLKRPK 75
          ++G + L+V  K  K
Sbjct: 69 RLGDRVLQVSFKTNK 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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.5 bits (99), Expect = 6e-07
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 14/71 (19%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
          P+G ++S+K  +D+ TN  KC G            +GFV FD+PA+A  A+ A+    + 
Sbjct: 30 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPAAAQKAVSALKASGVQ 75

Query: 64 MKRLKVQLKRP 74
           +  K Q + P
Sbjct: 76 AQMAKQQEQDP 86

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

 Score = 42.4 bits (99), Expect = 6e-07
 Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F PFG V + KV  D  TN  KC G            FGFV+  N   A  AI ++NG+
Sbjct: 21 LFGPFGAVTNVKVIRDFTTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 66

Query: 61 QIGMKRLKVQLKRPK 75
          ++G + L+V  K  K
Sbjct: 67 RLGDRVLQVSFKTSK 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|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 = 42.1 bits (99), Expect = 7e-07
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G +    V  DR T +S+ FG              FV+F+NP  A  A+ AMNG  
Sbjct: 21 FSKYGQISEVVVVKDRETQRSRGFG--------------FVTFENPDDAKDAMMAMNGKS 66

Query: 62 IGMKRLKV 69
          +  ++++V
Sbjct: 67 VDGRQIRV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 41.8 bits (99), Expect = 9e-07
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 18/62 (29%)

Query: 1  MFLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
          +F PFG +  S+V++  D+ T QS+ F               FV+F     A  AI+ +N
Sbjct: 19 LFRPFGPI--SRVYLAKDKETGQSRGFA--------------FVTFHTREDAERAIEKLN 62

Query: 59 GF 60
          GF
Sbjct: 63 GF 64

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 14/77 (18%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  FG+V+ +KV +DR T +S+ FG              FV+F++  +A  AI  M+G +
Sbjct: 55  FAHFGDVVDAKVIVDRETGRSRGFG--------------FVNFNDEGAATAAISEMDGKE 100

Query: 62  IGMKRLKVQLKRPKDAA 78
           +  + ++V     + +A
Sbjct: 101 LNGRHIRVNPANDRPSA 117

Length = 144

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

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 15/75 (20%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  FGN++S KV    AT++    G+         + +GFV F+   SA  AIQ +NG 
Sbjct: 108 TFSKFGNILSCKV----ATDE---NGK--------SRGYGFVHFEKEESAKAAIQKVNGM 152

Query: 61  QIGMKRLKVQLKRPK 75
            +  K + V     K
Sbjct: 153 LLNDKEVYVGRFIKK 167

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.9 bits (95), Expect = 3e-06
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 16/65 (24%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQ 61
          P+G ++S+K  +D+ TN  KC G            +GFV FD+P++A  A+ A+  +G Q
Sbjct: 24 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPSAAQKAVTALKASGVQ 69

Query: 62 IGMKR 66
            M +
Sbjct: 70 AQMAK 74

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

 Score = 40.7 bits (96), Expect = 3e-06
 Identities = 13/32 (40%), Positives = 22/32 (68%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
          FGF  F++P  A  A++ +NG ++G K+L V+
Sbjct: 44 FGFCEFEDPEGALRALRLLNGLELGGKKLLVK 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 40.4 bits (95), Expect = 3e-06
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 14/61 (22%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F P+G +I+S++  D  T  S       R V       GF+ FD    A  AI+A+NG 
Sbjct: 20 LFSPYGRIITSRILCDNVTGLS-------RGV-------GFIRFDKRIEAERAIKALNGT 65

Query: 61 Q 61
           
Sbjct: 66 I 66

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

 Score = 41.9 bits (97), Expect = 6e-06
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG V   ++  DR T +S+ F               FV F++  SA  AI+ +NG 
Sbjct: 135 LFKKFGPVKRVRLVRDRETGKSRGFA--------------FVEFESEESAEKAIEELNGK 180

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           ++  + L+VQ  +P    R 
Sbjct: 181 ELEGRPLRVQKAQPASQPRS 200

Length = 306

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

 Score = 39.7 bits (92), Expect = 9e-06
 Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 14/75 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F PFG V + KV  D  TN  KC G            FGFV+  N   A  AI ++NG+
Sbjct: 23 LFGPFGAVNNVKVIRDFNTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 68

Query: 61 QIGMKRLKVQLKRPK 75
          ++G + L+V  K  K
Sbjct: 69 RLGDRVLQVSFKTNK 83

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|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 = 39.1 bits (92), Expect = 1e-05
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 14/70 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +   FG + +  +  D AT  SK  G            + F  + +P+    AI  +NG 
Sbjct: 20 LLESFGKLKAFNLVKDSATGLSK--G------------YAFCEYLDPSVTDQAIAGLNGM 65

Query: 61 QIGMKRLKVQ 70
          Q+G K+L VQ
Sbjct: 66 QLGDKKLTVQ 75

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|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 = 38.8 bits (91), Expect = 1e-05
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 14/64 (21%)

Query: 6  GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK 65
          G V+S ++  DR T + K +G              F  F++  +A +AI+ +NG++   +
Sbjct: 23 GPVVSFRLVTDRDTGKPKGYG--------------FCEFEDIETAASAIRNLNGYEFNGR 68

Query: 66 RLKV 69
           L+V
Sbjct: 69 ALRV 72

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

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

 Score = 38.7 bits (91), Expect = 1e-05
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 14/58 (24%)

Query: 5  FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
          +G V    + IDR  N  +  G            + +V F++P  A  AI+ M+G QI
Sbjct: 22 YGTVKDVDLPIDREVNLPR--G------------YAYVEFESPEDAEKAIKHMDGGQI 65

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 19/79 (24%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  FG + S+ V  D +                  + F FV+F+    A  A++ MNG +
Sbjct: 199 FAKFGEITSAAVMKDGSGRS---------------RGFAFVNFEKHEDAAKAVEEMNGKK 243

Query: 62  IGM----KRLKVQLKRPKD 76
           IG+    K+L V   + + 
Sbjct: 244 IGLAKEGKKLYVGRAQKRA 262

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

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG + S  +  D  T +               K F FV ++ P +A  A++ MNG  
Sbjct: 21 FSPFGPIKSIDMSWDPVTMK--------------HKGFAFVEYEVPEAAQLALEQMNGVM 66

Query: 62 IGMKRLKV 69
          +G + +KV
Sbjct: 67 LGGRNIKV 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|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 38.4 bits (90), Expect = 2e-05
 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 23 KCFGECNRKVSV---NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
            FG     V V     K  GFV F + A+A  AIQ + G  IG  R+++ 
Sbjct: 20 SLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLS 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|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 = 38.4 bits (90), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 20/68 (29%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +   +VF D                    K + FV FD   +A TAI A+NG  
Sbjct: 21 FSPFGAIEEVRVFKD--------------------KGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 62 IGMKRLKV 69
          I  + +K 
Sbjct: 61 INGQTVKC 68

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

 Score = 38.7 bits (89), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 14/67 (20%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
          P+G ++S+K  +D+ TNQ               K +GFV FD+PA+A  A+ ++    + 
Sbjct: 27 PYGKIVSTKAILDKNTNQC--------------KGYGFVDFDSPAAAQKAVASLKANGVQ 72

Query: 64 MKRLKVQ 70
           +  K Q
Sbjct: 73 AQMAKQQ 79

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

 Score = 37.6 bits (88), Expect = 3e-05
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F+PFG++   ++ +D  T +               + F FV F+ P  A  AI  MN  +
Sbjct: 19 FIPFGDIKDIQIPLDYETQK--------------HRGFAFVEFEEPEDAAAAIDNMNESE 64

Query: 62 IGMKRLKV 69
          +  + ++V
Sbjct: 65 LFGRTIRV 72

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

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

 Score = 37.7 bits (88), Expect = 4e-05
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 15/76 (19%)

Query: 2  FLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          F  FG ++ + K+  D  T  SK F               F+S+D+  ++  AI+AMNG 
Sbjct: 22 FSAFGVILQTPKIMRDPDTGNSKGFA--------------FISYDSFEASDAAIEAMNGQ 67

Query: 61 QIGMKRLKVQLKRPKD 76
           +  + + V     KD
Sbjct: 68 YLCNRPITVSYAFKKD 83

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

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

 Score = 37.8 bits (87), Expect = 4e-05
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS   G            +GFV++ +P  A  AI  +NG 
Sbjct: 24 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYIDPKDAEKAINTLNGL 69

Query: 61 QIGMKRLKVQLKRP 74
          ++  K +KV   RP
Sbjct: 70 RLQTKTIKVSYARP 83

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

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

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 14/78 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS   G            +GFV++  P  A  A+ ++NG 
Sbjct: 23 LFTSIGEIESCKLVRDKVTGQS--LG------------YGFVNYVRPEDAEKAVNSLNGL 68

Query: 61 QIGMKRLKVQLKRPKDAA 78
          ++  K +KV   RP   +
Sbjct: 69 RLQNKTIKVSYARPSSDS 86

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.7 bits (88), Expect = 5e-05
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 14/76 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHT----AIQAM 57
          F PFG +  S++ +D  T QS   G C     V    F       P++AH     A+  +
Sbjct: 19 FRPFGEIEESELKLDPRTGQS--LGIC----RV---TFR-GDPLRPSAAHEAAKAAVDGL 68

Query: 58 NGFQIGMKRLKVQLKR 73
          NG +IG KR++V+L R
Sbjct: 69 NGRRIGGKRVRVELDR 84

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 36.7 bits (86), Expect = 5e-05
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 24 CFGECNR-KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
           FG   + K+   +  F FV F    +A  A+Q +NG   G + L+V  
Sbjct: 7  PFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 37.4 bits (86), Expect = 6e-05
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS   G            +GFV++ +P  A  AI  +NG 
Sbjct: 23 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYVDPNDADKAINTLNGL 68

Query: 61 QIGMKRLKVQLKRP 74
          ++  K +KV   RP
Sbjct: 69 KLQTKTIKVSYARP 82

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 36.9 bits (86), Expect = 7e-05
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 20/72 (27%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFGN+I+  + +++  N                   GFV+F+   SA  AI  +NG  
Sbjct: 23 FSPFGNIIN--ISMEKEKNC------------------GFVTFEKMESADRAIAELNGTT 62

Query: 62 IGMKRLKVQLKR 73
          +   +LKV L R
Sbjct: 63 VQGVQLKVSLAR 74

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

 Score = 36.4 bits (85), Expect = 8e-05
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
          F FV F++P  A  A++A++G +I   R++V+L R 
Sbjct: 38 FAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73

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

 Score = 37.0 bits (85), Expect = 9e-05
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 14/67 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +  ++V  D AT +SK +G              FVSF N   A  AIQ M G  
Sbjct: 22 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 67

Query: 62 IGMKRLK 68
          +G ++++
Sbjct: 68 LGGRQIR 74

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

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG V+S +V  D  T +S  +G              +V+F NPA A  A++ MN  +
Sbjct: 21 FKPFGPVLSVRVCRDSVTRRSLGYG--------------YVNFQNPADAERALETMNFKR 66

Query: 62 IGMKRLKV 69
          +G K +++
Sbjct: 67 LGGKPIRI 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS   G            +GFV++ +P  A  AI  +NG 
Sbjct: 22 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYIDPKDAEKAINTLNGL 67

Query: 61 QIGMKRLKVQLKRP 74
          ++  K +KV   RP
Sbjct: 68 RLQTKTIKVSYARP 81

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

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

 Score = 36.4 bits (85), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G +   +V  D+ T +S+ FG              FV F++   A  A + +NG +
Sbjct: 20 FSRYGPIEKVQVVYDQKTGRSRGFG--------------FVYFESVEDAKEAKERLNGME 65

Query: 62 IGMKRLKV 69
          I  +R++V
Sbjct: 66 IDGRRIRV 73

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

 Score = 36.5 bits (84), Expect = 1e-04
 Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 14/59 (23%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
          MF  FG +I+S+V +D+AT  S       R V+       F+ FD  + A  AI + NG
Sbjct: 20 MFSRFGRIINSRVLVDQATGLS-------RGVA-------FIRFDKRSEAEEAITSFNG 64

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

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

 Score = 36.1 bits (84), Expect = 1e-04
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG + S +V  D+ T  S                + F+ F+       A   M+   
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDS--------------LQYAFIEFETKEDCEEAYFKMDNVL 69

Query: 62 IGMKRLKV 69
          I  +R+ V
Sbjct: 70 IDDRRIHV 77

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

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 14/59 (23%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
           +F PFG +I+S++  D  T  S              K  GF+ FD    A  AI+ +NG
Sbjct: 109 IFSPFGQIITSRILSDNVTGLS--------------KGVGFIRFDKRDEADRAIKTLNG 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.8 bits (83), Expect = 2e-04
 Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 16/70 (22%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +    V  D+ T +SK  G              +V F   +SA  A++ MNG  
Sbjct: 23 FAPFGEIQDIWVVKDKQTKESK--GVA------------YVKFAKASSAARAMEEMNGKC 68

Query: 62 IG--MKRLKV 69
          +G   K LKV
Sbjct: 69 LGGDTKPLKV 78

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

 Score = 35.8 bits (82), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G V S+K+  D              KV+ +   +GFV++ N   A  AI  +NG 
Sbjct: 21 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVNAKDAERAINTLNGL 66

Query: 61 QIGMKRLKVQLKRP 74
          ++  K +KV   RP
Sbjct: 67 RLQSKTIKVSYARP 80

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

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

 Score = 35.3 bits (82), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 15/69 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   GNV+ + V  D            N   S   K FG V F++P  A  AI+  NG+
Sbjct: 18 LFRECGNVLRADVKTD------------NDGRS---KGFGTVLFESPEDAQRAIEMFNGY 62

Query: 61 QIGMKRLKV 69
           +  + L+V
Sbjct: 63 DLEGRELEV 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 35.3 bits (82), Expect = 2e-04
 Identities = 11/36 (30%), Positives = 20/36 (55%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
          + FV F+    A  A++ MNG ++    ++V L +P
Sbjct: 37 YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72

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

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

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 14/67 (20%)

Query: 4   PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
            FG++ +  +  D AT  SK +               F  + +P+    AI A+NG   G
Sbjct: 318 SFGDLKAFNLIKDIATGLSKGYA--------------FCEYKDPSVTDVAIAALNGKDTG 363

Query: 64  MKRLKVQ 70
             +L VQ
Sbjct: 364 DNKLHVQ 370

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

 Score = 35.4 bits (82), Expect = 3e-04
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
          + FV + +  SA  A+Q MNG  I  + +KV
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQEIKV 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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 35.0 bits (81), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 16/62 (25%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-- 59
          F  FG +    + +D+ T +SK F               FVSF  P  A  A   ++G  
Sbjct: 20 FEAFGEISEVHLPLDKETKRSKGFA--------------FVSFMFPEHAVKAYSELDGSI 65

Query: 60 FQ 61
          FQ
Sbjct: 66 FQ 67

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|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 = 35.1 bits (81), Expect = 4e-04
 Identities = 14/33 (42%), Positives = 24/33 (72%)

Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
          F +F +P  A T ++A+NG++I  +RL+V+ KR
Sbjct: 47 FANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79

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|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 = 35.2 bits (82), Expect = 4e-04
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 16/60 (26%)

Query: 1  MFLPFGNVISSKVFIDRATNQSK-CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
          +F  +GN+    +  D+ T QSK C                FV F +   A  AI+A++G
Sbjct: 19 LFEEYGNIEEVTIIRDKDTGQSKGC---------------AFVKFSSREEAQKAIEALHG 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 35.2 bits (81), Expect = 4e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 31 KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
          K + N K +GF+ F NP  A  A ++MN + +  K L+V 
Sbjct: 35 KKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVH 74

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

 Score = 35.0 bits (81), Expect = 4e-04
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 14/70 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G V+ +K+  +  +  +              +CFGFV+  +   A   IQ ++  
Sbjct: 19 LFSKYGKVVGAKIVTNARSPGA--------------RCFGFVTMASVEEAAKCIQHLHRT 64

Query: 61 QIGMKRLKVQ 70
          ++  + + V+
Sbjct: 65 ELHGRVISVE 74

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

 Score = 34.8 bits (81), Expect = 5e-04
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 14/57 (24%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
          F P G V+S +V  D  T +S   G            + +V+F NPA A  A+  +N
Sbjct: 20 FSPAGPVLSIRVCRDLITRRS--LG------------YAYVNFQNPADAERALDTLN 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 36.4 bits (84), Expect = 5e-04
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 14/69 (20%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG++   ++  D  T +SK FG              F+ F +   A  A++ MNGF
Sbjct: 206 IFEPFGDIEDVQLHRDPETGRSKGFG--------------FIQFHDAEEAKEALEVMNGF 251

Query: 61  QIGMKRLKV 69
           ++  + +KV
Sbjct: 252 ELAGRPIKV 260

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

 Score = 34.6 bits (80), Expect = 6e-04
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
            K F FV+F +  S   AIQ +NG ++  + L+++
Sbjct: 40 KPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 34.6 bits (79), Expect = 6e-04
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 14/71 (19%)

Query: 5  FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
          F   I++++  DR T  SK FG              FV F +   A  A +AM   +I  
Sbjct: 21 FDGSIAARIVTDRDTGSSKGFG--------------FVDFSSEEDAKAAKEAMEDGEIDG 66

Query: 65 KRLKVQLKRPK 75
           ++ +   +PK
Sbjct: 67 NKVTLDFAKPK 77

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

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 34.2 bits (79), Expect = 6e-04
 Identities = 10/33 (30%), Positives = 19/33 (57%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
          K +G+  + +  SA  AI  ++G ++   +LKV
Sbjct: 35 KNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67

This subfamily corresponds to the RRM4 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 = 68

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

 Score = 34.6 bits (80), Expect = 6e-04
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 14/65 (21%)

Query: 5  FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
          + +V  +KV +D  T +SK +G              FV F +      A+  MNG     
Sbjct: 26 YPSVRGAKVVMDPVTGRSKGYG--------------FVRFGDEDERDRALTEMNGVYCSS 71

Query: 65 KRLKV 69
          + ++V
Sbjct: 72 RPMRV 76

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

 Score = 34.3 bits (79), Expect = 7e-04
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 17/72 (23%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V+ +++  D  T +S              + FGFV+FD+ ++    + +    +
Sbjct: 20 FSQFGKVVDAQLMQDHDTGRS--------------RGFGFVTFDSESAVE-RVFSAGMLE 64

Query: 62 IGMKRLKVQLKR 73
          +G K  +V++KR
Sbjct: 65 LGGK--QVEVKR 74

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

 Score = 34.2 bits (79), Expect = 9e-04
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 14/55 (25%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
          F  +GNV S ++  D+ T +              ++ F FV+FD+       +  
Sbjct: 20 FSQYGNVESVEIVTDKETGK--------------KRGFAFVTFDDYDPVDKIVLQ 60

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

 Score = 34.3 bits (78), Expect = 9e-04
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 14/67 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +  ++V  D AT +SK +G              FVSF N   A  AI  M G  
Sbjct: 22 FAPFGKISDARVVKDMATGKSKGYG--------------FVSFYNKLDAENAIVHMGGQW 67

Query: 62 IGMKRLK 68
          +G ++++
Sbjct: 68 LGGRQIR 74

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

 Score = 34.1 bits (79), Expect = 0.001
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 14/69 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  + +   +KV  D+ T +SK +G              FVSF +P     A++ MNG  
Sbjct: 27 FSKYPSFQKAKVVRDKRTGKSKGYG--------------FVSFSDPNDYLKAMKEMNGKY 72

Query: 62 IGMKRLKVQ 70
          +G + +K++
Sbjct: 73 VGNRPIKLR 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 33.8 bits (78), Expect = 0.001
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
          FGFV F++P  A  A+  +NG ++  +R+ V+  R 
Sbjct: 35 FGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 33.8 bits (78), Expect = 0.001
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 14/67 (20%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
          PFG V    +    +T +SK  G            +GFV + + ASA  A   ++G QIG
Sbjct: 22 PFGAVERCFLVYSESTGESK--G------------YGFVEYASKASALKAKNQLDGKQIG 67

Query: 64 MKRLKVQ 70
           ++L+V 
Sbjct: 68 GRKLQVD 74

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

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 15/36 (41%), Positives = 21/36 (58%)

Query: 39  FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
           + FV F + A +  AI+ +NG  +  KRLKV   RP
Sbjct: 151 YAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP 186

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

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 14/79 (17%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F PFG + S  +  D AT +               K F FV ++ P +A  A++ MNG  
Sbjct: 128 FDPFGPIKSINMSWDPATGK--------------HKGFAFVEYEVPEAAQLALEQMNGQM 173

Query: 62  IGMKRLKVQLKRPKDAARP 80
           +G + +KV        A+P
Sbjct: 174 LGGRNIKVGRPSNMPQAQP 192

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 = 33.3 bits (77), Expect = 0.001
 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 14/55 (25%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
          F  +G V+   +  D  T +S+  G            FGFV+F +P+S    + A
Sbjct: 19 FSKYGEVVDCVIMKDPITGRSR--G------------FGFVTFADPSSVDKVLAA 59

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

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
          K   +V ++N +SA  A+  M+G +I  K + V +  P
Sbjct: 43 KGLAYVEYENESSASQAVLKMDGTEIKEKTISVAISNP 80

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

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

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 18/70 (25%)

Query: 1  MFLPFGNVISSK-VFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
          MF  FG ++  + +F +R +                 K FGFV+F N A A  A + ++G
Sbjct: 20 MFGQFGPILDVEIIFNERGS-----------------KGFGFVTFANSADADRAREKLHG 62

Query: 60 FQIGMKRLKV 69
            +  ++++V
Sbjct: 63 TVVEGRKIEV 72

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

 Score = 33.3 bits (77), Expect = 0.002
 Identities = 11/35 (31%), Positives = 18/35 (51%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
          + FGFV F +   A  A++  N   I   ++ V+L
Sbjct: 41 RRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVEL 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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 33.1 bits (76), Expect = 0.002
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
          F FV F++P  A  A++  +G+     RL+V+ 
Sbjct: 40 FAFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 32.9 bits (76), Expect = 0.003
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 25 FGECNRKVSV--------NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
          F +    +S+          + F +V F +P SA  A+  +NG      +L V++  P
Sbjct: 21 FEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVKISDP 78

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 32.6 bits (75), Expect = 0.003
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
          K +GFV FDN   A  A+   NG +I  ++L +
Sbjct: 35 KGYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 32.9 bits (75), Expect = 0.003
 Identities = 13/35 (37%), Positives = 18/35 (51%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
          FGFV F     A  A++AM+GF +    L V+   
Sbjct: 49 FGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 32.7 bits (75), Expect = 0.003
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 14/64 (21%)

Query: 8  VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRL 67
          V S K F  +A  +SK  G              +V F + A+A    + + G +   K+ 
Sbjct: 27 VKSIKFFEHKANGKSK--GFA------------YVEFASEAAAAAVKEKLEGREFNGKKC 72

Query: 68 KVQL 71
           V  
Sbjct: 73 VVTY 76

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

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

 Score = 32.5 bits (74), Expect = 0.004
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
          +GFV +     A  A+Q +NG QI    ++V
Sbjct: 41 YGFVEYHQSHDAEIALQTLNGRQIENNEIRV 71

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

 Score = 32.5 bits (74), Expect = 0.004
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
          F FV F++P  A  A+   NG+  G  RL+V+
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVE 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	81
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.7
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
KOG0146|consensus	371		99.62
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.62
KOG0122|consensus	270		99.59
KOG0148|consensus	321		99.58
KOG4207|consensus	256		99.56
KOG0125|consensus	376		99.55
smart00361	70	RRM_1 RNA recognition motif.	99.55
KOG0145|consensus	360		99.54
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.54
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.49
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.47
KOG0126|consensus	219		99.47
KOG0111|consensus	298		99.46
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.45
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.44
KOG0149|consensus	247		99.44
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.41
KOG0113|consensus	335		99.41
smart00360	71	RRM RNA recognition motif.	99.39
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.38
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.36
KOG0131|consensus	203		99.35
KOG0130|consensus	170		99.35
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.34
KOG0117|consensus	506		99.34
KOG0145|consensus	360		99.33
KOG0121|consensus	153		99.33
KOG0108|consensus	435		99.31
KOG0124|consensus	544		99.31
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.3
smart00362	72	RRM_2 RNA recognition motif.	99.29
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.29
KOG0107|consensus	195		99.28
KOG0127|consensus	678		99.27
PLN03120	260	nucleic acid binding protein; Provisional	99.26
PLN03213	759	repressor of silencing 3; Provisional	99.26
KOG4208|consensus	214		99.26
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.25
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.21
KOG0117|consensus	506		99.21
KOG0144|consensus	510		99.21
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.2
KOG0415|consensus	479		99.2
KOG0144|consensus	510		99.19
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.18
KOG0148|consensus	321		99.17
KOG0123|consensus	369		99.16
KOG0147|consensus	549		99.15
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.14
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.12
PLN03121	243	nucleic acid binding protein; Provisional	99.09
KOG0123|consensus	369		99.08
KOG0114|consensus	124		99.04
KOG4206|consensus	221		99.02
KOG0109|consensus	346		99.02
KOG0105|consensus	241		98.97
KOG0131|consensus	203		98.97
KOG4661|consensus	940		98.94
KOG0109|consensus	346		98.93
KOG0127|consensus	678		98.9
KOG0110|consensus	725		98.85
KOG0146|consensus	371		98.77
KOG0124|consensus	544		98.7
KOG0110|consensus	725		98.68
KOG4209|consensus	231		98.59
KOG0226|consensus	290		98.59
KOG4205|consensus	311		98.54
KOG4212|consensus	608		98.52
KOG1190|consensus	492		98.51
KOG4205|consensus	311		98.49
KOG0132|consensus	894		98.47
KOG2314|consensus	698		98.33
KOG0151|consensus	877		98.31
KOG0153|consensus	377		98.22
KOG0147|consensus	549		98.2
KOG0533|consensus	243		98.16
KOG0120|consensus	500		98.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.12
KOG0106|consensus	216		97.96
KOG1548|consensus	382		97.9
KOG4212|consensus	608		97.86
KOG4660|consensus	549		97.8
KOG0120|consensus	500		97.78
KOG4454|consensus	267		97.78
KOG1457|consensus	284		97.77
KOG0116|consensus	419		97.72
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.67
KOG1456|consensus	494		97.61
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.54
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.5
KOG1995|consensus	351		97.49
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.42
KOG1456|consensus	494		97.41
KOG1548|consensus	382		97.38
KOG2068|consensus	327		97.32
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.13
KOG2202|consensus	260		97.07
KOG4210|consensus	285		96.93
KOG0106|consensus	216		96.93
KOG1996|consensus	378		96.78
KOG4206|consensus	221		96.3
KOG4211|consensus	510		95.88
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.84
KOG4307|consensus	944		95.81
KOG1190|consensus	492		95.74
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.62
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.51
KOG4285|consensus	350		95.46
KOG1855|consensus	484		95.44
KOG0112|consensus	975		95.31
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.71
KOG0128|consensus	881		94.61
KOG2135|consensus	526		94.32
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.26
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.03
KOG4211|consensus	510		93.89
KOG4574|consensus	1007		93.01
KOG2193|consensus	584		92.02
KOG3152|consensus	278		92.01
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.13
KOG4660|consensus	549		90.82
KOG1365|consensus	508		90.78
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	89.02
KOG1457|consensus	284		88.77
KOG4849|consensus	498		87.62
KOG2416|consensus	718		85.99
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.22
KOG0128|consensus	881		83.48
KOG4676|consensus	479		81.83
KOG0115|consensus	275		81.22
KOG4210|consensus	285		80.81

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

Probab=99.71  E-value=7.1e-17  Score=99.54  Aligned_cols=63  Identities=33%  Similarity=0.667  Sum_probs=59.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.|+.+++++|              ||||+|.+.++|+.|++.||+..|+|+.|+|+++.++..
T Consensus        54 ~F~~~G~I~~v~i~~d~~tg~~kG--------------faFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         54 AFAHFGDVVDAKVIVDRETGRSRG--------------FGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             HHhcCCCeEEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            589999999999999999999999              999999999999999999999999999999999977653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.70  E-value=5.7e-17  Score=110.28  Aligned_cols=64  Identities=41%  Similarity=0.620  Sum_probs=60.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|++|+.|+.++|              ||||+|.+.++|..||..|||..++||.|+|+|+.++..+
T Consensus       289 ~F~~fG~v~~v~i~~d~~t~~skG--------------~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~~  352 (352)
T TIGR01661       289 LFGPFGAVQNVKIIRDLTTNQCKG--------------YGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR  352 (352)
T ss_pred             HHHhCCCeEEEEEeEcCCCCCccc--------------eEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCCC
Confidence            589999999999999999999999              9999999999999999999999999999999999887653

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

>PF13893 RRM_5: RNA recognition motif

Probab=99.63  E-value=2.6e-15  Score=78.71  Aligned_cols=53  Identities=36%  Similarity=0.599  Sum_probs=47.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.++.+..++     ++              +|||+|.+.++|+.|++.|||..+.|++|+|+||
T Consensus         4 ~f~~fG~V~~i~~~~~~-----~~--------------~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    4 LFSKFGEVKKIKIFKKK-----RG--------------FAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHTTTS-EEEEEEETTS-----TT--------------EEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             HhCCcccEEEEEEEeCC-----CC--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            48999999999987654     46              9999999999999999999999999999999986

(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 ....

>KOG0146|consensus

Probab=99.62  E-value=2.1e-16  Score=105.56  Aligned_cols=67  Identities=88%  Similarity=1.397  Sum_probs=65.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|-.||.|++.++..|+.|+.||+              ||||.|+++.+|+.||..|||+.|..++|+|++.+|++..+|
T Consensus       305 mF~PFGhivSaKVFvDRATNQSKC--------------FGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanRP  370 (371)
T KOG0146|consen  305 MFLPFGHIVSAKVFVDRATNQSKC--------------FGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDANRP  370 (371)
T ss_pred             Hhccccceeeeeeeehhccccccc--------------eeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccCCC
Confidence            488999999999999999999999              999999999999999999999999999999999999999999


Q ss_pred             C
Q psy16913         81 Y   81 (81)
Q Consensus        81 ~   81 (81)
                      |
T Consensus       371 Y  371 (371)
T KOG0146|consen  371 Y  371 (371)
T ss_pred             C
Confidence            8

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.62  E-value=1.6e-15  Score=103.13  Aligned_cols=63  Identities=33%  Similarity=0.629  Sum_probs=59.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|+|++|+.+|+++|              ||||+|.++++|++||+.|||..+.|+.|.|.++.+...
T Consensus        23 ~F~~~G~i~~v~i~~d~~~g~s~g--------------~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~   85 (352)
T TIGR01661        23 LFTSIGEIESCKLVRDKVTGQSLG--------------YGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD   85 (352)
T ss_pred             HHHccCCEEEEEEEEcCCCCccce--------------EEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc
Confidence            589999999999999999999999              999999999999999999999999999999999987653

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

>KOG0122|consensus

Probab=99.59  E-value=3.3e-15  Score=98.24  Aligned_cols=62  Identities=32%  Similarity=0.574  Sum_probs=59.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      ||.+||+|.++.+.+|+.||.++|              ||||+|.+.++|++||..|||+-+++-.|+|+|++|+.
T Consensus       209 Lf~~fg~i~rvylardK~TG~~kG--------------FAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~~  270 (270)
T KOG0122|consen  209 LFRPFGPITRVYLARDKETGLSKG--------------FAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPSN  270 (270)
T ss_pred             HhhccCccceeEEEEccccCcccc--------------eEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCCC
Confidence            688999999999999999999999              99999999999999999999999999999999999873

>KOG0148|consensus

Probab=99.58  E-value=4e-15  Score=99.22  Aligned_cols=61  Identities=43%  Similarity=0.653  Sum_probs=58.9

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      |.+||+|.+++|++|..|+++||              ||||.|.+.++|++||..|||.-|.+|.|+-+||..|.
T Consensus        83 F~pFGevS~akvirD~~T~KsKG--------------YgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   83 FAPFGEVSDAKVIRDMNTGKSKG--------------YGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             hccccccccceEeecccCCcccc--------------eeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            78999999999999999999999              99999999999999999999999999999999997765

>KOG4207|consensus

Probab=99.56  E-value=1.7e-15  Score=97.93  Aligned_cols=60  Identities=35%  Similarity=0.515  Sum_probs=57.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||.|-+|.|++|+.|+.++|              ||||-|.+..||+.|+++|+|.+|+|+.|.|++|+-
T Consensus        33 vFekYG~vgDVyIPrdr~Tr~sRg--------------FaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   33 VFEKYGRVGDVYIPRDRYTRQSRG--------------FAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             HHHHhCcccceecccccccccccc--------------eeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            599999999999999999999999              999999999999999999999999999999999854

>KOG0125|consensus

Probab=99.55  E-value=6.1e-15  Score=100.29  Aligned_cols=59  Identities=31%  Similarity=0.592  Sum_probs=53.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+|.||.+.  .-|||              ||||+|++++||++|.++|||..+.||+|.|+.|.++
T Consensus       116 MF~kfG~VldVEIIfNE--RGSKG--------------FGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  116 MFEKFGKVLDVEIIFNE--RGSKG--------------FGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHhhCceeeEEEEecc--CCCCc--------------cceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            59999999999999985  34566              9999999999999999999999999999999999664

>smart00361 RRM_1 RNA recognition motif

Probab=99.55  E-value=2.7e-14  Score=78.11  Aligned_cols=52  Identities=25%  Similarity=0.418  Sum_probs=47.6

Q ss_pred             CCceeeEEE-EEecCCC--CCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEE
Q psy16913          4 PFGNVISSK-VFIDRAT--NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV   69 (81)
Q Consensus         4 ~~G~i~~v~-i~~~~~~--~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V   69 (81)
                      +||+|.++. ++.++.+  +.++|              ||||+|.++++|.+|+..|||..+.|+.|++
T Consensus        15 ~fG~v~~v~~v~~~~~~~~~~~rG--------------~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       15 YFGEVGKINKIYIDNVGYENHKRG--------------NVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             hcCCeeEEEEEEeCCCCCCCCCcE--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            899999995 7777766  88888              9999999999999999999999999999986

>KOG0145|consensus

Probab=99.54  E-value=1.2e-14  Score=96.96  Aligned_cols=63  Identities=35%  Similarity=0.608  Sum_probs=60.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      ||+..|+|++|++++|+.+|++-|              ||||-|.+++||++||..|||..+..+.|+|.+|+|..+
T Consensus        61 LF~SiGeiEScKLvRDKitGqSLG--------------YGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~  123 (360)
T KOG0145|consen   61 LFGSIGEIESCKLVRDKITGQSLG--------------YGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD  123 (360)
T ss_pred             Hhhcccceeeeeeeeccccccccc--------------cceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh
Confidence            689999999999999999999999              999999999999999999999999999999999999754

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.54  E-value=1.6e-14  Score=99.66  Aligned_cols=61  Identities=33%  Similarity=0.558  Sum_probs=58.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||+|.+|+|+.|+.+++++|              ||||+|.++++|++|++.|||..+.+++|+|.++.+.
T Consensus       127 lF~~~G~V~~v~i~~d~~tg~srG--------------yaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~  187 (346)
T TIGR01659       127 LFRTIGPINTCRIMRDYKTGYSFG--------------YAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPG  187 (346)
T ss_pred             HHHhcCCEEEEEEEecCCCCccCc--------------EEEEEEccHHHHHHHHHHcCCCccCCceeeeeccccc
Confidence            589999999999999999999999              9999999999999999999999999999999998764

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

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

Probab=99.49  E-value=1.4e-13  Score=100.49  Aligned_cols=62  Identities=26%  Similarity=0.442  Sum_probs=58.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|+.||+|.+++|++|+.++.++|              ||||+|.+.++|.+||+.|||..++|+.|+|.++.++.
T Consensus       224 lFs~FG~I~svrl~~D~~tgksKG--------------fGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       224 VFEAFGEIVKCQLARAPTGRGHKG--------------YGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHhhcCCeeEEEEEecCCCCCcCC--------------eEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            589999999999999998999999              99999999999999999999999999999999997643

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.

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=2e-13  Score=73.22  Aligned_cols=53  Identities=30%  Similarity=0.612  Sum_probs=48.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK   68 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~   68 (81)
                      +|++||+|..+.++.+ .++.+++              +|||+|.+.++|+.|++.|||..+.|+.|+
T Consensus        18 ~f~~~g~i~~~~~~~~-~~~~~~~--------------~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   18 FFSQFGKIESIKVMRN-SSGKSKG--------------YAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             HHHTTSTEEEEEEEEE-TTSSEEE--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHHhhhccccccccc-ccccccc--------------eEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            4889999999999998 5778888              999999999999999999999999999885

(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 ....

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

Probab=99.47  E-value=1.3e-13  Score=100.56  Aligned_cols=60  Identities=35%  Similarity=0.552  Sum_probs=56.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+|+|+.|+.+++++|              ||||+|.++++|++|++.|||..++|+.|+|+++..
T Consensus       127 lF~~fG~I~sV~I~~D~~TgkskG--------------fAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~  186 (612)
T TIGR01645       127 AFDPFGPIKSINMSWDPATGKHKG--------------FAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  186 (612)
T ss_pred             HHHccCCEEEEEEeecCCCCCcCC--------------eEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccc
Confidence            589999999999999999999999              999999999999999999999999999999987543

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.

>KOG0126|consensus

Probab=99.47  E-value=3.1e-14  Score=90.58  Aligned_cols=58  Identities=24%  Similarity=0.525  Sum_probs=55.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||.|+.|.+++|+.||+|+|              |||++|++..+.--|+..|||..|.||.|+|+..
T Consensus        55 VFSqyGe~vdinLiRDk~TGKSKG--------------FaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   55 VFSQYGEIVDINLIRDKKTGKSKG--------------FAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             EeeccCceEEEEEEecCCCCcccc--------------eEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            599999999999999999999999              9999999999999999999999999999999875

>KOG0111|consensus

Probab=99.46  E-value=4.3e-14  Score=92.41  Aligned_cols=62  Identities=29%  Similarity=0.622  Sum_probs=59.0

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      |-+||.|..|.++.|-.++++||              ||||+|+..+||..||..||+.++.||.|+|++|+|.+.
T Consensus        31 FIPFGDI~dIqiPlDyesqkHRg--------------FgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   31 FIPFGDIKDIQIPLDYESQKHRG--------------FGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             cccccchhhcccccchhcccccc--------------eeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            67899999999999999999999              999999999999999999999999999999999998653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.45  E-value=3.2e-13  Score=93.27  Aligned_cols=63  Identities=24%  Similarity=0.432  Sum_probs=57.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~~~   77 (81)
                      +|++||.|..++|+.|+.+++++|              ||||+|.+.++|++||+.||+..+.+  ++|.|.++..+..
T Consensus       213 ~F~~fG~V~~v~i~~d~~tg~~kG--------------~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       213 IFGKYGQIVQKNILRDKLTGTPRG--------------VAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HHHhcCCEEEEEEeecCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            589999999999999999999999              99999999999999999999999876  7899999976543

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).

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

Probab=99.44  E-value=1.8e-13  Score=98.51  Aligned_cols=62  Identities=39%  Similarity=0.648  Sum_probs=58.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||.|.+++++.| .+|.++|              ||||+|.+.++|.+|+..|||..+.|++|.|.+|.++..
T Consensus       305 ~F~~~G~i~~~~i~~d-~~g~~~g--------------~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       305 LFSECGEITSAKVMLD-EKGVSRG--------------FGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             HHHhcCCeEEEEEEEC-CCCCcCC--------------eEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            5899999999999999 4899999              999999999999999999999999999999999987654

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

>KOG0149|consensus

Probab=99.44  E-value=1e-13  Score=90.78  Aligned_cols=57  Identities=30%  Similarity=0.508  Sum_probs=53.3

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      |++||+|+++.||.|+.||+|||              ||||+|.+.+.|.+|++..| -.|+||+-.+++|.
T Consensus        33 FeqfGeI~eavvitd~~t~rskG--------------yGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   33 FEQFGEIVEAVVITDKNTGRSKG--------------YGFVTFRDAEAATRACKDPN-PIIDGRKANCNLAS   89 (247)
T ss_pred             HHHhCceEEEEEEeccCCccccc--------------eeeEEeecHHHHHHHhcCCC-Ccccccccccchhh
Confidence            89999999999999999999999              99999999999999999655 67999999999974

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

Probab=99.41  E-value=7e-13  Score=95.51  Aligned_cols=60  Identities=37%  Similarity=0.643  Sum_probs=57.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+|+|++|+.|++++|              ||||+|.++++|++|++.+|+..+.|+.|+|.|+..
T Consensus        20 ~F~~~G~v~~v~v~~d~~t~~s~G--------------~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628        20 LFKPFGPVLSVRVCRDSVTRRSLG--------------YGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             HHHhcCCEEEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            589999999999999999999999              999999999999999999999999999999999854

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

>KOG0113|consensus

Probab=99.41  E-value=7.9e-13  Score=89.13  Aligned_cols=61  Identities=21%  Similarity=0.498  Sum_probs=57.9

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      |+.||+|..+.|+.|+.||+++|              ||||+|+++.+...|-+..+|.+|+|+.|.|++...+.
T Consensus       122 F~~YG~IkrirlV~d~vTgkskG--------------YAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRT  182 (335)
T KOG0113|consen  122 FEKYGPIKRIRLVRDKVTGKSKG--------------YAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRT  182 (335)
T ss_pred             HHhcCcceeEEEeeecccCCccc--------------eEEEEeccHHHHHHHHHhccCceecCcEEEEEeccccc
Confidence            88999999999999999999999              99999999999999999999999999999999876554

>smart00360 RRM RNA recognition motif

Probab=99.39  E-value=1.5e-12  Score=68.58  Aligned_cols=56  Identities=36%  Similarity=0.631  Sum_probs=51.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ   70 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~   70 (81)
                      +|++||+|..+.++.++.++.++|              +|||+|.+.++|..|+..+++..+.|+.|.|+
T Consensus        16 ~f~~~g~v~~~~i~~~~~~~~~~~--------------~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       16 LFSKFGKIESVRLVRDKDTGKSKG--------------FAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             HHHhhCCEeEEEEEeCCCCCCCCc--------------eEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            478899999999999887788888              99999999999999999999999999998874

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

Probab=99.38  E-value=2e-12  Score=90.90  Aligned_cols=60  Identities=33%  Similarity=0.667  Sum_probs=56.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|..|.++.++.+|.++|              ||||+|.+.++|..|++.|||..|.|+.|.|.++..
T Consensus       206 ~f~~~G~i~~v~~~~d~~~g~~~g--------------~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       206 IFEPFGDIEDVQLHRDPETGRSKG--------------FGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCeEEEEEEEcCCCCccce--------------EEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            589999999999999998899999              999999999999999999999999999999999753

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.

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

Probab=99.36  E-value=2.9e-12  Score=90.97  Aligned_cols=61  Identities=30%  Similarity=0.467  Sum_probs=57.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||+|..+.++.++.+|.++|              ||||+|.+.++|+.|++.|||..+.|+.|.|.+|...
T Consensus       315 ~f~~~G~i~~~~~~~~~~~g~~~g--------------~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       315 LLESFGDLKAFNLIKDIATGLSKG--------------YAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             HHHhcCCeeEEEEEecCCCCCcCe--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            588999999999999998999999              9999999999999999999999999999999998543

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

>KOG0131|consensus

Probab=99.35  E-value=6.6e-13  Score=84.38  Aligned_cols=59  Identities=24%  Similarity=0.426  Sum_probs=56.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      ||-+.|+|++++|++|+.+..++|              |||++|.++++|+-||+.||+..+.||+|+|+.+.
T Consensus        29 L~iqagpVv~i~iPkDrv~~~~qG--------------ygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   29 LFIQAGPVVNLHIPKDRVTQKHQG--------------YGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             HHHhcCceeeeecchhhhcccccc--------------eeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            467889999999999999999999              99999999999999999999999999999999886

>KOG0130|consensus

Probab=99.35  E-value=8.7e-13  Score=80.74  Aligned_cols=62  Identities=24%  Similarity=0.377  Sum_probs=58.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      .|..||+|+.+++-.|+.||-.+|              |++|+|+..++|+.|+..|||..|.|..|.|+|+..+.
T Consensus        92 ~F~dyGeiKNihLNLDRRtGy~KG--------------YaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen   92 KFADYGEIKNIHLNLDRRTGYVKG--------------YALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKG  153 (170)
T ss_pred             HHhhcccccceeeccccccccccc--------------eeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecC
Confidence            388999999999999999999999              99999999999999999999999999999999985443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.34  E-value=7.8e-12  Score=67.58  Aligned_cols=53  Identities=30%  Similarity=0.575  Sum_probs=49.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK   68 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~   68 (81)
                      +|+.||.|..+.++.++. +.+++              +|||+|.++++|.+|++.++|..++|+.|+
T Consensus        18 ~f~~~g~v~~v~~~~~~~-~~~~~--------------~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   18 FFSRFGPVEKVRLIKNKD-GQSRG--------------FAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             HCTTSSBEEEEEEEESTT-SSEEE--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHhcCCcceEEEEeeec-cccCC--------------EEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            488999999999999986 88888              999999999999999999999999999875

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 ....

>KOG0117|consensus

Probab=99.34  E-value=2.9e-12  Score=90.10  Aligned_cols=60  Identities=23%  Similarity=0.451  Sum_probs=56.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~~   74 (81)
                      ||++.|+|.+++|++|+.+|.+||              ||||+|.+.++|+.||+.||+++|. |+.|.|+.+..
T Consensus       103 lfEkiG~I~elRLMmD~~sG~nRG--------------YAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sva  163 (506)
T KOG0117|consen  103 LFEKIGKIYELRLMMDPFSGDNRG--------------YAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVA  163 (506)
T ss_pred             HHHhccceeeEEEeecccCCCCcc--------------eEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeee
Confidence            689999999999999999999999              9999999999999999999999986 99999887644

>KOG0145|consensus

Probab=99.33  E-value=6.6e-12  Score=83.96  Aligned_cols=61  Identities=43%  Similarity=0.682  Sum_probs=58.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||++||.|..|++++|..|.+.+|              ||||++.+.++|.-||..|||+.+.+|.|.|.+...+
T Consensus       298 lFgpFGAv~nVKvirD~ttnkCKG--------------fgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  298 LFGPFGAVTNVKVIRDFTTNKCKG--------------FGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             HhCcccceeeEEEEecCCcccccc--------------eeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            699999999999999999999999              9999999999999999999999999999999987664

>KOG0121|consensus

Probab=99.33  E-value=1.7e-12  Score=78.73  Aligned_cols=60  Identities=17%  Similarity=0.324  Sum_probs=56.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      ||+++|+|..|-|-.|+.+..+.|              ||||+|.+.++|..|+..++|+.++.++|+++|...
T Consensus        56 LFs~cG~irriiMGLdr~kktpCG--------------FCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   56 LFSKCGDIRRIIMGLDRFKKTPCG--------------FCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             HHHhccchheeEeccccCCcCccc--------------eEEEEEecchhHHHHHHHhccCcccccceeeecccc
Confidence            699999999999999999999999              999999999999999999999999999999998743

>KOG0108|consensus

Probab=99.31  E-value=2.8e-12  Score=90.71  Aligned_cols=63  Identities=30%  Similarity=0.560  Sum_probs=59.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|+..|+|.+++++.|+.||+++|              |||++|.++++|..|++.|||.++.|++|+|+|+...+.
T Consensus        38 ~~~~~g~v~s~~~v~D~~tG~~~G--------------~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~  100 (435)
T KOG0108|consen   38 IFSGVGPVLSFRLVYDRETGKPKG--------------FGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKN  100 (435)
T ss_pred             HHhccCccceeeecccccCCCcCc--------------eeeEecCchhhHHHHHHhcCCcccCCceEEeecccccch
Confidence            478899999999999999999999              999999999999999999999999999999999976554

>KOG0124|consensus

Probab=99.31  E-value=2.4e-12  Score=89.33  Aligned_cols=59  Identities=36%  Similarity=0.566  Sum_probs=55.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |..||+|+++.|-.|+.|++++|              |+||+|+-+|.|+-|++.|||.++.||.|+|....+
T Consensus       134 F~PFGPIKSInMSWDp~T~kHKg--------------FAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  134 FDPFGPIKSINMSWDPATGKHKG--------------FAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             ccCCCCcceeecccccccccccc--------------eEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            78999999999999999999999              999999999999999999999999999999985543

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

Probab=99.30  E-value=1.1e-11  Score=88.46  Aligned_cols=56  Identities=25%  Similarity=0.415  Sum_probs=51.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||+.||.|.+|+++.++     +|              ||||+|.+.++|+.|+..|||..|.|++|+|.+++.+
T Consensus       296 lF~~yG~V~~vki~~~~-----~g--------------~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       296 LFCVYGNVERVKFMKNK-----KE--------------TALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             HHHhcCCeEEEEEEeCC-----CC--------------EEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            68999999999999874     57              9999999999999999999999999999999998653

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).

>smart00362 RRM_2 RNA recognition motif

Probab=99.29  E-value=1.7e-11  Score=64.72  Aligned_cols=54  Identities=39%  Similarity=0.653  Sum_probs=48.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ   70 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~   70 (81)
                      +|++||+|..+.+..++  +.++|              +|||+|.+.++|+.|++.++|..+.|+.|.|+
T Consensus        19 ~~~~~g~v~~~~~~~~~--~~~~~--------------~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       19 LFSKFGPIESVKIPKDT--GKSKG--------------FAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             HHHhcCCEEEEEEecCC--CCCCc--------------eEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            47889999999988876  66777              99999999999999999999999999998874

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

Probab=99.29  E-value=1.1e-11  Score=87.19  Aligned_cols=59  Identities=24%  Similarity=0.334  Sum_probs=55.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+|.|+.|+.++.++|              ||||+|.+.++|.+|+. |+|..+.|++|.|+++..
T Consensus       109 ~F~~~G~v~~v~i~~d~~~~~skg--------------~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~  167 (457)
T TIGR01622       109 FFSKVGKVRDVQCIKDRNSRRSKG--------------VAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQA  167 (457)
T ss_pred             HHHhcCCeeEEEEeecCCCCCcce--------------EEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecch
Confidence            589999999999999999999999              99999999999999997 999999999999998654

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.

>KOG0107|consensus

Probab=99.28  E-value=5.4e-12  Score=79.83  Aligned_cols=57  Identities=28%  Similarity=0.477  Sum_probs=51.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|..||+|.+|.|-..+     .|              ||||+|+++.||+.|+..|||..|.|..|+|+++..+.
T Consensus        30 ~F~~yG~lrsvWvArnP-----PG--------------fAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   30 AFSKYGPLRSVWVARNP-----PG--------------FAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             HHHhcCcceeEEEeecC-----CC--------------ceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            48899999999888765     67              99999999999999999999999999999999986543

>KOG0127|consensus

Probab=99.27  E-value=8.4e-12  Score=89.70  Aligned_cols=62  Identities=26%  Similarity=0.404  Sum_probs=56.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|+.||.|.+|.|++.+ .|.-+|              ||||.|....+|..|++.+||.+|+||+|-|+||.+++.
T Consensus       137 vFs~~G~V~Ei~IP~k~-dgklcG--------------FaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  137 VFSNFGKVVEIVIPRKK-DGKLCG--------------FAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             HHhhcceEEEEEcccCC-CCCccc--------------eEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            58999999999999776 555569              999999999999999999999999999999999998864

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.26  E-value=1.8e-11  Score=81.59  Aligned_cols=56  Identities=18%  Similarity=0.311  Sum_probs=50.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|+.||+|.++.|+.++.   ++|              ||||+|.++++|+.|+. |||..|.|+.|.|.++..
T Consensus        24 fFS~~G~I~~V~I~~d~~---~~G--------------fAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         24 FFSFSGDIEYVEMQSENE---RSQ--------------IAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             HHHhcCCeEEEEEeecCC---CCC--------------EEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            589999999999998863   467              99999999999999996 999999999999999863

>PLN03213 repressor of silencing 3; Provisional

Probab=99.26  E-value=1.1e-11  Score=88.72  Aligned_cols=57  Identities=21%  Similarity=0.430  Sum_probs=51.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCH--HHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNP--ASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~--~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||.|.+|.|+  +.+|  ||              ||||+|...  .++.+||..|||..+.|+.|+|+.|++.
T Consensus        30 vFSeFGsVkdVEIp--RETG--RG--------------FAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         30 IFSPMGTVDAVEFV--RTKG--RS--------------FAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             HHHhcCCeeEEEEe--cccC--Cc--------------eEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            48999999999999  4466  88              999999988  6899999999999999999999999764

>KOG4208|consensus

Probab=99.26  E-value=1.6e-11  Score=79.18  Aligned_cols=60  Identities=27%  Similarity=0.463  Sum_probs=54.7

Q ss_pred             ccCC-ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPF-GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~-G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      |.+| |.+...++-+++.||.|+|              ||||+|++++.|.-|.+.||++.+.|+.|.+.+-.|.
T Consensus        70 ~~q~~g~v~r~rlsRnkrTGNSKg--------------YAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   70 FRQFGGTVTRFRLSRNKRTGNSKG--------------YAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             hhhcCCeeEEEEeecccccCCcCc--------------eEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            4555 8899999999999999999              9999999999999999999999999999999876654

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

Probab=99.25  E-value=2.1e-11  Score=77.91  Aligned_cols=59  Identities=36%  Similarity=0.588  Sum_probs=56.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|.+||+|..+.+..++.++.++|              ||||+|.++++|..|+..++|..+.|+.|.|.++.
T Consensus       135 ~F~~~g~~~~~~~~~d~~~~~~~g--------------~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         135 LFKKFGPVKRVRLVRDRETGKSRG--------------FAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             HHHhcCceeEEEeeeccccCccCc--------------eEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            488999999999999998999999              99999999999999999999999999999999965

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

Probab=99.21  E-value=2.2e-11  Score=88.69  Aligned_cols=58  Identities=22%  Similarity=0.438  Sum_probs=52.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~   73 (81)
                      +|++||+|.+++|++| .+++++|              ||||+|.+.++|++||+.||+..+. |+.|.|.++.
T Consensus        78 ~F~~~G~I~~vrl~~D-~sG~sRG--------------faFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        78 LFEKAGPIYELRLMMD-FSGQNRG--------------YAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             HHHhhCCEEEEEEEEC-CCCCccc--------------eEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            5899999999999999 6999999              9999999999999999999999985 7888777664

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.

>KOG0117|consensus

Probab=99.21  E-value=1.9e-11  Score=86.06  Aligned_cols=56  Identities=30%  Similarity=0.479  Sum_probs=52.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|.+|+.++|                      ||||+|.+.++|.+|++.|||+.|+|..|.|.+|+|.++.
T Consensus       279 ~F~~~G~veRVkk~rD----------------------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  279 LFNEFGKVERVKKPRD----------------------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             HHHhccceEEeecccc----------------------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            5899999999998866                      9999999999999999999999999999999999997654

>KOG0144|consensus

Probab=99.21  E-value=1.7e-11  Score=86.05  Aligned_cols=67  Identities=66%  Similarity=1.047  Sum_probs=62.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|..||.|.++++..|+.|+-+++              |+||+|++..+|..||..|||..|.+++++|++.+.+....|
T Consensus       444 ~f~pfG~Vlsakvfidk~tnlskc--------------fgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~np~~  509 (510)
T KOG0144|consen  444 TFQPFGGVLSAKVFIDKVTNLSKC--------------FGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNNPYP  509 (510)
T ss_pred             HhccccceeEEEEEEecccCHhhh--------------cCcccccchhhhHHHHHHhcchhhccccceEEeeeccCCCCC
Confidence            478999999999999999999999              999999999999999999999999999999999988887666


Q ss_pred             C
Q psy16913         81 Y   81 (81)
Q Consensus        81 ~   81 (81)
                      |
T Consensus       510 ~  510 (510)
T KOG0144|consen  510 R  510 (510)
T ss_pred             C
Confidence            4

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

Probab=99.20  E-value=5.3e-11  Score=84.57  Aligned_cols=60  Identities=17%  Similarity=0.232  Sum_probs=51.8

Q ss_pred             CccCCceeeEEEEEecCC---CCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRA---TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~---~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||.|.+|.|+++..   ++...|              ++||+|.+.++|++|+..|||..+.|+.|.|.|...
T Consensus       439 ~f~~~G~v~~v~i~~~~~~~~~~~~~G--------------~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       439 EFSKYGPLINIVIPRPNGDRNSTPGVG--------------KVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHhcCCeeEEEeeccCcCCCcCCCcc--------------eEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            378999999999987632   234456              999999999999999999999999999999998754

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

>KOG0415|consensus

Probab=99.20  E-value=1.9e-11  Score=84.46  Aligned_cols=60  Identities=30%  Similarity=0.552  Sum_probs=57.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      ||+.||+|.+|.||+|+.||.+-.              ||||+|++.+++++|.-.|+...|+.++|.|.++++
T Consensus       259 IFSrFG~i~sceVIRD~ktgdsLq--------------yaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  259 IFSRFGKIVSCEVIRDRKTGDSLQ--------------YAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             HHhhcccceeeeEEecccccchhh--------------eeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            699999999999999999999998              999999999999999999999999999999999854

>KOG0144|consensus

Probab=99.19  E-value=1.7e-11  Score=86.09  Aligned_cols=63  Identities=27%  Similarity=0.415  Sum_probs=57.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcE-ECC--EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ-IGM--KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~-i~g--~~i~V~~a~~~~~   77 (81)
                      ||++||.|.+|.|++|. .+.+||              ||||+|...+.|..||+.|||.. +.|  .+|.|+||.++++
T Consensus       144 iFs~fG~Ied~~ilrd~-~~~sRG--------------caFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  144 IFSRFGHIEDCYILRDP-DGLSRG--------------CAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             HHHhhCccchhhheecc-cccccc--------------eeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            69999999999999997 789999              99999999999999999999976 555  7999999998876


Q ss_pred             C
Q psy16913         78 A   78 (81)
Q Consensus        78 ~   78 (81)
                      +
T Consensus       209 k  209 (510)
T KOG0144|consen  209 K  209 (510)
T ss_pred             c
Confidence            5

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

Probab=99.18  E-value=7.3e-11  Score=86.02  Aligned_cols=55  Identities=29%  Similarity=0.528  Sum_probs=49.6

Q ss_pred             CccCC--ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPF--GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~--G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++|  |+|.+|+++        ++              ||||+|.+.++|++|++.|||..|+|+.|+|+|++|+..
T Consensus       253 ~F~~f~~G~I~rV~~~--------rg--------------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       253 SFSEFKPGKVERVKKI--------RD--------------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHhcCCCceEEEEee--------cC--------------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            48899  999998765        34              999999999999999999999999999999999988643

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.

>KOG0148|consensus

Probab=99.17  E-value=1.3e-10  Score=77.85  Aligned_cols=57  Identities=32%  Similarity=0.559  Sum_probs=52.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      .|++||+|.+|++..++      |              |+||.|++.|.|.+||..||+.+|.|..+++.|-+....
T Consensus       184 ~Fs~fG~I~EVRvFk~q------G--------------YaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  184 TFSPFGPIQEVRVFKDQ------G--------------YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             hcccCCcceEEEEeccc------c--------------eEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            48999999999999885      6              999999999999999999999999999999999876543

>KOG0123|consensus

Probab=99.16  E-value=6.1e-11  Score=82.62  Aligned_cols=61  Identities=38%  Similarity=0.594  Sum_probs=55.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|+.||+|++|++.++. .| ++|              | ||+|+++++|++||+.+||..+.|+.|.|....++..+
T Consensus        96 ~f~~~g~ilS~kv~~~~-~g-~kg--------------~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   96 TFSEFGNILSCKVATDE-NG-SKG--------------Y-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             HHHhhcCeeEEEEEEcC-CC-cee--------------e-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            48999999999999997 44 788              9 99999999999999999999999999999998776654

>KOG0147|consensus

Probab=99.15  E-value=8.4e-11  Score=84.21  Aligned_cols=61  Identities=33%  Similarity=0.640  Sum_probs=57.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||+|..|.+++|..||.++|              |||++|.+.++|.+|+..|||..|-|+.|+|..-..+
T Consensus       298 ifepfg~Ie~v~l~~d~~tG~skg--------------fGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  298 IFEPFGKIENVQLTKDSETGRSKG--------------FGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hccCcccceeeeeccccccccccC--------------cceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            699999999999999999999999              9999999999999999999999999999998876443

>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=99.14  E-value=3.2e-10  Score=60.06  Aligned_cols=56  Identities=38%  Similarity=0.695  Sum_probs=49.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      +|+.+|+|..+.+..++.+ .++|              +|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus        19 ~~~~~g~i~~~~~~~~~~~-~~~~--------------~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          19 LFSKFGKVESVRIVRDKDT-KSKG--------------FAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             HHHhcCCEEEEEEeeCCCC-Ccce--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            3678899999999988744 6667              999999999999999999999999999999864

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).

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

Probab=99.12  E-value=2.2e-10  Score=81.75  Aligned_cols=57  Identities=30%  Similarity=0.481  Sum_probs=49.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~   75 (81)
                      +|+.||+|.+|.|++++.    ++              +|||+|.+.++|.+|++.|||..|.|  ..|+|+|+++.
T Consensus       116 ~F~~~G~V~~v~i~~~~~----~~--------------~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       116 IFNPYGKVLRIVTFTKNN----VF--------------QALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             HHhccCCEEEEEEEecCC----ce--------------EEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            589999999999887642    36              99999999999999999999999975  58999998764

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.09  E-value=3.3e-10  Score=74.87  Aligned_cols=54  Identities=19%  Similarity=0.338  Sum_probs=48.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|+.||+|.+|+|++|.   ..++              ||||+|.++++|+.|+. |||..|.+++|.|..+
T Consensus        25 fFS~~G~I~~V~I~~D~---et~g--------------fAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121         25 FFSHCGAIEHVEIIRSG---EYAC--------------TAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             HHHhcCCeEEEEEecCC---Ccce--------------EEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            59999999999999884   4456              99999999999999995 9999999999998874

>KOG0123|consensus

Probab=99.08  E-value=3e-10  Score=79.14  Aligned_cols=59  Identities=31%  Similarity=0.435  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|+.+|++.++++.+|- |  +-|              ||||.|.++.+|.+|++.||...+.|++|++.|+....
T Consensus        18 ~f~~~~~v~s~rvc~d~-t--slg--------------y~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen   18 KFSPAGPVLSIRVCRDA-T--SLG--------------YAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             HhcccCCceeEEEeecC-C--ccc--------------eEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            58999999999999998 6  888              99999999999999999999999999999999987653

>KOG0114|consensus

Probab=99.04  E-value=6.6e-10  Score=65.43  Aligned_cols=59  Identities=19%  Similarity=0.406  Sum_probs=52.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      ||++||+|..++|-..+.   .+|              -|||.|++..+|.+|+..|+|+-+.++.+.|-+-++.+
T Consensus        38 lFGkyg~IrQIRiG~~k~---TrG--------------TAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   38 LFGKYGTIRQIRIGNTKE---TRG--------------TAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             HhhcccceEEEEecCccC---cCc--------------eEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            699999999999876653   477              99999999999999999999999999999998876643

>KOG4206|consensus

Probab=99.02  E-value=3.2e-10  Score=73.85  Aligned_cols=60  Identities=25%  Similarity=0.502  Sum_probs=53.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      ||++||.|..|....   |.+.+|              -|||.|.+.+.|..|+..|+|..+.|+++++++|+.+.+
T Consensus        33 LFsqfG~ildI~a~k---t~KmRG--------------QA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sd   92 (221)
T KOG4206|consen   33 LFSQFGKILDISAFK---TPKMRG--------------QAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSD   92 (221)
T ss_pred             HHHhhCCeEEEEecC---CCCccC--------------ceEEEecChhHHHHHHHHhcCCcccCchhheecccCccc
Confidence            699999999987664   567788              999999999999999999999999999999999987653

>KOG0109|consensus

Probab=99.02  E-value=3.7e-10  Score=76.32  Aligned_cols=55  Identities=22%  Similarity=0.577  Sum_probs=51.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      ||++||+|.+|.|+++                      ||||..++...|..||..|+|+.|+|..|+|+-+++|..
T Consensus        22 lFe~ygkVlECDIvKN----------------------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk   76 (346)
T KOG0109|consen   22 LFEQYGKVLECDIVKN----------------------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK   76 (346)
T ss_pred             HHHhhCceEeeeeecc----------------------cceEEeecccccHHHHhhcccceecceEEEEEeccccCC
Confidence            6999999999999976                      999999999999999999999999999999999988743

>KOG0105|consensus

Probab=98.97  E-value=6.8e-10  Score=71.26  Aligned_cols=58  Identities=26%  Similarity=0.480  Sum_probs=49.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||.+||.|..|.+...+   ....              ||||+|+++.||+.||..-||+.++|..|+|+++..-
T Consensus        26 lFyKyg~i~~ieLK~r~---g~pp--------------fafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen   26 LFYKYGRIREIELKNRP---GPPP--------------FAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             HHhhhcceEEEEeccCC---CCCC--------------eeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            68999999998765433   2234              9999999999999999999999999999999998653

>KOG0131|consensus

Probab=98.97  E-value=4.6e-10  Score=71.52  Aligned_cols=63  Identities=32%  Similarity=0.511  Sum_probs=57.5

Q ss_pred             CccCCceeeEE-EEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v-~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|+.||.|.+. ++++++.||.++|              ||||.|.+.+.+++|+..|||..+..+++.|.++..++.
T Consensus       116 tFsafG~l~~~P~i~rd~~tg~~~~--------------~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  116 TFSAFGVLISPPKIMRDPDTGNPKG--------------FGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHhccccccCCcccccccCCCCCC--------------CeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            48899998774 8899999999999              999999999999999999999999999999999977653

>KOG4661|consensus

Probab=98.94  E-value=1.1e-09  Score=79.62  Aligned_cols=61  Identities=21%  Similarity=0.527  Sum_probs=53.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||++||+|+-++|+++..+--.              +||+||++.+.++|.+||+.|+.+.|.|+.|.|..+++.
T Consensus       425 lFSKyGKVvGAKVVTNaRsPGa--------------RCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  425 LFSKYGKVVGAKVVTNARSPGA--------------RCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             HHHHhcceeceeeeecCCCCCc--------------ceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            6999999999999987644333              459999999999999999999999999999999988653

>KOG0109|consensus

Probab=98.93  E-value=1.7e-09  Score=73.23  Aligned_cols=57  Identities=30%  Similarity=0.501  Sum_probs=52.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      .|++||+|.+++|++|                      |+||.|+-.++|..||..||++++.|+++.|+++.++-...
T Consensus        98 ~fe~ygpviecdivkd----------------------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrta  154 (346)
T KOG0109|consen   98 KFEKYGPVIECDIVKD----------------------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA  154 (346)
T ss_pred             hhcccCCceeeeeecc----------------------eeEEEEeeccchHHHHhcccccccccceeeeeeeccccccC
Confidence            4899999999999876                      99999999999999999999999999999999998875543

>KOG0127|consensus

Probab=98.90  E-value=1.6e-09  Score=78.12  Aligned_cols=63  Identities=17%  Similarity=0.340  Sum_probs=59.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|+.+|+|..+.++.++.++.++|              ||||+|.-.+|+++|+..+++..+.|+.|+|..|.++..
T Consensus        25 ~FS~vGPik~~~vVt~~gs~~~RG--------------fgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r   87 (678)
T KOG0127|consen   25 FFSYVGPIKHAVVVTNKGSSEKRG--------------FGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRAR   87 (678)
T ss_pred             hhhcccCcceeEEecCCCcccccC--------------ccceeeehHhHHHHHHHHhhcCcccceeccccccccccc
Confidence            589999999999999998889999              999999999999999999999999999999999977653

>KOG0110|consensus

Probab=98.85  E-value=1.5e-09  Score=79.76  Aligned_cols=62  Identities=24%  Similarity=0.448  Sum_probs=56.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      ||..||.|.+|+|+.-...+.++|              ||||+|.++.+|.+|+.+|.++.++||+|.++||....
T Consensus       633 LF~aFGqlksvRlPKK~~k~a~rG--------------F~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  633 LFTAFGQLKSVRLPKKIGKGAHRG--------------FGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HHhcccceeeeccchhhcchhhcc--------------ceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            699999999999998755566788              99999999999999999999999999999999997653

>KOG0146|consensus

Probab=98.77  E-value=1.1e-08  Score=68.88  Aligned_cols=63  Identities=32%  Similarity=0.458  Sum_probs=55.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-C--EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-M--KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g--~~i~V~~a~~~~~   77 (81)
                      ||..||.|.+|.+.+.. .|.+||              ++||.|.+..+|+.||..|+|.... |  ..|.|+++...++
T Consensus        39 lf~pfG~~~e~tvlrg~-dg~sKG--------------CAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkE  103 (371)
T KOG0146|consen   39 LFQPFGNIEECTVLRGP-DGNSKG--------------CAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKE  103 (371)
T ss_pred             HhcccCCcceeEEecCC-CCCCCC--------------ceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccchHH
Confidence            58999999999999987 789999              9999999999999999999997644 3  6889999987665


Q ss_pred             C
Q psy16913         78 A   78 (81)
Q Consensus        78 ~   78 (81)
                      |
T Consensus       104 R  104 (371)
T KOG0146|consen  104 R  104 (371)
T ss_pred             H
Confidence            4

>KOG0124|consensus

Probab=98.70  E-value=1.9e-08  Score=70.20  Aligned_cols=59  Identities=27%  Similarity=0.471  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|+.||+|+.|.+-+++.++.++|              |||++|.+......||..||-+.+.|..|+|-.+.
T Consensus       230 VFEAFG~I~~C~LAr~pt~~~HkG--------------yGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  230 VFEAFGEIVKCQLARAPTGRGHKG--------------YGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             HHHhhcceeeEEeeccCCCCCccc--------------eeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            488999999999999998888999              99999999999999999999999999999998764

>KOG0110|consensus

Probab=98.68  E-value=6.5e-08  Score=71.36  Aligned_cols=62  Identities=27%  Similarity=0.502  Sum_probs=50.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|...|.|.++.|..-+.... +-          .++|||||+|.++++|++|++.|+|+.|+|+.|.|+++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~-k~----------lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPAN-KY----------LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHhcCeEEEEEEeccccccc-cc----------cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            377889999998876653221 21          233499999999999999999999999999999999987

>KOG4209|consensus

Probab=98.59  E-value=1.1e-07  Score=62.83  Aligned_cols=59  Identities=25%  Similarity=0.380  Sum_probs=54.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      |+.||.|..+.|+.|+.+++++|              |+||+|.+.+.+..|+. |||..|.|+.+.|.+.+-+
T Consensus       122 f~~Cg~i~~~ti~~d~~~~~~k~--------------~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  122 FESCGGINRVTVPKDKFRGHPKG--------------FAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             eeccCCccceeeeccccCCCcce--------------eEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            78899999999999999999999              99999999999999999 9999999999999887543

>KOG0226|consensus

Probab=98.59  E-value=2.1e-08  Score=66.82  Aligned_cols=58  Identities=36%  Similarity=0.592  Sum_probs=50.9

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      |.+|-.-...++++|+.||+++|              |+||.|.++.|+.+|+.+|||.-++.+.|++.-+.
T Consensus       211 f~Kfpsf~~akviRdkRTgKSkg--------------ygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  211 FKKFPSFQKAKVIRDKRTGKSKG--------------YGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             HHhccchhhcccccccccccccc--------------ceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            45566666788999999999999              99999999999999999999999999998876543

>KOG4205|consensus

Probab=98.54  E-value=6.1e-08  Score=66.40  Aligned_cols=62  Identities=24%  Similarity=0.482  Sum_probs=54.9

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      |++||+|.++.+++|+.+++++|              |+||+|.+++...+++.. .-..|+|+.|.+..|.++...
T Consensus        27 f~~~Gev~d~~vm~d~~t~rsrg--------------Fgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~   88 (311)
T KOG4205|consen   27 FSQFGEVTDCVVMRDPSTGRSRG--------------FGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSREDQ   88 (311)
T ss_pred             hcccCceeeEEEeccCCCCCccc--------------ccceecCCCcchheeecc-cccccCCccccceeccCcccc
Confidence            68999999999999999999999              999999999998888774 347799999999999887653

>KOG4212|consensus

Probab=98.52  E-value=2.3e-07  Score=66.00  Aligned_cols=55  Identities=18%  Similarity=0.414  Sum_probs=50.4

Q ss_pred             cCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         3 ~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      ++-|+|..|.+..|. +|+++|              +|.|+|.++|.+++|++.||.+.+.||+|.|+-.
T Consensus        67 ekvGev~yveLl~D~-~GK~rG--------------cavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   67 EKVGEVEYVELLFDE-SGKARG--------------CAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             HhcCceEeeeeeccc-CCCcCC--------------ceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            356899999999986 899999              9999999999999999999999999999999854

>KOG1190|consensus

Probab=98.51  E-value=3.8e-07  Score=64.27  Aligned_cols=56  Identities=20%  Similarity=0.412  Sum_probs=51.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||+.||.|.+|+|..++.     -              -|.|+|.+...|+-|++.|+|..+.|++|+|.+++-.
T Consensus       318 lFgvYGdVqRVkil~nkk-----d--------------~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  318 LFGVYGDVQRVKILYNKK-----D--------------NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             HHhhhcceEEEEeeecCC-----c--------------ceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            689999999999998873     3              7899999999999999999999999999999998644

>KOG4205|consensus

Probab=98.49  E-value=1.6e-07  Score=64.37  Aligned_cols=62  Identities=27%  Similarity=0.484  Sum_probs=56.6

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      |++||.|..+.++.|+.+.+++|              |+||+|.+++.+++++. ..-+.|.|+.+.|..|.|+...
T Consensus       118 fe~~g~v~~~~~~~d~~~~~~rg--------------Fgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  118 FEQFGKVADVVIMYDKTTSRPRG--------------FGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             hhccceeEeeEEeeccccccccc--------------ceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            78999999999999999999999              99999999999998876 6778999999999999998654

>KOG0132|consensus

Probab=98.47  E-value=2.4e-07  Score=69.20  Aligned_cols=59  Identities=19%  Similarity=0.317  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|+.||+|.+|.++..      +|              +|||++....+|.+|+..|+...+.++.|+|.||..+..+.
T Consensus       441 ~feefGeiqSi~li~~------R~--------------cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  441 LFEEFGEIQSIILIPP------RG--------------CAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             HHHhcccceeEeeccC------Cc--------------eeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            5899999999988865      45              99999999999999999999999999999999998765543

>KOG2314|consensus

Probab=98.33  E-value=6.8e-07  Score=65.11  Aligned_cols=56  Identities=23%  Similarity=0.398  Sum_probs=48.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEe
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQL   71 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~   71 (81)
                      +|+++|+|+...++.+..+| .+|              |.|++|.+..+|+.|++.|||+.++ .+.+.|..
T Consensus        84 vfsk~gk~vn~~~P~~e~gg-tkG--------------~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen   84 VFSKAGKIVNMYYPIDEEGG-TKG--------------YLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             HHHhhccccceeeccCccCC-eee--------------EEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            58999999999999888655 888              9999999999999999999999998 45555553

>KOG0151|consensus

Probab=98.31  E-value=7.2e-07  Score=66.31  Aligned_cols=63  Identities=25%  Similarity=0.448  Sum_probs=52.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      .|+.||+|.+++|+..+....++           +.+.+|||.|.+..||++|++.|+|..+.++.+++-|+++
T Consensus       194 tfGrfgPlasvKimwpRtEeEk~-----------r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  194 TFGRFGPLASVKIMWPRTEEEKR-----------RERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKA  256 (877)
T ss_pred             HhcccCcccceeeecccchhhhc-----------cccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccc
Confidence            38899999999999877332221           1234899999999999999999999999999999999843

>KOG0153|consensus

Probab=98.22  E-value=3.9e-06  Score=58.07  Aligned_cols=54  Identities=30%  Similarity=0.518  Sum_probs=46.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHh-hCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA-MNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~-lng~~i~g~~i~V~~a~~~   75 (81)
                      |.+||+|.++.+...+      +              +|||+|.+.+.|+.|... +|-..|+|++|.|.|..++
T Consensus       249 FyqyGeirsi~~~~~~------~--------------CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~~  303 (377)
T KOG0153|consen  249 FYQYGEIRSIRILPRK------G--------------CAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRPK  303 (377)
T ss_pred             HhhcCCeeeEEeeccc------c--------------cceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCCc
Confidence            7899999999887653      4              899999999999998766 6767799999999999883

>KOG0147|consensus

Probab=98.20  E-value=1.2e-06  Score=63.26  Aligned_cols=58  Identities=28%  Similarity=0.366  Sum_probs=54.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|+.+|+|..|.||.|+.++.++|              .+||+|.+.+....||. |.|..+.|.+|.|+...
T Consensus       199 fFs~~gkVrdVriI~Dr~s~rskg--------------i~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  199 FFSIVGKVRDVRIIGDRNSRRSKG--------------IAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             HHHhhcCcceeEeeccccchhhcc--------------eeEEEEecccchhhHhh-hcCCcccCceeEecccH
Confidence            589999999999999999999999              99999999999999995 99999999999998753

>KOG0533|consensus

Probab=98.16  E-value=4.6e-06  Score=55.53  Aligned_cols=60  Identities=25%  Similarity=0.407  Sum_probs=54.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||..||.+..+-+-+++ +|.+.|              .|-|.|...+||..|++.+||..++|+.|.+....+.
T Consensus       103 LF~~~~~~~r~~vhy~~-~G~s~G--------------ta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen  103 LFAEFGELKRVAVHYDR-AGRSLG--------------TADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             HHHHhccceEEeeccCC-CCCCCc--------------cceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            58899999999888887 888888              9999999999999999999999999999998887554

>KOG0120|consensus

Probab=98.14  E-value=9.4e-06  Score=58.68  Aligned_cols=62  Identities=16%  Similarity=0.217  Sum_probs=49.4

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +++||.|.+|.++++-..+..           ....|--||+|.+.+++++|.++|+|.++.||.+...|-.+
T Consensus       430 c~k~g~v~~v~ipr~~~~~~~-----------~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  430 CAKFGAVRSVEIPRPYPDENP-----------VPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             hcccCceeEEecCCCCCCCCc-----------CCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            478999999999988323221           12244789999999999999999999999999988877543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.12  E-value=6.7e-06  Score=57.19  Aligned_cols=63  Identities=14%  Similarity=0.212  Sum_probs=45.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      .|++||.|..+.|-+...+..+..         +.  .=.|++|...+||.+||.+.+|..++||.|+..+...
T Consensus       140 yFGQyGkI~KIvvNkkt~s~nst~---------~h--~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTT  202 (480)
T COG5175         140 YFGQYGKIKKIVVNKKTSSLNSTA---------SH--AGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTT  202 (480)
T ss_pred             hhhhccceeEEEeccccccccccc---------cc--ceEEEEecchHHHHHHHHHhccccccCceEeeecCch
Confidence            489999999875433221111111         00  0149999999999999999999999999999887643

>KOG0106|consensus

Probab=97.96  E-value=3.4e-06  Score=55.27  Aligned_cols=52  Identities=29%  Similarity=0.563  Sum_probs=45.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|..||.|.++.|..        |              |+||+|++..+|..|+..+|+..+.|-.+.|+++..
T Consensus        21 ~f~~yg~~~d~~mk~--------g--------------f~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen   21 FFKGYGKIPDADMKN--------G--------------FGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             HHhhccccccceeec--------c--------------cceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            477788888776543        4              999999999999999999999999998899999875

>KOG1548|consensus

Probab=97.90  E-value=6.2e-05  Score=52.29  Aligned_cols=55  Identities=31%  Similarity=0.376  Sum_probs=46.0

Q ss_pred             cCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         3 ~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ++||+|.+|.|. ++   .+.|              .+-|.|.+.++|+.||+.|+|.-++||.|..++...+
T Consensus       298 ~K~G~v~~vvv~-d~---hPdG--------------vvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  298 EKFGQVRKVVVY-DR---HPDG--------------VVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHhCCcceEEEe-cc---CCCc--------------eeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            578999888654 32   4566              9999999999999999999999999999998876443

>KOG4212|consensus

Probab=97.86  E-value=1.7e-05  Score=56.74  Aligned_cols=52  Identities=29%  Similarity=0.441  Sum_probs=43.5

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      |-.||.|..+.|+   ..|+++|                .|.|.++++|++|+..|||..++||.|+|.+.
T Consensus       557 fre~G~v~yadim---e~GkskG----------------VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  557 FREIGHVLYADIM---ENGKSKG----------------VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             HHhccceehhhhh---ccCCccc----------------eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            5567888877773   2466665                89999999999999999999999999999873

>KOG4660|consensus

Probab=97.80  E-value=3.5e-06  Score=60.99  Aligned_cols=49  Identities=29%  Similarity=0.440  Sum_probs=42.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK   68 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~   68 (81)
                      +|+.||+|..++.     |-..+|              ..||+|.|..+|++|+++||+..+.|+.|+
T Consensus        95 ~f~~yGeir~ir~-----t~~~~~--------------~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   95 IFGAYGEIREIRE-----TPNKRG--------------IVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             HHHhhcchhhhhc-----ccccCc--------------eEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            5889999998653     334467              999999999999999999999999999887

>KOG0120|consensus

Probab=97.78  E-value=1.2e-05  Score=58.18  Aligned_cols=60  Identities=33%  Similarity=0.501  Sum_probs=54.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      .+.||++..-.++.|..+|.++|              |||.+|.++.....|+..|||..+.++.|.|+.|.+.
T Consensus       310 l~~fg~lk~f~lv~d~~~g~skg--------------~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  310 LDSFGPLKAFRLVKDSATGNSKG--------------FAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             HHhcccchhheeecccccccccc--------------eeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            35689999999999998899999              9999999999999999999999999999999998654

>KOG4454|consensus

Probab=97.78  E-value=1.5e-05  Score=52.59  Aligned_cols=57  Identities=25%  Similarity=0.308  Sum_probs=48.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      ||-+-|+|..|.|+.++ .++.+               ||||.|.++-...-|++.|||..+.++.+.+++-.
T Consensus        29 lfiqaGPV~kv~ip~~~-d~~~k---------------Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   29 LFIQAGPVYKVGIPSGQ-DQEQK---------------FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             HhhccCceEEEeCCCCc-cCCCc---------------eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            46678999999998876 33333               99999999999999999999999999999888643

>KOG1457|consensus

Probab=97.77  E-value=0.00012  Score=48.63  Aligned_cols=38  Identities=24%  Similarity=0.451  Sum_probs=34.9

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEEC---CEEEEEEeeCCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIG---MKRLKVQLKRPKD   76 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~---g~~i~V~~a~~~~   76 (81)
                      +|||+|.+..+|..|+..|||..++   +..|.+++|+...
T Consensus        79 vaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNt  119 (284)
T KOG1457|consen   79 VAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNT  119 (284)
T ss_pred             eEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCc
Confidence            9999999999999999999999998   7899999986654

>KOG0116|consensus

Probab=97.72  E-value=6.6e-05  Score=53.47  Aligned_cols=60  Identities=35%  Similarity=0.702  Sum_probs=47.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|.+||+|+...|..-...+...+              ||||+|.+.++++.||++ +-..|+++++.|+.-++.
T Consensus       308 ~Fk~FG~Ik~~~I~vr~~~~~~~~--------------fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  308 VFKQFGPIKEGGIQVRSPGGKNPC--------------FGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             HHhhcccccccceEEeccCCCcCc--------------eEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            488999999988776542333335              999999999999999985 467889999999976653

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.67  E-value=6.9e-05  Score=42.65  Aligned_cols=47  Identities=21%  Similarity=0.261  Sum_probs=32.9

Q ss_pred             ccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913         27 ECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus        27 ~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      .|.+++..-..+-|.|.|.+++.|++|.+.|+|..+.|..|.|++..
T Consensus        29 NCGGkVl~v~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   29 NCGGKVLSVSGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             TTT--EEE--TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             ccCCEEEEEeCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            35556655556799999999999999999999999999999999873

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

>KOG1456|consensus

Probab=97.61  E-value=0.00023  Score=50.25  Aligned_cols=55  Identities=18%  Similarity=0.300  Sum_probs=49.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      ||..||.|.+|+.++.+     .|              -|.|++.++...++|+..||+..+-|.+|.|..++.
T Consensus       308 l~ClYGNV~rvkFmkTk-----~g--------------tamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  308 LFCLYGNVERVKFMKTK-----PG--------------TAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             hhhhcCceeeEEEeecc-----cc--------------eeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence            57889999999999876     45              899999999999999999999999999999888754

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

Probab=97.54  E-value=0.0004  Score=43.08  Aligned_cols=51  Identities=31%  Similarity=0.576  Sum_probs=39.4

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      |..||.+.-++..-+                      --.|+|.+.+.|-+|+. ++|.++.|+.|.|.+..|.
T Consensus        57 ~~~~GevvLvRfv~~----------------------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   57 FAQYGEVVLVRFVGD----------------------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHCCS-ECEEEEETT----------------------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHhCCceEEEEEeCC----------------------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            567888777766654                      35899999999999988 9999999999999987664

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.50  E-value=0.00059  Score=39.66  Aligned_cols=56  Identities=23%  Similarity=0.243  Sum_probs=45.1

Q ss_pred             ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC----CEEEEEEeeCCC
Q psy16913          6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG----MKRLKVQLKRPK   75 (81)
Q Consensus         6 G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~----g~~i~V~~a~~~   75 (81)
                      |...-+-++.|-.++.+.|              ||||-|.+++.|.+-.+.++|..+.    .+.+.|.+|+-+
T Consensus        28 g~yDF~YLPiDf~~~~N~G--------------YAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAriQ   87 (97)
T PF04059_consen   28 GKYDFFYLPIDFKNKCNLG--------------YAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARIQ   87 (97)
T ss_pred             CcceEEEeeeeccCCCceE--------------EEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHhh
Confidence            3444456777777777777              9999999999999999999999986    577788888643

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

>KOG1995|consensus

Probab=97.49  E-value=5.7e-05  Score=52.41  Aligned_cols=52  Identities=27%  Similarity=0.417  Sum_probs=44.4

Q ss_pred             EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913         11 SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus        11 v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +.|-+|+.|+.+||              =|.|+|+++..|+.||..+++..+.+..|+|.+|..+.
T Consensus       104 i~~y~dkeT~~~KG--------------eatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  104 IKIYTDKETGAPKG--------------EATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             hhccccccccCcCC--------------ceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            34556666777777              99999999999999999999999999999999886654

>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=97.42  E-value=0.00061  Score=39.79  Aligned_cols=35  Identities=29%  Similarity=0.356  Sum_probs=28.7

Q ss_pred             eEEEEEEcCHHHHHHHHHhhCCcEECCEEE-EEEeeC
Q psy16913         38 CFGFVSFDNPASAHTAIQAMNGFQIGMKRL-KVQLKR   73 (81)
Q Consensus        38 ~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i-~V~~a~   73 (81)
                      ++-.|+|.++.+|.+|+. -||..+.|..| -|.+.+
T Consensus        55 NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   55 NWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             TEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-H
T ss_pred             CEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEcH
Confidence            389999999999999998 69999998644 476663

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.

>KOG1456|consensus

Probab=97.41  E-value=0.00071  Score=47.82  Aligned_cols=56  Identities=29%  Similarity=0.387  Sum_probs=45.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-C-EEEEEEeeCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-M-KRLKVQLKRPKD   76 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g-~~i~V~~a~~~~   76 (81)
                      .-..|+|.+|.|.+.  +|-                 -|.|+|++.+.|++|-..|||..|+ | ..|+|++|+|.+
T Consensus       143 cnp~GkVlRIvIfkk--ngV-----------------QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  143 CNPQGKVLRIVIFKK--NGV-----------------QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             cCCCCceEEEEEEec--cce-----------------eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            345788888877754  333                 6899999999999999999999988 3 688999998854

>KOG1548|consensus

Probab=97.38  E-value=0.0004  Score=48.36  Aligned_cols=58  Identities=17%  Similarity=0.271  Sum_probs=46.5

Q ss_pred             CccCCceeeE--------EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVIS--------SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~--------v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||-|.+        |++-++. .|..+|              =|.++|...++..-|++.|++..+.|+.|+|+.|
T Consensus       154 ~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKG--------------DaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerA  218 (382)
T KOG1548|consen  154 VMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKG--------------DALCCYIKRESVELAIKILDEDELRGKKLRVERA  218 (382)
T ss_pred             HHHhcceEeccCCCCCeeEEEEecC-CCCccC--------------ceEEEeecccHHHHHHHHhCcccccCcEEEEehh
Confidence            3567776653        4455554 466666              8999999999999999999999999999999988


Q ss_pred             C
Q psy16913         73 R   73 (81)
Q Consensus        73 ~   73 (81)
                      +
T Consensus       219 k  219 (382)
T KOG1548|consen  219 K  219 (382)
T ss_pred             h
Confidence            4

>KOG2068|consensus

Probab=97.32  E-value=8.5e-05  Score=51.22  Aligned_cols=63  Identities=21%  Similarity=0.359  Sum_probs=47.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      |++||.|.++.+-.++....+.+           ..+-++|+|...++|..||...+|..++|+.++..+..++
T Consensus       101 fgqygki~ki~~~~~~S~~s~~~-----------~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gttk  163 (327)
T KOG2068|consen  101 FGQYGKINKIVKNKDPSSSSSSG-----------GTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTTK  163 (327)
T ss_pred             ccccccceEEeecCCcccccCCC-----------CCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCCc
Confidence            78999999988776652111111           2234899999999999999999999999998877766554

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

Probab=97.13  E-value=0.00055  Score=35.48  Aligned_cols=33  Identities=18%  Similarity=0.406  Sum_probs=26.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHH
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAI   54 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai   54 (81)
                      |.+||+|....+...      ..              +.+|.|.+..+|++|+
T Consensus        21 F~~fGeI~~~~~~~~------~~--------------~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   21 FASFGEIVDIYVPES------TN--------------WMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHhcCCEEEEEcCCC------Cc--------------EEEEEECCHHHHHhhC
Confidence            778999999876621      22              8999999999999985

>KOG2202|consensus

Probab=97.07  E-value=0.00015  Score=48.53  Aligned_cols=55  Identities=15%  Similarity=0.207  Sum_probs=45.4

Q ss_pred             CCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         4 ~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +||+|.++.|..+. .-.-.|              -.+|.|...++|++|++.||+.-+.|++|...+..
T Consensus        92 kygEiee~~Vc~Nl-~~hl~G--------------NVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   92 KYGEIEELNVCDNL-GDHLVG--------------NVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             Hhhhhhhhhhhccc-chhhhh--------------hhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            78998887655443 334456              79999999999999999999999999999988763

>KOG4210|consensus

Probab=96.93  E-value=0.00037  Score=47.46  Aligned_cols=61  Identities=25%  Similarity=0.441  Sum_probs=54.7

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      |..+|.|..++++.++.++..+|              |++|.|....++..|+.. +...+.++++.+....++..
T Consensus       206 ~~~~~~i~~~r~~~~~~s~~~kg--------------~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  206 FVSSGEITSVRLPTDEESGDSKG--------------FAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             ccCcCcceeeccCCCCCccchhh--------------hhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            66789999999999999999999              999999999999999887 78889999999998877643

>KOG0106|consensus

Probab=96.93  E-value=0.00038  Score=45.74  Aligned_cols=36  Identities=25%  Similarity=0.562  Sum_probs=32.6

Q ss_pred             ceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913         37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus        37 ~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      .+++||+|...++|.+|+..|++..+.++.|.+..+
T Consensus       133 ~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  133 RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            349999999999999999999999999999998443

>KOG1996|consensus

Probab=96.78  E-value=0.0043  Score=42.75  Aligned_cols=58  Identities=21%  Similarity=0.241  Sum_probs=44.3

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      .++||.|..|-|.-++..-....             .--||+|...++|-+|+-.|||.-+.||.+...+-
T Consensus       307 ceKyg~V~~viifeip~~p~dea-------------vRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  307 CEKYGKVGNVIIFEIPSQPEDEA-------------VRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHhhcceeeEEEEecCCCccchh-------------heeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            36799999987766642222111             14699999999999999999999999998876653

>KOG4206|consensus

Probab=96.30  E-value=0.0091  Score=39.36  Aligned_cols=54  Identities=24%  Similarity=0.431  Sum_probs=42.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~   73 (81)
                      +|.+|.--..++++...     ++              .|||+|.+...|..|.+.+.|..|- ...+.|.++.
T Consensus       166 lf~qf~g~keir~i~~~-----~~--------------iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPR-----SG--------------IAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccCC-----Cc--------------eeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            46667777777766544     34              9999999999999999999999987 7777877664

>KOG4211|consensus

Probab=95.88  E-value=0.02  Score=41.66  Aligned_cols=48  Identities=15%  Similarity=0.221  Sum_probs=39.5

Q ss_pred             EEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913         13 VFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus        13 i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ++..+.+|+..|              =|||+|.+++|+++|++ .|...+..|-|.|=.+.+.
T Consensus        39 ~~~~r~~Gr~sG--------------eA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   39 LEIPRRNGRPSG--------------EAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             EEEeccCCCcCc--------------ceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            445555788888              99999999999999998 6878888899998776544

>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=95.84  E-value=0.022  Score=33.39  Aligned_cols=40  Identities=25%  Similarity=0.438  Sum_probs=23.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF   60 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~   60 (81)
                      +|++||+|..|.+.....                    -|+|-|.+++.|+.|+..+.-.
T Consensus        21 ~f~~~g~V~yVD~~~G~~--------------------~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen   21 AFSQFGEVAYVDFSRGDT--------------------EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             HT-SS--EEEEE--TT-S--------------------EEEEEESS---HHHHHHHHHHT
T ss_pred             HHHhcCCcceEEecCCCC--------------------EEEEEECCcchHHHHHHHHHhc
Confidence            378899888887665431                    6899999999999999876433

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

>KOG4307|consensus

Probab=95.81  E-value=0.02  Score=43.56  Aligned_cols=33  Identities=18%  Similarity=0.334  Sum_probs=31.2

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      -|-|-|++.++|.+|...|++..|..+.+++.+
T Consensus       911 e~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  911 ECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             ceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            899999999999999999999999999988764

>KOG1190|consensus

Probab=95.74  E-value=0.014  Score=41.80  Aligned_cols=54  Identities=26%  Similarity=0.437  Sum_probs=39.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a   72 (81)
                      +|++||.|..+--.. +    .-|+             -|.|+|.+++.|+.|-..|+|.-|..  ..|+++++
T Consensus       170 vFS~fG~VlKIiTF~-K----nn~F-------------QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  170 VFSKFGFVLKIITFT-K----NNGF-------------QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             HHhhcceeEEEEEEe-c----ccch-------------hhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            599999998764322 1    2331             38999999999999999999999874  45555554

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.62  E-value=0.028  Score=35.10  Aligned_cols=50  Identities=18%  Similarity=0.189  Sum_probs=39.0

Q ss_pred             cCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         3 ~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +.||+|.+|.+.-     +  -              -|.|+|.+..+|=+|+.++.. ...|..+.+.|-.+
T Consensus       112 s~fGpI~SVT~cG-----r--q--------------savVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqqr  161 (166)
T PF15023_consen  112 SVFGPIQSVTLCG-----R--Q--------------SAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQR  161 (166)
T ss_pred             HhcCCcceeeecC-----C--c--------------eEEEEehhhHHHHHHHHhhcC-CCCCceEEeecccc
Confidence            5789999886442     1  2              689999999999999998875 66788888887654

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.51  E-value=0.048  Score=29.79  Aligned_cols=33  Identities=30%  Similarity=0.515  Sum_probs=20.7

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      |.||+-.. +.|+.++..|++..+.|++++|+.|
T Consensus        42 ~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   42 FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             -EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            89999876 4789999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4285|consensus

Probab=95.46  E-value=0.021  Score=39.46  Aligned_cols=50  Identities=20%  Similarity=0.259  Sum_probs=38.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEE-EEEe
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRL-KVQL   71 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i-~V~~   71 (81)
                      +|++||.|++....       +.|+             +-+|.|.+..+|++||. -||..|+|-.+ -|..
T Consensus       216 ~F~~cG~Vvkhv~~-------~ngN-------------wMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  216 LFSRCGEVVKHVTP-------SNGN-------------WMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             HHHhhCeeeeeecC-------CCCc-------------eEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            48899998875432       2232             89999999999999998 79999998644 3544

>KOG1855|consensus

Probab=95.44  E-value=0.0041  Score=44.53  Aligned_cols=55  Identities=18%  Similarity=0.239  Sum_probs=37.5

Q ss_pred             CccCCceeeEEEEEec---CCCCC--cccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcE
Q psy16913          1 MFLPFGNVISSKVFID---RATNQ--SKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ   61 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~---~~~~~--~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~   61 (81)
                      ||+.+|.|..|+|...   +.+.+  +++..      +...+-+|+|+|+..+.|.+|.+.||-..
T Consensus       251 iFg~~G~IksIRIckPgaip~d~r~~~~~~~------~~~tk~~AlvEye~~~~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  251 IFGTVGSIKSIRICKPGAIPEDVRGFPKKYF------ELQTKECALVEYEEVEAARKARELLNPEQ  310 (484)
T ss_pred             HhhcccceeeeeecCCCCCCcccccCCccch------hhhhhhhhhhhhhhhHHHHHHHHhhchhh
Confidence            6999999999998766   33222  22100      00122389999999999999999876443

>KOG0112|consensus

Probab=95.31  E-value=0.011  Score=45.70  Aligned_cols=55  Identities=25%  Similarity=0.512  Sum_probs=44.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~   75 (81)
                      .|..||+|..|.+-..      .-              |++|.|++...|+.|+..|-|..+.+  +.+.|.++.+.
T Consensus       475 ~fd~fGpir~Idy~hg------q~--------------yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  475 EFDRFGPIRIIDYRHG------QP--------------YAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             HhhccCcceeeecccC------Cc--------------ceeeecccCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence            3788999988654322      12              99999999999999999999999985  77999998654

>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=94.71  E-value=0.077  Score=28.72  Aligned_cols=29  Identities=17%  Similarity=0.386  Sum_probs=26.4

Q ss_pred             EEEEcCHHHHHHHHHhhCCcEECCEEEEE
Q psy16913         41 FVSFDNPASAHTAIQAMNGFQIGMKRLKV   69 (81)
Q Consensus        41 fV~f~~~~~A~~Ai~~lng~~i~g~~i~V   69 (81)
                      ||.|.+.++|++|....||..+.+..|.+
T Consensus        37 YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   37 YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            79999999999999999999998887764

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

>KOG0128|consensus

Probab=94.61  E-value=0.01  Score=45.45  Aligned_cols=59  Identities=20%  Similarity=0.219  Sum_probs=51.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |++.+|.+.+..++..+ .|+++|              .++|.|.++.++.+++..++...+..+.+.|+.+.|
T Consensus       756 l~~~~gn~~~~~~vt~r-~gkpkg--------------~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  756 LASKTGNVTSLRLVTVR-AGKPKG--------------KARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hccccCCccccchhhhh-cccccc--------------ceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            46788888888888776 788888              999999999999999999998888888888888655

>KOG2135|consensus

Probab=94.32  E-value=0.022  Score=41.36  Aligned_cols=53  Identities=23%  Similarity=0.327  Sum_probs=43.3

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      |.+||+|..|-+-...      -              -|.|+|....+|-.|.. ..+..|++|.|+|-|..+.
T Consensus       394 fA~fG~i~n~qv~~~~------~--------------~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  394 FAQFGEIENIQVDYSS------L--------------HAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhcCccccccccCch------h--------------hheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            7889999988655442      1              57999999999977765 6899999999999998773

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

Probab=94.26  E-value=0.13  Score=33.13  Aligned_cols=37  Identities=35%  Similarity=0.449  Sum_probs=28.3

Q ss_pred             EEEEEEcCHHHHHHHHHhhC--CcEECCEEEEEEeeCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMN--GFQIGMKRLKVQLKRPK   75 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~ln--g~~i~g~~i~V~~a~~~   75 (81)
                      =..|.|.+.++|.+|...|+  +..+.|..+++-++.+.
T Consensus        33 Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen   33 RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            46899999999999999999  99999999999988543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

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

Probab=94.03  E-value=0.18  Score=28.67  Aligned_cols=36  Identities=25%  Similarity=0.520  Sum_probs=29.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN   58 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln   58 (81)
                      ||+.||.|. |..+.|.                     -|||...+.+.|..++..++
T Consensus        28 lFspfG~I~-VsWi~dT---------------------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   28 LFSPFGQIY-VSWINDT---------------------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             HCCCCCCEE-EEEECTT---------------------EEEEEECCCHHHHHHHHHHT
T ss_pred             HhccCCcEE-EEEEcCC---------------------cEEEEeecHHHHHHHHHHhc
Confidence            589999984 5666665                     79999999999999988776

; 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.

>KOG4211|consensus

Probab=93.89  E-value=0.11  Score=38.00  Aligned_cols=36  Identities=25%  Similarity=0.301  Sum_probs=29.7

Q ss_pred             cceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913         36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus        36 ~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      ++|-|||+|++.+.|+.|+. -|...|..|-|.|-.+
T Consensus       144 ~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  144 PTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             cccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            33499999999999999998 5667888888887654

>KOG4574|consensus

Probab=93.01  E-value=0.043  Score=42.43  Aligned_cols=56  Identities=23%  Similarity=0.328  Sum_probs=47.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC--CEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG--MKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~--g~~i~V~~a~~~~   76 (81)
                      ||+.||.|.++...++-.                    .+.|+|...+.|-.|++++.|+++-  |-+.+|.+|+.-.
T Consensus       318 l~s~yg~v~s~wtlr~~N--------------------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  318 LCSDYGSVASAWTLRDLN--------------------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             HHHhhcchhhheeccccc--------------------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            477899999988777642                    7899999999999999999999865  7788999887644

>KOG2193|consensus

Probab=92.02  E-value=0.065  Score=38.80  Aligned_cols=41  Identities=27%  Similarity=0.389  Sum_probs=36.2

Q ss_pred             ceEEEEEEcCHHHHHHHHHhhCCcE-ECCEEEEEEeeCCCCC
Q psy16913         37 KCFGFVSFDNPASAHTAIQAMNGFQ-IGMKRLKVQLKRPKDA   77 (81)
Q Consensus        37 ~~~~fV~f~~~~~A~~Ai~~lng~~-i~g~~i~V~~a~~~~~   77 (81)
                      .||+||.+.+...|.+|++.++|.. +.|+++.|....+++.
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            3599999999999999999999875 7899999998877654

>KOG3152|consensus

Probab=92.01  E-value=0.036  Score=37.47  Aligned_cols=56  Identities=18%  Similarity=0.206  Sum_probs=40.7

Q ss_pred             CccCCceeeEEEEEecCCC--------CCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEE
Q psy16913          1 MFLPFGNVISSKVFIDRAT--------NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR   66 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~--------~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~   66 (81)
                      ||++||.|-+|-+-....+        |....          ..---|.|+|.+...|..+...||+..|.|+.
T Consensus        94 il~~yGeVGRvylqpE~~s~~~~r~~~~~n~~----------~~y~EGWvEF~~KrvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen   94 ILSQYGEVGRVYLQPEDDSKRAARKRKGGNYK----------KLYSEGWVEFISKRVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             HHHhccccceEEecchhhHHHHHHhhcCCCcc----------ccchhHHHHHHHHHHHHHHHHHhCCCccCCCC
Confidence            4788999999988766544        11111          00002579999999999999999999999864

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=91.13  E-value=1.2  Score=26.36  Aligned_cols=41  Identities=15%  Similarity=0.280  Sum_probs=32.3

Q ss_pred             eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC
Q psy16913          8 VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM   64 (81)
Q Consensus         8 i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g   64 (81)
                      |..++|++|..  ..+-              -+.+.|.+.++|+.=...+||+.+..
T Consensus        41 i~~~riird~~--pnry--------------mVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   41 IEHIRIIRDGT--PNRY--------------MVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEEEeeCCC--CceE--------------EEEEEECCHHHHHHHHHHhCCCccCC
Confidence            66778887642  2333              68899999999999999999998873

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

>KOG4660|consensus

Probab=90.82  E-value=0.57  Score=34.74  Aligned_cols=41  Identities=17%  Similarity=0.264  Sum_probs=32.5

Q ss_pred             CcceEEEEEEcCHHHHHHHHHhhCCcEEC----CEEEEEEeeCCC
Q psy16913         35 NQKCFGFVSFDNPASAHTAIQAMNGFQIG----MKRLKVQLKRPK   75 (81)
Q Consensus        35 ~~~~~~fV~f~~~~~A~~Ai~~lng~~i~----g~~i~V~~a~~~   75 (81)
                      -+.|||||-|-+++++..+.++.||+.+.    .+...+.||+-+
T Consensus       429 cNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQ  473 (549)
T KOG4660|consen  429 CNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQ  473 (549)
T ss_pred             cccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhh
Confidence            34559999999999999999999999875    355567776543

>KOG1365|consensus

Probab=90.78  E-value=0.22  Score=35.78  Aligned_cols=35  Identities=17%  Similarity=0.149  Sum_probs=28.9

Q ss_pred             ceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913         37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus        37 ~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      +|-|||+|.+.++|..|....+.+....|.|.|--
T Consensus       324 SGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  324 SGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             ChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            33999999999999999988887777788887643

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=89.02  E-value=0.6  Score=31.73  Aligned_cols=35  Identities=26%  Similarity=0.344  Sum_probs=26.0

Q ss_pred             EEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913         40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus        40 ~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      |||+|.+..+|+.|++.+....  .+.+.+..|.+.+
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~--~~~~~v~~APeP~   35 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKR--PNSWRVSPAPEPD   35 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCC--CCCceEeeCCCcc
Confidence            6999999999999999655333  3556777775544

; GO: 0016020 membrane

>KOG1457|consensus

Probab=88.77  E-value=0.3  Score=32.79  Aligned_cols=28  Identities=18%  Similarity=0.316  Sum_probs=24.5

Q ss_pred             cceEEEEEEcCHHHHHHHHHhhCCcEEC
Q psy16913         36 QKCFGFVSFDNPASAHTAIQAMNGFQIG   63 (81)
Q Consensus        36 ~~~~~fV~f~~~~~A~~Ai~~lng~~i~   63 (81)
                      ..+.+|++|++.+.|..|+..|.|..|.
T Consensus       247 g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  247 GMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             CcceEeecHHHHHHHHHHHHHhhcceec
Confidence            3458999999999999999999998874

>KOG4849|consensus

Probab=87.62  E-value=0.43  Score=33.97  Aligned_cols=48  Identities=19%  Similarity=0.283  Sum_probs=39.1

Q ss_pred             eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEE
Q psy16913          8 VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV   69 (81)
Q Consensus         8 i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V   69 (81)
                      +.+++...++.+|++||              ||+|...+.....+.++.|.-+.|.|+.=.|
T Consensus       109 ~~dmKFFENR~NGQSKG--------------~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen  109 FADMKFFENRTNGQSKG--------------YALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             HhhhhhhhcccCCcccc--------------eEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34455666778899999              9999999999899999999999999865443

>KOG2416|consensus

Probab=85.99  E-value=1.3  Score=33.58  Aligned_cols=36  Identities=22%  Similarity=0.292  Sum_probs=31.6

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEEC---CEEEEEEeeCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIG---MKRLKVQLKRP   74 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~---g~~i~V~~a~~   74 (81)
                      .|||.|.+.++|...+.+|||..+-   .+.|.+.|...
T Consensus       483 hCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~  521 (718)
T KOG2416|consen  483 HCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRA  521 (718)
T ss_pred             ceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecch
Confidence            7999999999999999999998874   68888888754

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

Probab=85.22  E-value=2.7  Score=22.41  Aligned_cols=19  Identities=26%  Similarity=0.274  Sum_probs=16.6

Q ss_pred             EEEEEEcCHHHHHHHHHhh
Q psy16913         39 FGFVSFDNPASAHTAIQAM   57 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~l   57 (81)
                      -|-|.|.+++.|.+|+.+|
T Consensus        44 ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen   44 SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             cEEEEECCHHHHHHHHHcC
Confidence            5779999999999999764

>KOG0128|consensus

Probab=83.48  E-value=0.17  Score=39.17  Aligned_cols=45  Identities=20%  Similarity=0.361  Sum_probs=30.4

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF   60 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~   60 (81)
                      |+.+|.+..+.+..-...++.+|              +||++|..++++.+||.-.++.
T Consensus       688 ~~~~~~~e~vqi~~h~n~~~~rG--------------~~Y~~F~~~~~~~aaV~f~d~~  732 (881)
T KOG0128|consen  688 FSPSGTIEVVQIVIHKNEKRFRG--------------KAYVEFLKPEHAGAAVAFRDSC  732 (881)
T ss_pred             cCccchhhhHHHHHHhhcccccc--------------ceeeEeecCCchhhhhhhhhhh
Confidence            44555555544433334566666              9999999999999999844433

>KOG4676|consensus

Probab=81.83  E-value=1.3  Score=31.98  Aligned_cols=59  Identities=19%  Similarity=0.194  Sum_probs=37.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      ||+-.|+|..+.+.....  .++.         .-....|||-|.++..+..| +.|..+.+-++-|.|-.
T Consensus        27 lFg~lGkI~elrlyp~~~--d~~~---------pv~sRtcyVkf~d~~sv~va-QhLtntvfvdraliv~p   85 (479)
T KOG4676|consen   27 LFGNLGKIPELRLYPNVD--DSKI---------PVISRTCYVKFLDSQSVTVA-QHLTNTVFVDRALIVRP   85 (479)
T ss_pred             HHhhccccccccccCCCC--CccC---------cceeeeEEEeccCCcceeHH-hhhccceeeeeeEEEEe
Confidence            578888998887764321  1111         01122799999999888877 45666776666665543

>KOG0115|consensus

Probab=81.22  E-value=1.2  Score=30.31  Aligned_cols=42  Identities=21%  Similarity=0.326  Sum_probs=34.4

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN   58 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln   58 (81)
                      |+.||+|.+..++.|. .+++.+              -++|.|...-.|.+|+...+
T Consensus        52 f~~fg~~e~av~~vD~-r~k~t~--------------eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   52 FRRFGPIERAVAKVDD-RGKPTR--------------EGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             hhhcCccchheeeecc-cccccc--------------cchhhhhcchhHHHHHHHhc
Confidence            7889999998887775 566656              78999999999999888764

>KOG4210|consensus

Probab=80.81  E-value=1.2  Score=30.47  Aligned_cols=36  Identities=11%  Similarity=0.001  Sum_probs=26.6

Q ss_pred             eEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913         38 CFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus        38 ~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      |++.+.|...+.+..|+...-...+.+..+...+..
T Consensus       131 ~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen  131 GGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             cceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            399999999999999998544456666665554443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	81
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		5e-22
2khc_A	118	Bruno Rrm3+ Length = 118		6e-19
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-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 = 99.0 bits (245), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 58/79 (73%), Gaps = 14/79 (17%)
Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNV+S+KVFID+ TN SKCFG              FVS+DNP SA  AIQ+MNGF
Sbjct: 45  MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQSMNGF 90
Query: 61  QIGMKRLKVQLKRPKDAAR 79
           QIGMKRLKVQLKR K+ ++
Sbjct: 91  QIGMKRLKVQLKRSKNDSK 109

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 89.0 bits (219), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/72 (63%), Positives = 52/72 (72%), Gaps = 14/72 (19%)
Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           FLPFGNVIS+KVFID+ T+ SKCFG              FVSFDNP SA  AI+AMNGFQ
Sbjct: 61  FLPFGNVISAKVFIDKQTSLSKCFG--------------FVSFDNPDSAQVAIKAMNGFQ 106
Query: 62  IGMKRLKVQLKR 73
           +G KRLKVQLK+
Sbjct: 107 VGTKRLKVQLKK 118

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G + S K+  DR T QS+ +G              FV F + +SA  AI  +NGF
Sbjct: 62  LFERYGPIESVKIVCDRETRQSRGYG--------------FVKFQSGSSAQQAIAGLNGF 107
Query: 61  QIGMKRLKVQL 71
            I  KRLKV L
Sbjct: 108 NILNKRLKVAL 118

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 16/65 (24%)
Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQ 61
          P+G ++S+K  +D+ TN  KC G            +GFV FD+P++A  A+ A+  +G Q
Sbjct: 28 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPSAAQKAVTALKASGVQ 73
Query: 62 IGMKR 66
            M +
Sbjct: 74 AQMAK 78

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 14/78 (17%)
Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G++ S K+  D+ T QS   G            +GFV++ +P  A  AI  +NG 
Sbjct: 24 LFGSIGDIESCKLVRDKITGQS--LG------------YGFVNYSDPNDADKAINTLNGL 69
Query: 61 QIGMKRLKVQLKRPKDAA 78
          ++  K +KV   RP  A+
Sbjct: 70 KLQTKTIKVSYARPSSAS 87

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G++ S K+  D+ T QS  +G              FV++ +P  A  AI  +NG 
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYG--------------FVNYSDPNDADKAINTLNGL 69
Query: 61 QIGMKRLKVQLKRPKDAA 78
          ++  K +KV   RP  A+
Sbjct: 70 KLQTKTIKVSYARPSSAS 87

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS  +G              FV++ +P  A  AI  +NG 
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYG--------------FVNYIDPKDAEKAINTLNGL 67
Query: 61 QIGMKRLKVQLKRPKDAA 78
          ++  K +KV   RP  A+
Sbjct: 68 RLQTKTIKVSYARPSSAS 85

>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 = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +  ++V  D AT +SK +G              FVSF N   A  AIQ M G  
Sbjct: 36 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 81
Query: 62 IGMKRLKVQL 71
          +G ++++   
Sbjct: 82 LGGRQIRTNW 91

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-30
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-28
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-27
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-24
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-19
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-19
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-19
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-17
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-15
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-15
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	9e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-10
2div_A	99	TRNA selenocysteine associated protein; structural	5e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	7e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-04

>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 =  102 bits (256), Expect = 2e-30
 Identities = 49/79 (62%), Positives = 58/79 (73%), Gaps = 14/79 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF+PFGNV+S+KVFID+ TN SKCFG              FVS+DNP SA  AIQ+MNGF
Sbjct: 45  MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQSMNGF 90

Query: 61  QIGMKRLKVQLKRPKDAAR 79
           QIGMKRLKVQLKR K+ ++
Sbjct: 91  QIGMKRLKVQLKRSKNDSK 109

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 97.4 bits (243), Expect = 2e-28
 Identities = 46/73 (63%), Positives = 52/73 (71%), Gaps = 14/73 (19%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            FLPFGNVIS+KVFID+ T+ SKCFG              FVSFDNP SA  AI+AMNGF
Sbjct: 60  TFLPFGNVISAKVFIDKQTSLSKCFG--------------FVSFDNPDSAQVAIKAMNGF 105

Query: 61  QIGMKRLKVQLKR 73
           Q+G KRLKVQLK+
Sbjct: 106 QVGTKRLKVQLKK 118

>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 = 95.6 bits (238), Expect = 2e-27
 Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 14/76 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G + S K+  DR T QS+ +G              FV F + +SA  AI  +NGF
Sbjct: 62  LFERYGPIESVKIVCDRETRQSRGYG--------------FVKFQSGSSAQQAIAGLNGF 107

Query: 61  QIGMKRLKVQLKRPKD 76
            I  KRLKV L     
Sbjct: 108 NILNKRLKVALAASGH 123

>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 = 86.4 bits (215), Expect = 2e-24
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 14/73 (19%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +  P+G ++S+K  +D+ TN+ K +G              FV FD+P++A  A+ A+   
Sbjct: 25 LCQPYGKIVSTKAILDKTTNKCKGYG--------------FVDFDSPSAAQKAVTALKAS 70

Query: 61 QIGMKRLKVQLKR 73
           +  +  K     
Sbjct: 71 GVQAQMAKQSGPS 83

>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 = 74.6 bits (184), Expect = 1e-19
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 20/80 (25%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F PFGN+I   +                       +   FV+++   SA  A+  +NG 
Sbjct: 33 AFSPFGNIIDLSMDPP--------------------RNCAFVTYEKMESADQAVAELNGT 72

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          Q+   +LKV + R +     
Sbjct: 73 QVESVQLKVNIARKQPMLDS 92

>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 = 74.2 bits (183), Expect = 2e-19
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 16/76 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F  FGN++S KV  D   +                K +GFV F+   +A  AI+ MNG 
Sbjct: 25 TFSAFGNILSCKVVCDENGS----------------KGYGFVHFETQEAAERAIEKMNGM 68

Query: 61 QIGMKRLKVQLKRPKD 76
           +  +++ V   + + 
Sbjct: 69 LLNDRKVFVGRFKSRK 84

>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 = 73.8 bits (182), Expect = 4e-19
 Identities = 16/76 (21%), Positives = 23/76 (30%), Gaps = 15/76 (19%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           M  PFG VIS+++  D  +  S+  G              F   ++       I   NG 
Sbjct: 45  MLKPFGQVISTRILRDS-SGTSRGVG--------------FARMESTEKCEAVIGHFNGK 89

Query: 61  QIGMKRLKVQLKRPKD 76
            I           P  
Sbjct: 90  FIKTPPGVSAPTEPLL 105

>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 = 68.8 bits (169), Expect = 3e-17
 Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 16/76 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F PFG + S+KV ++    +SK FG              FV F +P  A  A+  MNG 
Sbjct: 35 AFSPFGTITSAKVMME--GGRSKGFG--------------FVCFSSPEEATKAVTEMNGR 78

Query: 61 QIGMKRLKVQLKRPKD 76
           +  K L V L + K+
Sbjct: 79 IVATKPLYVALAQRKE 94

>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 = 66.5 bits (163), Expect = 2e-16
 Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG++    +  D+ T QSK F               F+SF     A  AI  ++GF
Sbjct: 35  LFRPFGSISRIYLAKDKTTGQSKGFA--------------FISFHRREDAARAIAGVSGF 80

Query: 61  QIGMKRLKVQLKRPKDAARP 80
                 L V+  +P   + P
Sbjct: 81  GYDHLILNVEWAKPSTNSGP 100

>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 = 64.4 bits (158), Expect = 7e-16
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 14/75 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  F + +S  V  D  T  S+ +G              FVSF +   A  A+ +M G  
Sbjct: 22 FKDFPSYLSGHVMWDMQTGSSRGYG--------------FVSFTSQDDAQNAMDSMQGQD 67

Query: 62 IGMKRLKVQLKRPKD 76
          +  + L++      +
Sbjct: 68 LNGRPLRINWAAKLE 82

>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 = 66.4 bits (163), Expect = 9e-16
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 14/75 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + + ++  D  T  S  +               FV F +   +  AI+ +NG 
Sbjct: 23 LFRAIGPINTCRIMRDYKTGYSYGYA--------------FVDFTSEMDSQRAIKVLNGI 68

Query: 61 QIGMKRLKVQLKRPK 75
           +  KRLKV   RP 
Sbjct: 69 TVRNKRLKVSYARPG 83

>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 = 61.4 bits (150), Expect = 7e-14
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 16/73 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G+++   +  D+ T + +                 FV ++    A  AI A+N  
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRGVA--------------FVRYNKREEAQEAISALNNV 154

Query: 61  QI--GMKRLKVQL 71
               G + L V+L
Sbjct: 155 IPEGGSQPLSVRL 167

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.0 bits (164), Expect = 1e-15
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 16/82 (19%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG + S+ +  D  T + K +G              F+ ++   S+  A+ +MN F
Sbjct: 145 VFEAFGKIKSATLARDPTTGKHKGYG--------------FIEYEKAQSSQDAVSSMNLF 190

Query: 61  QIGMKRLKVQL--KRPKDAARP 80
            +G + L+V      P     P
Sbjct: 191 DLGGQYLRVGKAVTPPMPLLTP 212

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 62.3 bits (152), Expect = 9e-14
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F PFG + S  +  D  T + K F               FV ++ P +A  A++ MN  
Sbjct: 48  AFAPFGPIKSIDMSWDSVTMKHKGFA--------------FVEYEVPEAAQLALEQMNSV 93

Query: 61  QIGMKRLKVQLKRPKDAARP 80
            +G + +KV        A+P
Sbjct: 94  MLGGRNIKVGRPSNIGQAQP 113

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 64.1 bits (157), Expect = 2e-15
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 16/79 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F   G+V+ + + ++    +SK  G               V F++P  A  A + MNG 
Sbjct: 28 KFNECGHVLYADIKME--NGKSKGCG--------------VVKFESPEVAERACRMMNGM 71

Query: 61 QIGMKRLKVQLKRPKDAAR 79
          ++  + + V++ R      
Sbjct: 72 KLSGREIDVRIDRNASGPS 90

>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 = 64.2 bits (157), Expect = 2e-15
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 14/79 (17%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F+PFG++   ++ +D  T + +  G            F FV F+    A  AI  MN  +
Sbjct: 33 FIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNESE 78

Query: 62 IGMKRLKVQLKRPKDAARP 80
          +  + ++V L +P      
Sbjct: 79 LFGRTIRVNLAKPMRIKES 97

>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 = 64.2 bits (157), Expect = 2e-15
 Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  F       +     T + +                 F++F N   A  A+  +NG+
Sbjct: 45  LFARFQEKKGPPIQFRMMTGRMRGQA--------------FITFPNKEIAWQALHLVNGY 90

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           ++  K L ++  + K     
Sbjct: 91  KLYGKILVIEFGKNKKQRSS 110

>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 = 64.3 bits (157), Expect = 2e-15
 Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 14/79 (17%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F PFG +  ++V  D AT +SK +G              FVSF N   A  AIQ M G  
Sbjct: 36  FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 81

Query: 62  IGMKRLKVQLKRPKDAARP 80
           +G ++++      K  A  
Sbjct: 82  LGGRQIRTNWATRKPPAPK 100

>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 = 63.0 bits (154), Expect = 3e-15
 Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 14/74 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F PFG +  ++V  D AT +SK +G              FVSF N   A  AIQ M G  
Sbjct: 27 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 72

Query: 62 IGMKRLKVQLKRPK 75
          +G ++++      K
Sbjct: 73 LGGRQIRTNWATRK 86

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 62.7 bits (153), Expect = 7e-15
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 14/76 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG + S ++ +D  T +SK  G            +GF++F +   A  A++ +NGF
Sbjct: 46  IFEPFGRIESIQLMMDSETGRSK--G------------YGFITFSDSECAKKALEQLNGF 91

Query: 61  QIGMKRLKVQLKRPKD 76
           ++  + +KV     + 
Sbjct: 92  ELAGRPMKVGHVTERT 107

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 64.1 bits (157), Expect = 8e-15
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 14/76 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S K+  D+ T QS  +G              FV++ +P  A  AI  +NG 
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYG--------------FVNYIDPKDAEKAINTLNGL 67

Query: 61 QIGMKRLKVQLKRPKD 76
          ++  K +KV   RP  
Sbjct: 68 RLQTKTIKVSYARPSS 83

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 61.4 bits (150), Expect = 7e-14
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 16/73 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG- 59
           +F  +G +I+S++ +D+ T  S+  G              F+ FD    A  AI+ +NG 
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVG--------------FIRFDKRIEAEEAIKGLNGQ 153

Query: 60  -FQIGMKRLKVQL 71
                 + + V+ 
Sbjct: 154 KPSGATEPITVKF 166

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 62.7 bits (153), Expect = 8e-15
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 15/81 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F   G V+ + +  D+   +S+  G               V+F+    A  AI   NG 
Sbjct: 35  VFSMAGVVVRADILEDK-DGKSRGIG--------------TVTFEQSIEAVQAISMFNGQ 79

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
            +  + + V++         +
Sbjct: 80  LLFDRPMHVKMDERALPKGDF 100

>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 = 61.9 bits (151), Expect = 1e-14
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 14/79 (17%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G +    V  DR T +S+  G            FGFV+F+N   A  A+ AMNG  
Sbjct: 33 FSKYGQISEVVVVKDRETQRSR--G------------FGFVTFENIDDAKDAMMAMNGKS 78

Query: 62 IGMKRLKVQLKRPKDAARP 80
          +  ++++V         R 
Sbjct: 79 VDGRQIRVDQAGKSSDNRS 97

>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 = 60.6 bits (148), Expect = 2e-14
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F+PFG++   ++ +D  T + +  G            F FV F+    A  AI  MN  +
Sbjct: 28 FIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNESE 73

Query: 62 IGMKRLKV 69
          +  + ++V
Sbjct: 74 LFGRTIRV 81

>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 = 61.0 bits (149), Expect = 3e-14
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 14/76 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F PFG + +  +  D  T +SK  G            +GF++F +   A  A++ +NGF
Sbjct: 25 IFEPFGKIDNIVLMKDSDTGRSK--G------------YGFITFSDSECARRALEQLNGF 70

Query: 61 QIGMKRLKVQLKRPKD 76
          ++  + ++V     + 
Sbjct: 71 ELAGRPMRVGHVTERL 86

>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 = 62.6 bits (153), Expect = 3e-14
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 12/79 (15%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G V    V  DR+ N  +             K   FV+F    +A  A  A++  
Sbjct: 23 LFEQYGAVYEINVLRDRSQNPPQS------------KGCCFVTFYTRKAALEAQNALHNM 70

Query: 61 QIGMKRLKVQLKRPKDAAR 79
          ++          +P D+ +
Sbjct: 71 KVLPGMHHPIQMKPADSEK 89

>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 = 52.6 bits (127), Expect = 2e-10
 Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 18/74 (24%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF  FG +   ++        S+                 FV+F   A A TAI+AM+  
Sbjct: 115 MFSSFGQIEECRILRG-PDGLSRGCA--------------FVTFTTRAMAQTAIKAMHQA 159

Query: 61  QI---GMKRLKVQL 71
           Q        + V+ 
Sbjct: 160 QTMEGCSSPMVVKF 173

>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 = 60.7 bits (148), Expect = 3e-14
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 14/80 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +    G VI+ K+  D  T +SK  G            + F+ F +  S+ +A++ +NG+
Sbjct: 22 LCSNVGPVINLKMMFDPQTGRSK--G------------YAFIEFRDLESSASAVRNLNGY 67

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          Q+G + LK       D +  
Sbjct: 68 QLGSRFLKCGYSSNSDISGV 87

>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 = 60.8 bits (148), Expect = 3e-14
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 16/75 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          MF  FG ++  ++  +   +                K FGFV+F+N A A  A + ++G 
Sbjct: 35 MFGQFGKILDVEIIFNERGS----------------KGFGFVTFENSADADRAREKLHGT 78

Query: 61 QIGMKRLKVQLKRPK 75
           +  ++++V     +
Sbjct: 79 VVEGRKIEVNNATAR 93

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 62.2 bits (152), Expect = 4e-14
 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 14/69 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
              FG + +  +  D AT  SK +               F  + +      AI  +NG Q
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYA--------------FCEYVDINVTDQAIAGLNGMQ 160

Query: 62  IGMKRLKVQ 70
           +G K+L VQ
Sbjct: 161 LGDKKLLVQ 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 = 39.9 bits (94), Expect = 1e-05
 Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 22/80 (27%)

Query: 2  FLPFGNVIS-----SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
          F     +           +    NQ K F               F+ F +      A+ A
Sbjct: 25 FNAQMRLGGLTQAPGNPVLAVQINQDKNFA--------------FLEFRSVDETTQAM-A 69

Query: 57 MNGFQIGMKRLKVQLKRPKD 76
           +G     + LK+  +RP D
Sbjct: 70 FDGIIFQGQSLKI--RRPHD 87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 60.9 bits (148), Expect = 4e-14
 Identities = 10/79 (12%), Positives = 22/79 (27%), Gaps = 14/79 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          M   +G V   ++ +   T +    G               V F +   A   ++ ++  
Sbjct: 26 MCRKYGEVEEVEILLHPRTRKHL--G------------LARVLFTSTRGAKETVKNLHLT 71

Query: 61 QIGMKRLKVQLKRPKDAAR 79
           +    +  QL        
Sbjct: 72 SVMGNIIHAQLDIKGQQRM 90

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 62.4 bits (152), Expect = 5e-14
 Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 16/78 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
              FG + +  +  D AT  SK +               F  + +      AI  +NG Q
Sbjct: 135 LTSFGPLKAFNLVKDSATGLSKGYA--------------FCEYVDINVTDQAIAGLNGMQ 180

Query: 62  IGMKRLKVQL--KRPKDA 77
           +G K+L VQ      K+A
Sbjct: 181 LGDKKLLVQRASVGAKNA 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 = 41.6 bits (98), Expect = 4e-06
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 22/81 (27%)

Query: 1  MFLPFGNVIS-----SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQ 55
           F     +           +    NQ K F               F+ F +      A+ 
Sbjct: 24 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFA--------------FLEFRSVDETTQAM- 68

Query: 56 AMNGFQIGMKRLKVQLKRPKD 76
          A +G     + LK++  RP D
Sbjct: 69 AFDGIIFQGQSLKIR--RPHD 87

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 61.3 bits (149), Expect = 6e-14
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 14/69 (20%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F+PFG++   ++ +D  T + +  G            F FV F+    A  AI  MN  
Sbjct: 83  AFIPFGDITDIQIPLDYETEKHR--G------------FAFVEFELAEDAAAAIDNMNES 128

Query: 61  QIGMKRLKV 69
           ++  + ++V
Sbjct: 129 ELFGRTIRV 137

>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 = 63.5 bits (155), Expect = 6e-14
 Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 14/78 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +  PFG++    +     T QSK +G              F  +    SA  A   + G 
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYG--------------FAEYMKKDSAARAKSDLLGK 160

Query: 61  QIGMKRLKVQLKRPKDAA 78
            +G + L V         
Sbjct: 161 PLGPRTLYVHWTDAGQLT 178

>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 = 60.4 bits (147), Expect = 8e-13
 Identities = 12/79 (15%), Positives = 22/79 (27%), Gaps = 15/79 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
                 +    ++   +   Q K F                + ++    A  A Q  +G 
Sbjct: 205 ALSAVHSPTFCQLACGQ-DGQLKGFA--------------VLEYETAEMAEEAQQQADGL 249

Query: 61  QIGMKRLKVQLKRPKDAAR 79
            +G   L+V    P    R
Sbjct: 250 SLGGSHLRVSFCAPGPPGR 268

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 46.5 bits (111), Expect = 8e-08
 Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          +      V    K   FV+  N   A  AI A +  ++  + L VQL+   
Sbjct: 46 YELKYCFVDKY-KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 59.9 bits (146), Expect = 7e-14
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 15/76 (19%)

Query: 2  FLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          F  FG ++ + K+  D  T  SK +               F++F +  ++  AI+AMNG 
Sbjct: 26 FSAFGVILQTPKIMRDPDTGNSKGYA--------------FINFASFDASDAAIEAMNGQ 71

Query: 61 QIGMKRLKVQLKRPKD 76
           +  + + V     KD
Sbjct: 72 YLCNRPITVSYAFKKD 87

>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 = 59.1 bits (144), Expect = 1e-13
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 15/75 (20%)

Query: 2  FLPFGNVISSKVFIDRA-TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          F  +G +    + ++R   + SK +               +V F+NP  A  A++ M+G 
Sbjct: 25 FSTYGKIKMIDMPVERMHPHLSKGYA--------------YVEFENPDEAEKALKHMDGG 70

Query: 61 QIGMKRLKVQLKRPK 75
          QI  + +        
Sbjct: 71 QIDGQEITATAVLAP 85

>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 = 59.6 bits (145), Expect = 1e-13
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 11/80 (13%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + S  +   +                     FGFV +  P  A  A++ + G 
Sbjct: 25 VFSKVGAIKSCTISKKKNKAGVLLS-----------MGFGFVEYKKPEQAQKALKQLQGH 73

Query: 61 QIGMKRLKVQLKRPKDAARP 80
           +   +L+V++         
Sbjct: 74 TVDGHKLEVRISERATKPAS 93

>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 = 59.1 bits (144), Expect = 1e-13
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 16/83 (19%)

Query: 1  MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
               G  +++  K F +RA  QSK  G            F  V   + AS+   +  + 
Sbjct: 21 AVHSLGVNDILEIKFFENRANGQSK--G------------FALVGVGSEASSKKLMDLLP 66

Query: 59 GFQIGMKRLKVQLKRPKDAARPY 81
            ++  +   V      +    +
Sbjct: 67 KRELHGQNPVVTPSNKLEHHHHH 89

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 62.3 bits (152), Expect = 1e-13
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +      V  S        N S+ F               ++   +   A   ++ +NG 
Sbjct: 137 LLQDINVVALSIRLPSLRFNTSRRFA--------------YIDVTSKEDARYCVEKLNGL 182

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           +I    L  ++  P + ++ 
Sbjct: 183 KIEGYTLVTKVSNPLEKSKR 202

>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 = 53.1 bits (128), Expect = 3e-10
 Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 14/75 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  FG++    +   +  +                 C  F+ F+N  SA  A+Q MN  
Sbjct: 231 SFEGFGSIEKINIPAGQKEHS-------------FNNCCAFMVFENKDSAERALQ-MNRS 276

Query: 61  QIGMKRLKVQLKRPK 75
            +G + + V L   K
Sbjct: 277 LLGNREISVSLADKK 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 = 41.1 bits (97), Expect = 5e-06
 Identities = 12/69 (17%), Positives = 17/69 (24%), Gaps = 17/69 (24%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F   G +I   V      N                  F  + F     A  AI   +  
Sbjct: 61  YFKHCGPIIHVDVADSLKKN----------------FRFARIEFARYDGALAAITKTHKV 104

Query: 61  QIGMKRLKV 69
            +G   + V
Sbjct: 105 -VGQNEIIV 112

>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 = 59.2 bits (144), Expect = 2e-13
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 14/76 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +FL  G V+++ +  DR T Q +  G            +GFV F +   A  AI+ M+  
Sbjct: 35 LFLQAGPVVNTHMPKDRVTGQHQ--G------------YGFVEFLSEEDADYAIKIMDMI 80

Query: 61 QIGMKRLKVQLKRPKD 76
          ++  K ++V      +
Sbjct: 81 KLYGKPIRVNKASAHN 96

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 60.6 bits (148), Expect = 2e-13
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 14/71 (19%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  F + +S  V  D  T  S+ +G              FVSF +   A  A+ +M G 
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYG--------------FVSFTSQDDAQNAMDSMQGQ 152

Query: 61  QIGMKRLKVQL 71
            +  + L++  
Sbjct: 153 DLNGRPLRINW 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 = 49.8 bits (120), Expect = 2e-09
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 15/69 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F   G + + K+ ID+  N++  +               FV +     A+ A+Q +NG 
Sbjct: 20 YFQVGGPIANIKIMIDK-NNKNVNYA--------------FVEYHQSHDANIALQTLNGK 64

Query: 61 QIGMKRLKV 69
          QI    +K+
Sbjct: 65 QIENNIVKI 73

>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 = 59.3 bits (144), Expect = 2e-13
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 15/75 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G +    +  DR T++S+ F               F++F+NPA A  A + MNG 
Sbjct: 27 VFGKHGPISEVLLIKDR-TSKSRGFA--------------FITFENPADAKNAAKDMNGK 71

Query: 61 QIGMKRLKVQLKRPK 75
           +  K +KV+  +  
Sbjct: 72 SLHGKAIKVEQAKKP 86

>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 = 58.8 bits (143), Expect = 2e-13
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 14/76 (18%)

Query: 5  FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
          F   + +++  DR T  SK  G            FGFV F++   A  A +AM   +I  
Sbjct: 36 FDGSVRARIVTDRETGSSK--G------------FGFVDFNSEEDAKAAKEAMEDGEIDG 81

Query: 65 KRLKVQLKRPKDAARP 80
           ++ +   +PK     
Sbjct: 82 NKVTLDWAKPKGEGGS 97

>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 = 58.8 bits (143), Expect = 2e-13
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 14/80 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G V    +  +  T   +  G            F FV F +   A  A  AM+G 
Sbjct: 33 VFEKYGRVGDVYIPREPHTKAPR--G------------FAFVRFHDRRDAQDAEAAMDGA 78

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          ++  + L+VQ+ R       
Sbjct: 79 ELDGRELRVQVARYGRRDLS 98

>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 = 58.4 bits (142), Expect = 3e-13
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 14/70 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G +    +  D+ + +S+ F               FV F+N   A  A +  NG 
Sbjct: 35 VFSKYGPIADVSIVYDQQSRRSRGFA--------------FVYFENVDDAKEAKERANGM 80

Query: 61 QIGMKRLKVQ 70
          ++  +R++V 
Sbjct: 81 ELDGRRIRVS 90

>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 = 58.0 bits (141), Expect = 4e-13
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G V+   +  D+ T +SK  G              F+ F +  SA    +A+N  
Sbjct: 36 IFSKYGKVVKVTIMKDKDTRKSK--G------------VAFILFLDKDSAQNCTRAINNK 81

Query: 61 QIGMKRLKV 69
          Q+  + +K 
Sbjct: 82 QLFGRVIKA 90

>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 = 60.0 bits (146), Expect = 5e-13
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 16/80 (20%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  FGN++S KV  D   N SK +G              FV F+   +A  AI+ MNG 
Sbjct: 123 TFSAFGNILSCKVVCD--ENGSKGYG--------------FVHFETQEAAERAIEKMNGM 166

Query: 61  QIGMKRLKVQLKRPKDAARP 80
            +  +++ V   + +     
Sbjct: 167 LLNDRKVFVGRFKSRKEREA 186

>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 = 55.4 bits (134), Expect = 3e-11
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F P G ++S +V  D  T +S  +               +V+F  PA A  A+  MN  
Sbjct: 35 KFSPAGPILSIRVCRDMITRRSLGYA--------------YVNFQQPADAERALDTMNFD 80

Query: 61 QIGMKRLKV 69
           I  K +++
Sbjct: 81 VIKGKPVRI 89

>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 = 58.6 bits (142), Expect = 6e-13
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 17/80 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G +    +  D+ + +S+ F               FV F+N   A  A +  NG 
Sbjct: 66  VFSKYGPIADVSIVYDQQSRRSRGFA--------------FVYFENVDDAKEAKERANGM 111

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           ++  +R++V     K   RP
Sbjct: 112 ELDGRRIRVDFSITK---RP 128

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.7 bits (140), Expect = 7e-13
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 16/75 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           MF  FG ++  ++  +     SK FG              FV+F+N A A  A + ++G 
Sbjct: 49  MFGQFGKILDVEIIFNE--RGSKGFG--------------FVTFENSADADRAREKLHGT 92

Query: 61  QIGMKRLKVQLKRPK 75
            +  ++++V     +
Sbjct: 93  VVEGRKIEVNNATAR 107

>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 = 57.7 bits (140), Expect = 7e-13
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 15/71 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG +  + V  DR + +S                   V F+  A A  A++  NG 
Sbjct: 49  LFAEFGTLKKAAVHYDR-SGRSLGTA--------------DVHFERKADALKAMKQYNGV 93

Query: 61  QIGMKRLKVQL 71
            +  + + +QL
Sbjct: 94  PLDGRPMNIQL 104

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 57.8 bits (140), Expect = 9e-13
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G V    +  DR T +S+  G            F FV F +   A  A+ AM+G 
Sbjct: 67  VFEKYGRVGDVYIPRDRYTKESR--G------------FAFVRFHDKRDAEDAMDAMDGA 112

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
            +  + L+VQ+ R       +
Sbjct: 113 VLDGRELRVQMARYGRPPDSH 133

>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 = 57.2 bits (139), Expect = 9e-13
 Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 14/79 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G +      ID  T + K F               FV+F  P  A  A   ++G 
Sbjct: 28 LFSAYGPLSELHYPIDSLTKKPKGFA--------------FVTFMFPEHAVKAYAEVDGQ 73

Query: 61 QIGMKRLKVQLKRPKDAAR 79
              + L V     K  A 
Sbjct: 74 VFQGRMLHVLPSTIKKEAS 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 = 57.6 bits (139), Expect = 2e-12
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 16/81 (19%)

Query: 1   MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
           +    G  +V+  K   +RA  QSK  G            +  V   +  S H  ++ + 
Sbjct: 75  VIRSIGVYDVVELKFAENRANGQSK--G------------YAEVVVASENSVHKLLELLP 120

Query: 59  GFQIGMKRLKVQLKRPKDAAR 79
           G  +  +++ V+    ++ ++
Sbjct: 121 GKVLNGEKVDVRPATRQNLSQ 141

>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 = 59.0 bits (142), Expect = 2e-12
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 16/81 (19%)

Query: 1   MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
                G  +++  K F +RA  QSK F                V   + AS+   +  + 
Sbjct: 88  AVHSLGVNDILEIKFFENRANGQSKGFA--------------LVGVGSEASSKKLMDLLP 133

Query: 59  GFQIGMKRLKVQLKRPKDAAR 79
             ++  +   V     +  ++
Sbjct: 134 KRELHGQNPVVTPVNKQFLSQ 154

>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 = 56.1 bits (136), Expect = 2e-12
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 15/69 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +FL  G +    +  DR   + K FG              FV F +P S   AI  +NG 
Sbjct: 36 LFLQAGPLTKVTICKDR-EGKPKSFG--------------FVCFKHPESVSYAIALLNGI 80

Query: 61 QIGMKRLKV 69
          ++  + + V
Sbjct: 81 RLYGRPINV 89

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 56.6 bits (137), Expect = 2e-12
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 15/81 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG +  + V  DR + +S   G               V F+  A A  A++   G 
Sbjct: 55  LFAEFGTLKKAAVDYDR-SGRSL--G------------TADVHFERRADALKAMKQYKGV 99

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
            +  + + +QL   +     +
Sbjct: 100 PLDGRPMDIQLVASQIDLEHH 120

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.7 bits (135), Expect = 3e-12
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 14/75 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  +G + +  + +DR T   K  G            +  V ++    A  A++ +NG 
Sbjct: 43  KFAEYGEIKNIHLNLDRRTGYLK--G------------YTLVEYETYKEAQAAMEGLNGQ 88

Query: 61  QIGMKRLKVQLKRPK 75
            +  + + V     +
Sbjct: 89  DLMGQPISVDWCFVR 103

>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 = 55.7 bits (135), Expect = 4e-12
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 16/79 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G   S K+  +  +N                  + FV F     A  A+ AMNG 
Sbjct: 35 LFSQIGPCKSCKMITEHTSNDP----------------YCFVEFYEHRDAAAALAAMNGR 78

Query: 61 QIGMKRLKVQLKRPKDAAR 79
          +I  K +KV       + +
Sbjct: 79 KILGKEVKVNWATTPSSQK 97

>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 = 55.3 bits (134), Expect = 5e-12
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 14/80 (17%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G V+S ++  DR T + K  G            +GF  + +  +A +A++ +NG 
Sbjct: 28 IFSEVGPVVSFRLVYDRETGKPK--G------------YGFCEYQDQETALSAMRNLNGR 73

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          +   + L+V     +     
Sbjct: 74 EFSGRALRVDNAASEKNKEE 93

>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 = 56.4 bits (136), Expect = 5e-12
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 14/81 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G V    +  DR T +S+  G            F FV F +   A  A+ AM+G 
Sbjct: 90  VFEKYGRVGDVYIPRDRYTKESR--G------------FAFVRFHDKRDAEDAMDAMDGA 135

Query: 61  QIGMKRLKVQLKRPKDAARPY 81
            +  + L+VQ+ R       +
Sbjct: 136 VLDGRELRVQMARYGRPPDSH 156

>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 = 54.5 bits (132), Expect = 7e-12
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 15/81 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG V + K+  DR T +               K FGFV      S   AI  ++  
Sbjct: 21 LFSQFGKVFNVKLIYDRETKKP--------------KGFGFVEMQE-ESVSEAIAKLDNT 65

Query: 61 QIGMKRLKVQLKRPKDAARPY 81
              + ++V    PK +   +
Sbjct: 66 DFMGRTIRVTEANPKKSLEHH 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 = 56.4 bits (136), Expect = 8e-12
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 14/80 (17%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  +G + +  + +DR T  SK +                V ++    A  A +A+NG 
Sbjct: 92  KFCDYGEIKNIHLNLDRRTGFSKGYA--------------LVEYETHKQALAAKEALNGA 137

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           +I  + ++V     K   R 
Sbjct: 138 EIMGQTIQVDWCFVKGPKRV 157

>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 = 54.9 bits (132), Expect = 1e-11
 Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 11/75 (14%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  FG +    +    +   S+                 +V++     A  AIQ +N  
Sbjct: 38  YFGKFGKIHKVVINNSTSYAGSQ-----------GPSASAYVTYIRSEDALRAIQCVNNV 86

Query: 61  QIGMKRLKVQLKRPK 75
            +  + LK  L   K
Sbjct: 87  VVDGRTLKASLGTTK 101

>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 = 54.6 bits (132), Expect = 1e-11
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 14/75 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  +G + +  + +DR T  SK +                V ++    A  A +A+NG 
Sbjct: 46  KFCDYGEIKNIHLNLDRRTGFSKGYA--------------LVEYETHKQALAAKEALNGA 91

Query: 61  QIGMKRLKVQLKRPK 75
           +I  + ++V     K
Sbjct: 92  EIMGQTIQVDWCFVK 106

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 53.8 bits (130), Expect = 2e-11
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 15/78 (19%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +    G V   ++  +R   + K  G              +V ++N + A  A+  M+G 
Sbjct: 37 ICKAHGTVKDLRLVTNR-AGKPK--G------------LAYVEYENESQASQAVMKMDGM 81

Query: 61 QIGMKRLKVQLKRPKDAA 78
           I    +KV +     ++
Sbjct: 82 TIKENIIKVAISNSGPSS 99

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 53.9 bits (130), Expect = 2e-11
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 20/75 (26%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F PFG ++  +VF +                    K + FV F    SA  AI ++NG 
Sbjct: 45 TFSPFGQIMEIRVFPE--------------------KGYSFVRFSTHESAAHAIVSVNGT 84

Query: 61 QIGMKRLKVQLKRPK 75
           I    +K    +  
Sbjct: 85 TIEGHVVKCYWGKES 99

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 53.1 bits (128), Expect = 3e-11
 Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 20/75 (26%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG ++  K + +                    K   F+ +D    A   I A+  F
Sbjct: 47  LFQNFGFILDFKHYPE--------------------KGCCFIKYDTHEQAAVCIVALANF 86

Query: 61  QIGMKRLKVQLKRPK 75
               + L+    + +
Sbjct: 87  PFQGRNLRTGWGKER 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 53.6 bits (129), Expect = 3e-11
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 22/83 (26%)

Query: 1   MFLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHT 52
            F   G V  +         +++D+ T + K                  VS+++P +A  
Sbjct: 35  FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA--------------TVSYEDPPTAKA 80

Query: 53  AIQAMNGFQIGMKRLKVQLKRPK 75
           A++  +G      +LKV L R K
Sbjct: 81  AVEWFDGKDFQGSKLKVSLARKK 103

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 52.8 bits (127), Expect = 5e-11
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 17/79 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          + + +G V S +     +                       V++ +   A  A+  +NGF
Sbjct: 35 LLVQYGVVESCEQVNTDSETAV-----------------VNVTYSSKDQARQALDKLNGF 77

Query: 61 QIGMKRLKVQLKRPKDAAR 79
          Q+    LKV     + AA+
Sbjct: 78 QLENFTLKVAYIPDEMAAQ 96

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 52.6 bits (127), Expect = 5e-11
 Identities = 11/80 (13%), Positives = 24/80 (30%), Gaps = 20/80 (25%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G      +  D+                     FGF+  +    A  A   ++  
Sbjct: 35 LFEKYGKAGEVFIHKDKG--------------------FGFIRLETRTLAEIAKVELDNM 74

Query: 61 QIGMKRLKVQLKRPKDAARP 80
           +  K+L+V+      +   
Sbjct: 75 PLRGKQLRVRFACHSASLTS 94

>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 = 52.4 bits (126), Expect = 7e-11
 Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 9   ISSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGF 60
           I+S+VFI                F +  R    +  K + FV + N   A  A+   NG 
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85

Query: 61  QIGMKRLKVQLKRPKDAARP 80
            +  + L + +       R 
Sbjct: 86  VLAGQTLDINMAGEPKPDRS 105

>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 = 51.9 bits (125), Expect = 9e-11
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 19/79 (24%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F     +      +     +SK  G              ++ F + A A   ++   G 
Sbjct: 36 VFEDALEIR-----LVSQDGKSK--G------------IAYIEFKSEADAEKNLEEKQGA 76

Query: 61 QIGMKRLKVQLKRPKDAAR 79
          +I  + + +     K   R
Sbjct: 77 EIDGRSVSLYYTGEKGGTR 95

>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 = 52.3 bits (126), Expect = 9e-11
 Identities = 19/83 (22%), Positives = 26/83 (31%), Gaps = 18/83 (21%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG +    V        SK                 FV F +   A  AI A++G 
Sbjct: 35  LFQPFGVIDECTVLRGP-DGSSKGCA--------------FVKFSSHTEAQAAIHALHGS 79

Query: 61  QI---GMKRLKVQLKRPKDAARP 80
           Q        L V+       + P
Sbjct: 80  QTMPGASSSLVVKFADTDKESGP 102

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 51.7 bits (125), Expect = 9e-11
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 15/75 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F   G+V    +  D+ +   K  G            F ++ F +  S  T++ A++  
Sbjct: 26 HFHGCGSVNRVTILCDKFSGHPK--G------------FAYIEFSDKESVRTSL-ALDES 70

Query: 61 QIGMKRLKVQLKRPK 75
              +++KV  KR  
Sbjct: 71 LFRGRQIKVIPKRTN 85

>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 = 52.4 bits (126), Expect = 1e-10
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 14/75 (18%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
            F  +G + +  + +DR T   K  G            +  V ++    A  A++ +NG 
Sbjct: 42  KFAEYGEIKNIHLNLDRRTGYLK--G------------YTLVEYETYKEAQAAMEGLNGQ 87

Query: 61  QIGMKRLKVQLKRPK 75
            +  + + V     +
Sbjct: 88  DLMGQPISVDWCFVR 102

>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 = 52.0 bits (125), Expect = 1e-10
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 20/86 (23%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN-- 58
           +   FG++   +V +   T  SK  G              F  F    +A   + A +  
Sbjct: 35  VLQQFGDLKYVRVVLHPDTEHSK--G------------CAFAQFMTQEAAQKCLAAASLE 80

Query: 59  ----GFQIGMKRLKVQLKRPKDAARP 80
               G ++  ++LKV L   +D A  
Sbjct: 81  AEGGGLKLDGRQLKVDLAVTRDEAAS 106

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 52.9 bits (127), Expect = 1e-10
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 14/80 (17%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F   G++    + +D+    +   G            F FV + + A A  A++ +NG +
Sbjct: 60  FSKSGDIKKIIMGLDKMKKTAC--G------------FCFVEYYSRADAENAMRYINGTR 105

Query: 62  IGMKRLKVQLKRPKDAARPY 81
           +  + ++          R Y
Sbjct: 106 LDDRIIRTDWDAGFKEGRQY 125

>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 = 51.1 bits (123), Expect = 2e-10
 Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 22/80 (27%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F  FG +   K                        K + F+ FD    A  A++ MNG 
Sbjct: 31 AFSQFGKLERVKKL----------------------KDYAFIHFDERDGAVKAMEEMNGK 68

Query: 61 QIGMKRLKVQLKRPKDAARP 80
           +  + +++   +P D  R 
Sbjct: 69 DLEGENIEIVFAKPPDQKRK 88

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 53.5 bits (129), Expect = 2e-10
 Identities = 14/79 (17%), Positives = 23/79 (29%), Gaps = 19/79 (24%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  FG V  + V +D    ++   G              FV F     A  A++      
Sbjct: 117 FSQFGPVEKAVVVVD-DRGRATGKG--------------FVEFAAKPPARKALERCGDGA 161

Query: 62  IGMKR----LKVQLKRPKD 76
             +      + V+     D
Sbjct: 162 FLLTTTPRPVIVEPMEQFD 180

>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 = 48.9 bits (117), Expect = 8e-09
 Identities = 11/69 (15%), Positives = 23/69 (33%), Gaps = 20/69 (28%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G      +  DR                     FGF+  ++   A  A   ++G 
Sbjct: 42 LFERYGEPSEVFINRDR--------------------GFGFIRLESRTLAEIAKAELDGT 81

Query: 61 QIGMKRLKV 69
           +  + L++
Sbjct: 82 ILKSRPLRI 90

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 51.1 bits (123), Expect = 2e-10
 Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 16/78 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
                     V +D  T  ++ FG              +V F++      A++ + G +
Sbjct: 38 ISELFAKNDLAV-VDVRTGTNRKFG--------------YVDFESAEDLEKALE-LTGLK 81

Query: 62 IGMKRLKVQLKRPKDAAR 79
          +    +K++  + +D  R
Sbjct: 82 VFGNEIKLEKPKGRDGTR 99

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 52.6 bits (127), Expect = 2e-10
 Identities = 11/80 (13%), Positives = 29/80 (36%), Gaps = 16/80 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
                      V +D  T  ++ FG              +V F++      A++ + G 
Sbjct: 33 AISELFAKNDLAV-VDVRTGTNRKFG--------------YVDFESAEDLEKALE-LTGL 76

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          ++    +K++  + +D+ + 
Sbjct: 77 KVFGNEIKLEKPKGRDSKKV 96

>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 = 49.5 bits (119), Expect = 3e-09
 Identities = 9/75 (12%), Positives = 21/75 (28%), Gaps = 19/75 (25%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F     +            +SK                 ++ F + A A   ++   G 
Sbjct: 119 VFEDALEIRL-----VSQDGKSKGIA--------------YIEFKSEADAEKNLEEKQGA 159

Query: 61  QIGMKRLKVQLKRPK 75
           +I  + + +     K
Sbjct: 160 EIDGRSVSLYYTGEK 174

>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 = 51.2 bits (123), Expect = 2e-10
 Identities = 12/80 (15%), Positives = 27/80 (33%), Gaps = 17/80 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G +   +V     T                 +   +V +++   A  A+  ++GF
Sbjct: 28 IFGKYGPIRQIRVGNTPET-----------------RGTAYVVYEDIFDAKNAVDHLSGF 70

Query: 61 QIGMKRLKVQLKRPKDAARP 80
           +  + L V       A + 
Sbjct: 71 NVSNRYLVVLYYNANRAFQK 90

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 52.2 bits (125), Expect = 4e-10
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 15/74 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  FG +  + V  DR + +S   G               V F+  A A  A++   G  
Sbjct: 109 FAEFGTLKKAAVDYDR-SGRSL--G------------TADVHFERRADALKAMKQYKGVP 153

Query: 62  IGMKRLKVQLKRPK 75
           +  + + +QL   +
Sbjct: 154 LDGRPMDIQLVASQ 167

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 50.4 bits (121), Expect = 4e-10
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 16/77 (20%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ-I 62
           + +    KV +D+ T  SK +G              FV F +      A+    G   +
Sbjct: 33 VYPSCRGGKVVLDQ-TGVSKGYG--------------FVKFTDELEQKRALTECQGAVGL 77

Query: 63 GMKRLKVQLKRPKDAAR 79
          G K +++ +  PK +  
Sbjct: 78 GSKPVRLSVAIPKASRV 94

>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 = 50.4 bits (121), Expect = 5e-10
 Identities = 13/55 (23%), Positives = 22/55 (40%)

Query: 27  ECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY 81
           + + K       F FV F++P  A  A+   +G+     RL+V+  R        
Sbjct: 51  DIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 50.0 bits (120), Expect = 5e-10
 Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 15/73 (20%)

Query: 1  MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
           F   G  V+S K+  +R T     +               FV F + A+A   +  +NG
Sbjct: 29 AFATMGETVMSVKIIRNRLTGIPAGYC--------------FVEFADLATAEKCLHKING 74

Query: 60 FQIGMKRLKVQLK 72
            +       + K
Sbjct: 75 KPLPGATPAKRFK 87

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 50.0 bits (120), Expect = 5e-10
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 18/77 (23%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F     +            +SK  G            + F+ F +   A  A+ + N  
Sbjct: 35 VFEKATFI----KVPQNQNGKSK--G------------YAFIEFASFEDAKEALNSCNKR 76

Query: 61 QIGMKRLKVQLKRPKDA 77
          +I  + ++++L+ P+ +
Sbjct: 77 EIEGRAIRLELQGPRGS 93

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 50.0 bits (120), Expect = 6e-10
 Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 22/76 (28%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F PFG +   K+                         F FV F+   SA  AI+ ++G 
Sbjct: 51  IFGPFGPMKEVKI----------------------LNGFAFVEFEEAESAAKAIEEVHGK 88

Query: 61  QIGMKRLKVQLKRPKD 76
               + L+V   +   
Sbjct: 89  SFANQPLEVVYSKLPA 104

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 50.1 bits (120), Expect = 6e-10
 Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 22/82 (26%)

Query: 2  FLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTA 53
          F   G + ++         ++ DR T + K  G               VSFD+P SA  A
Sbjct: 28 FKQIGIIKTNKKTGQPMINLYTDRETGKLK--G------------EATVSFDDPPSAKAA 73

Query: 54 IQAMNGFQIGMKRLKVQLKRPK 75
          I   +G +     +KV     +
Sbjct: 74 IDWFDGKEFSGNPIKVSFATRR 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 = 50.5 bits (121), Expect = 7e-10
 Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 15/74 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F   G++    +  D+ +   K  G            + ++ F    S   A+ AM+   
Sbjct: 57  FSSCGSINRITILCDKFSGHPK--G------------YAYIEFAERNSVDAAV-AMDETV 101

Query: 62  IGMKRLKVQLKRPK 75
              + +KV  KR  
Sbjct: 102 FRGRTIKVLPKRTN 115

>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 = 49.6 bits (119), Expect = 9e-10
 Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 16/68 (23%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG +    V  DR T   K                 F+++    SA  A  A++  
Sbjct: 33 LFEEFGKIYELTVLKDRFTGMHKGCA--------------FLTYCERESALKAQSALHEQ 78

Query: 61 QI--GMKR 66
          +   GM R
Sbjct: 79 KTLPGMNR 86

>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 = 49.2 bits (118), Expect = 2e-09
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 15/74 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F   G V   ++  DR + +SK  G              +V F    S   AI  + G +
Sbjct: 46  FSAVGKVRDVRIISDRNSRRSK--G------------IAYVEFCEIQSVPLAI-GLTGQR 90

Query: 62  IGMKRLKVQLKRPK 75
           +    + VQ  + +
Sbjct: 91  LLGVPIIVQASQAE 104

>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 = 48.4 bits (116), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 20/75 (26%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F         +V   R                     + FV F N   A  A++A+NG  
Sbjct: 36 FNNIKPGAVERVKKIR--------------------DYAFVHFSNREDAVEAMKALNGKV 75

Query: 62 IGMKRLKVQLKRPKD 76
          +    ++V L +P D
Sbjct: 76 LDGSPIEVTLAKPVD 90

>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 = 48.0 bits (115), Expect = 2e-09
 Identities = 10/44 (22%), Positives = 23/44 (52%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
          K +GFV  ++  +A  AI+ ++ +++    + V+  + K  A  
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.0 bits (115), Expect = 3e-09
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 10 SSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGFQ 61
           S++FI        + +   + F      + +N +  FGF+ FDNP S   AI+  +   
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEM 69

Query: 62 IGMKRLKVQLKRPKDAARPY 81
             K+L +++       +  
Sbjct: 70 NFGKKLILEVSSSNARPQFD 89

>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 = 48.7 bits (116), Expect = 4e-09
 Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 9/79 (11%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  + +  S    I       K             K   F+   N  +A  A++  NG+
Sbjct: 65  IFGRYVDFSSETQRIMFDIRLMK---------EGRMKGQAFIGLPNEKAAAKALKEANGY 115

Query: 61  QIGMKRLKVQLKRPKDAAR 79
            +  K + VQ  R     +
Sbjct: 116 VLFGKPMVVQFARSARPKQ 134

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 47.6 bits (114), Expect = 4e-09
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 17/75 (22%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG ++   V                       +   FV F   +SA  A+++M GF
Sbjct: 32 IFSRFGQILDILVSRSL-----------------KMRGQAFVIFKEVSSATNALRSMQGF 74

Query: 61 QIGMKRLKVQLKRPK 75
              K +++Q  +  
Sbjct: 75 PFYDKPMRIQYAKTD 89

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.8 bits (114), Expect = 4e-09
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 15/69 (21%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F   G V++ +  ID AT ++K F               FV   +   A   I++ +G +
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFL--------------FVECGSMNDAKKIIKSFHGKR 78

Query: 62 I-GMKRLKV 69
          +    RL +
Sbjct: 79 LDLKHRLFL 87

>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 = 46.8 bits (112), Expect = 7e-09
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 10 SSKVFI----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAIQAMNGFQI 62
          + K+F+       T+Q     F    R +  +  K + FV  +  A A  AI  +NG ++
Sbjct: 9  TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV 68

Query: 63 GMKRLKVQLKRPKD 76
            KR+ V+L     
Sbjct: 69 KGKRINVELSTKGQ 82

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.1 bits (112), Expect = 7e-09
 Identities = 11/46 (23%), Positives = 22/46 (47%)

Query: 30 RKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          R      +   F+ + + A+A  A+  + G ++G   L+V L R +
Sbjct: 49 RLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 47.3 bits (113), Expect = 8e-09
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 15/79 (18%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  FG++  + V  DR T +S+ +G              FV+  + A+A  A +  N   
Sbjct: 38  FEGFGDIEEAVVITDRQTGKSRGYG--------------FVTMADRAAAERACKDPNP-I 82

Query: 62  IGMKRLKVQLKRPKDAARP 80
           I  ++  V L       R 
Sbjct: 83  IDGRKANVNLAYLGAKPRS 101

>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 = 46.9 bits (112), Expect = 9e-09
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 3  LPFGNVISSKVFI-----DRATNQS--KCFGECNRKVSVN-QKCFGFVSFDNPASAHTAI 54
          +P G+ + S++FI        + +   + F      + +N +  FGF+ FDNP S   AI
Sbjct: 15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 74

Query: 55 QAMNGFQIGMKRLKVQLKRPK 75
          +  +      K+L +++    
Sbjct: 75 EXESQEMNFGKKLILEVSSSN 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 46.9 bits (112), Expect = 1e-08
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 25 FGECNR-KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          +G      ++ N   F FV F++P  A  A++ ++G  I   R++V+L    
Sbjct: 24 YGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM 75

>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 = 48.0 bits (114), Expect = 1e-08
 Identities = 13/45 (28%), Positives = 25/45 (55%)

Query: 31  KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
            V+ N   F FV F++P  A  A++ ++G  +   R++V+L   +
Sbjct: 104 WVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.1 bits (116), Expect = 1e-08
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 17/79 (21%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG ++   V                       +   FV F   +SA  A+++M GF
Sbjct: 33 IFSQFGQILDILVSRSL-----------------KMRGQAFVIFKEVSSATNALRSMQGF 75

Query: 61 QIGMKRLKVQLKRPKDAAR 79
              K +++Q  +      
Sbjct: 76 PFYDKPMRIQYAKTDSDII 94

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 3e-07
 Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 20/74 (27%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  F      ++   R                       FV FDN   A  A  A+ GF
Sbjct: 227 LFNQFPGFKEVRLVPGRHD-------------------IAFVEFDNEVQAGAARDALQGF 267

Query: 61  QI-GMKRLKVQLKR 73
           +I     +K+   +
Sbjct: 268 KITQNNAMKISFAK 281

>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 = 46.5 bits (111), Expect = 1e-08
 Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 22/77 (28%)

Query: 2  FLPFGNVISS--------KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTA 53
          F   G + ++         ++ DR T + K  G               VSFD+P SA  A
Sbjct: 34 FKQIGIIKTNKKTGQPMINLYTDRETGKLK--G------------EATVSFDDPPSAKAA 79

Query: 54 IQAMNGFQIGMKRLKVQ 70
          I   +G +     +KV 
Sbjct: 80 IDWFDGKEFSGNPIKVS 96

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 46.5 bits (111), Expect = 1e-08
 Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 17/75 (22%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G+V   K+  DR T  SK +G              FVSF N       ++  +   
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYG--------------FVSFYNDVDVQKIVE--SQIN 72

Query: 62 IGMKRLKVQLKRPKD 76
             K+LK+     K 
Sbjct: 73 FHGKKLKLGPAIRKQ 87

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 45.8 bits (109), Expect = 2e-08
 Identities = 12/80 (15%), Positives = 27/80 (33%), Gaps = 20/80 (25%)

Query: 1  MFLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
             P+ ++  + + +  D+ T Q++ F               FV   +   A   +Q + 
Sbjct: 29 ALSPYASLAVNNIRLIKDKQTQQNRGFA--------------FVQLSSAMDASQLLQILQ 74

Query: 59 G----FQIGMKRLKVQLKRP 74
                +I  K + V   + 
Sbjct: 75 SLHPPLKIDGKTIGVDFAKS 94

>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 = 45.8 bits (109), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 16/78 (20%)

Query: 1  MFLPFGNVISSKVFIDR-ATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-N 58
          +F  FG + + ++      T   +  G            FGFV F     A  A  A+ +
Sbjct: 35 LFSTFGELKTVRLPKKMTGTGAHR--G------------FGFVDFITKQDAKKAFNALCH 80

Query: 59 GFQIGMKRLKVQLKRPKD 76
             +  +RL ++    + 
Sbjct: 81 STHLYGRRLVLEWADSEV 98

>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 = 45.3 bits (108), Expect = 3e-08
 Identities = 10/42 (23%), Positives = 18/42 (42%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
          + FV  +    A  AI+ ++  +   KR+ VQL   +     
Sbjct: 46 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAS 87

>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 = 46.8 bits (111), Expect = 4e-08
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 19/80 (23%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G+V   K+  ++                   K    V   +   A  A+  +NG 
Sbjct: 24 LFGVYGDVQRVKILFNK-------------------KENALVQMADGNQAQLAMSHLNGH 64

Query: 61 QIGMKRLKVQLKRPKDAARP 80
          ++  K +++ L + ++   P
Sbjct: 65 KLHGKPIRITLSKHQNVQLP 84

>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 = 40.7 bits (95), Expect = 7e-06
 Identities = 9/76 (11%), Positives = 21/76 (27%), Gaps = 19/76 (25%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F   G V+    F  +                   +    +   +   A  A+  ++  
Sbjct: 140 LFSSNGGVVKGFKFFQK------------------DRKMALIQMGSVEEAVQALIDLHNH 181

Query: 61  QIGMKR-LKVQLKRPK 75
            +G    L+V   +  
Sbjct: 182 DLGENHHLRVSFSKST 197

>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 = 44.5 bits (106), Expect = 7e-08
 Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-FQIGMKRLKVQLKRPKD 76
                   + +  + FV + +   A  AI+ ++G  ++  K ++V     K 
Sbjct: 32 RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 84

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.9 bits (106), Expect = 1e-07
 Identities = 8/76 (10%), Positives = 20/76 (26%), Gaps = 17/76 (22%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +    G+++   V +                   +     ++ F    SA   ++A  G+
Sbjct: 53  LASSQGDILDIVVDLSD-----------------DNSGKAYIVFATQESAQAFVEAFQGY 95

Query: 61  QIGMKRLKVQLKRPKD 76
                 L +       
Sbjct: 96  PFQGNPLVITFSETPQ 111

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 17/70 (24%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG + +   F      ++K +               F+ + +PA A  A++  +G+
Sbjct: 41 IFSKFGKITN--DFYPEEDGKTKGYI--------------FLEYASPAHAVDAVKNADGY 84

Query: 61 QIGMK-RLKV 69
          ++  +   +V
Sbjct: 85 KLDKQHTFRV 94

>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 = 43.3 bits (103), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 15/79 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V    +  D    +               + FGF++F++  S   A+  M+   
Sbjct: 31 FKKFGVVTEVVMIYDAEKQRP--------------RGFGFITFEDEQSVDQAV-NMHFHD 75

Query: 62 IGMKRLKVQLKRPKDAARP 80
          I  K+++V+   P+D+   
Sbjct: 76 IMGKKVEVKRAEPRDSKSS 94

>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 = 45.0 bits (106), Expect = 3e-07
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 19/80 (23%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  +G+V   K+  ++                   K    V   +   A  A+  +NG 
Sbjct: 55  LFGVYGDVQRVKILFNK-------------------KENALVQMADGNQAQLAMSHLNGH 95

Query: 61  QIGMKRLKVQLKRPKDAARP 80
           ++  K +++ L + ++   P
Sbjct: 96  KLHGKPIRITLSKHQNVQLP 115

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 40.4 bits (94), Expect = 9e-06
 Identities = 9/76 (11%), Positives = 20/76 (26%), Gaps = 19/76 (25%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F   G V+    F                      +    +   +   A  A+  ++  
Sbjct: 171 LFSSNGGVVKGFKFFQ------------------KDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 61  QIGMKR-LKVQLKRPK 75
            +G    L+V   +  
Sbjct: 213 DLGENHHLRVSFSKST 228

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.8 bits (101), Expect = 3e-07
 Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 17/70 (24%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  FG + +   F      ++K +               F+ + +PA A  A++  +G+
Sbjct: 27 IFSKFGKITN--DFYPEEDGKTKGYI--------------FLEYASPAHAVDAVKNADGY 70

Query: 61 QIGMK-RLKV 69
          ++  +   +V
Sbjct: 71 KLDKQHTFRV 80

>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 = 42.6 bits (101), Expect = 4e-07
 Identities = 12/71 (16%), Positives = 21/71 (29%), Gaps = 21/71 (29%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NG 59
           F  FG + +  V                       +   F+ F    +A  A +   N 
Sbjct: 32 HFYQFGEIRTITVVQR--------------------QQCAFIQFATRQAAEVAAEKSFNK 71

Query: 60 FQIGMKRLKVQ 70
            +  +RL V+
Sbjct: 72 LIVNGRRLNVK 82

>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 = 42.6 bits (101), Expect = 5e-07
 Identities = 17/79 (21%), Positives = 25/79 (31%), Gaps = 16/79 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  FG V+  +V  D  T  S              K FGFV F    +    +   +   
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHS--------------KGFGFVRFTEYETQVKVMSQRH--M 79

Query: 62 IGMKRLKVQLKRPKDAARP 80
          I  +    +L   K +   
Sbjct: 80 IDGRWCDCKLPNSKQSQDS 98

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 42.2 bits (100), Expect = 6e-07
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG--MKRLKVQLKRPK 75
          FG       V    F ++ +++  +A  A   M GF +G   +RL+V   +  
Sbjct: 41 FGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 41.8 bits (99), Expect = 7e-07
 Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 14/57 (24%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
          F  FG V+   + +D  T +S              + FGF+ F + AS    +    
Sbjct: 32 FTKFGEVVDCTIKMDPNTGRS--------------RGFGFILFKDAASVEKVLDQKE 74

>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 = 43.5 bits (102), Expect = 7e-07
 Identities = 7/69 (10%), Positives = 20/69 (28%), Gaps = 14/69 (20%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +    G    + V +    ++    G               + +D+ + A   +  +N +
Sbjct: 143 ICDELGVKRPTSVKVFSGKSERSSSG--------------LLEWDSKSDALETLGFLNHY 188

Query: 61  QIGMKRLKV 69
           Q+       
Sbjct: 189 QMKNPNGPY 197

>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 = 41.2 bits (96), Expect = 4e-06
 Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 19/71 (26%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +GNV   K    +                        V   +  +   AI  +N  
Sbjct: 25 VFCLYGNVEKVKFMKSK-------------------PGAAMVEMADGYAVDRAITHLNNN 65

Query: 61 QIGMKRLKVQL 71
           +  +++ V +
Sbjct: 66 FMFGQKMNVCV 76

>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 = 42.9 bits (102), Expect = 8e-07
 Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 15/74 (20%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  +G +I +++ +D+ T QS              + FGFV++D+  +            
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQS--------------RGFGFVTYDSADAVDRVC-QNKFID 152

Query: 62  IGMKRLKVQLKRPK 75
              ++++++   P+
Sbjct: 153 FKDRKIEIKRAEPR 166

>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 = 40.6 bits (96), Expect = 7e-06
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 16/79 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G V   K+  D AT +S              + FGF+SF+ P+S    ++  +   
Sbjct: 24 FGKYGTVTDLKIMKDPATGRS--------------RGFGFLSFEKPSSVDEVVKTQH--I 67

Query: 62 IGMKRLKVQLKRPKDAARP 80
          +  K +  +   P+D    
Sbjct: 68 LDGKVIDPKRAIPRDEQDK 86

>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 = 40.9 bits (96), Expect = 2e-06
 Identities = 13/39 (33%), Positives = 17/39 (43%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          K   FV+  N   A  AIQ  + +    K L VQL+   
Sbjct: 40 KRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 40.6 bits (95), Expect = 3e-06
 Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 1/56 (1%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
           G+      V +   G V F        A++ ++  +      +    R K     
Sbjct: 39 AGDVCY-ADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR 93

>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 = 40.4 bits (95), Expect = 3e-06
 Identities = 11/77 (14%), Positives = 23/77 (29%), Gaps = 14/77 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +  +  S                              V+F++   A  A+  +N   
Sbjct: 36 FYGYQVIPGSVCLKYNEKGMPTGEA--------------MVAFESRDEATAAVIDLNDRP 81

Query: 62 IGMKRLKVQLKRPKDAA 78
          IG +++K+ L     + 
Sbjct: 82 IGSRKVKLVLGSGPSSG 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.9 bits (94), Expect = 5e-06
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 15/73 (20%)

Query: 7  NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR 66
          ++ S ++  D+ T++ K  G            F +V FD   S   A+   +G  +G + 
Sbjct: 40 SIRSVRLVRDKDTDKFK--G------------FCYVEFDEVDSLKEAL-TYDGALLGDRS 84

Query: 67 LKVQLKRPKDAAR 79
          L+V +   +   +
Sbjct: 85 LRVDIAEGRKQDK 97

>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 = 40.0 bits (94), Expect = 6e-06
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 18/69 (26%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
           +  +G +    V  D A+ +S              + FGFV+F + A    A+ A    +
Sbjct: 48  YEQWGKLTDCVVMRDPASKRS--------------RGFGFVTFSSMAEVDAAMAARPHSI 93

Query: 58  NGFQIGMKR 66
           +G  +  KR
Sbjct: 94  DGRVVEPKR 102

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 39.8 bits (93), Expect = 6e-06
 Identities = 8/56 (14%), Positives = 16/56 (28%), Gaps = 1/56 (1%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
           G+      V +   G V F        A++ ++  +      +    R K     
Sbjct: 40 AGDVCY-ADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR 94

>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 = 39.9 bits (94), Expect = 6e-06
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 18/69 (26%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
          F  +G V+   +  D+ TNQS              + FGFV F +P    T + +    +
Sbjct: 37 FSQYGEVVDCVIMKDKTTNQS--------------RGFGFVKFKDPNCVGTVLASRPHTL 82

Query: 58 NGFQIGMKR 66
          +G  I  K 
Sbjct: 83 DGRNIDPKP 91

>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 = 39.4 bits (92), Expect = 8e-06
 Identities = 9/46 (19%), Positives = 15/46 (32%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
          FG   R +         V F  P  A  A + +   +     L ++
Sbjct: 34 FGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE 79

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 38.6 bits (91), Expect = 9e-06
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 18/69 (26%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
          F  FG V  + +  D+ TN+               + FGFV+F++        +     +
Sbjct: 20 FEQFGKVDDAMLMFDKTTNRH--------------RGFGFVTFESEDIVEKVCEIHFHEI 65

Query: 58 NGFQIGMKR 66
          N   +  K+
Sbjct: 66 NNKMVECKK 74

>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 = 39.0 bits (91), Expect = 1e-05
 Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 14/77 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN-- 58
                  +   +    A ++ K             + F FV +++  +A  A + +   
Sbjct: 28 EIAKVTEGVLDVIVYASAADKMK------------NRGFAFVEYESHRAAAMARRKLMPG 75

Query: 59 GFQIGMKRLKVQLKRPK 75
            Q+   ++ V    P+
Sbjct: 76 RIQLWGHQIAVDWAEPE 92

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 15/79 (18%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  +G +   ++  DR + +               + F FV+FD+  S    +       
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKK--------------RGFAFVTFDDHDSVDKIV-IQKYHT 169

Query: 62  IGMKRLKVQLKRPKDAARP 80
           +     +V+    K     
Sbjct: 170 VNGHNCEVRKALSKQEMAS 188

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 38.8 bits (91), Expect = 4e-05
 Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 15/79 (18%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +G +    V  D  T +S              + FGFV++        A+      +
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRS--------------RGFGFVTYATVEEVDAAM-NARPHK 78

Query: 62 IGMKRLKVQLKRPKDAARP 80
          +  + ++ +    ++ ++ 
Sbjct: 79 VDGRVVEPKRAVSREDSQR 97

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 37.9 bits (89), Expect = 2e-05
 Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 14/55 (25%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
          F  FG V    V  D  T +S              + FGFV+F + A     +  
Sbjct: 21 FGQFGEVKECLVMRDPLTKRS--------------RGFGFVTFMDQAGVDKVLAQ 61

>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 = 38.4 bits (90), Expect = 2e-05
 Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 18/69 (26%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
           F  FG V    V  D  T +S              + FGFV+F + A     +      +
Sbjct: 46  FGQFGEVKECLVMRDPLTKRS--------------RGFGFVTFMDQAGVDKVLAQSRHEL 91

Query: 58  NGFQIGMKR 66
           +   I  K 
Sbjct: 92  DSKTIDPKV 100

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 38.5 bits (89), Expect = 2e-05
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 20/78 (25%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG V+    F      Q                    + + +P SA  A  +++G 
Sbjct: 48  IFSKFGTVLKIITFTKNNQFQ------------------ALLQYADPVSAQHAKLSLDGQ 89

Query: 61  QI--GMKRLKVQLKRPKD 76
            I      L++   +   
Sbjct: 90  NIYNACCTLRIDFSKLTS 107

>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 = 37.5 bits (88), Expect = 3e-05
 Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 18/69 (26%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA----M 57
          F  FG V S ++ +D  TN+               + F F++F         ++     +
Sbjct: 20 FGGFGEVESIELPMDNKTNKR--------------RGFCFITFKEEEPVKKIMEKKYHNV 65

Query: 58 NGFQIGMKR 66
             +  +K 
Sbjct: 66 GLSKCEIKV 74

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 39.0 bits (90), Expect = 3e-05
 Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 20/76 (26%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F   G++   +                     V  K  GFV F   A+A  A +AM+  
Sbjct: 163 VFSRLGDIDRIRY--------------------VESKNCGFVKFKYQANAEFAKEAMSNQ 202

Query: 61  QIGMKRLKVQLKRPKD 76
            + +   K    R + 
Sbjct: 203 TLLLPSDKEWDDRREG 218

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 20/78 (25%)

Query: 1   MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           +F  FG V+    F      Q                    + + +P SA  A  +++G 
Sbjct: 66  IFSKFGTVLKIITFTKNNQFQ------------------ALLQYADPVSAQHAKLSLDGQ 107

Query: 61  QI--GMKRLKVQLKRPKD 76
            I      L++   +   
Sbjct: 108 NIYNACCTLRIDFSKLTS 125

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 37.7 bits (88), Expect = 3e-05
 Identities = 10/68 (14%), Positives = 21/68 (30%), Gaps = 14/68 (20%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          F  +  +  S                              V+F++   A  A+  +N   
Sbjct: 36 FYGYQVIPGSVCLKYNEKGMPTGEA--------------MVAFESRDEATAAVIDLNDRP 81

Query: 62 IGMKRLKV 69
          IG +++K+
Sbjct: 82 IGSRKVKL 89

>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 = 39.1 bits (90), Expect = 4e-05
 Identities = 10/74 (13%), Positives = 31/74 (41%), Gaps = 14/74 (18%)

Query: 2   FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
           F  +G +    +   + + + + +               F+ +++    H+A +  +G +
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYA--------------FIEYEHERDMHSAYKHADGKK 168

Query: 62  IGMKRLKVQLKRPK 75
           I  +R+ V ++R +
Sbjct: 169 IDGRRVLVDVERGR 182

>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 = 37.6 bits (87), Expect = 4e-05
 Identities = 6/38 (15%), Positives = 14/38 (36%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
           G  +  +    K + F  +     +  A   +NG ++
Sbjct: 51 CGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 88

>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 = 37.1 bits (86), Expect = 6e-05
 Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 2/58 (3%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKDAARP 80
          FG     + +  K    V F+N  SA   +         I  ++        K   RP
Sbjct: 39 FGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRP 96

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 36.9 bits (86), Expect = 7e-05
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 20/79 (25%)

Query: 2  FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
          FL FG V  + V +D+                     F  V   +  +    + + +   
Sbjct: 29 FLAFGPV--ASVVMDKDKG-----------------VFAIVEMGDVGAREAVL-SQSQHS 68

Query: 62 IGMKRLKVQLKRPKDAARP 80
          +G  RL+V+ +  K+   P
Sbjct: 69 LGGHRLRVRPREQKEFQSP 87

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 37.2 bits (86), Expect = 8e-05
 Identities = 8/58 (13%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 25  FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQLKRPKDAARP 80
           FG+    + +  K   F+  +   +A+T +         +  + + +Q    K+    
Sbjct: 55  FGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 112

>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 = 35.9 bits (83), Expect = 2e-04
 Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
                      K F F+ F +      A+   +G     + LK+  +RP
Sbjct: 41 GNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI--RRP 87

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 36.0 bits (83), Expect = 2e-04
 Identities = 8/58 (13%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQA--MNGFQIGMKRLKVQLKRPKDAARP 80
          FG+    + +  K   F+  +   +A+T +         +  + + +Q    K+    
Sbjct: 40 FGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 97

>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 = 35.2 bits (81), Expect = 3e-04
 Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQLKRPKD 76
          FG+    + +  K   F+      +A T +   +     +  + + +Q    K+
Sbjct: 39 FGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92

>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 = 34.5 bits (80), Expect = 6e-04
 Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
          FG+  F++  S  +A+ ++N   +G KR++V +     
Sbjct: 59 FGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ 95

>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 = 34.7 bits (80), Expect = 7e-04
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 10/55 (18%)

Query: 5  FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
          FG V   +V I +     +   E   K+        FV F   +  H AIQA+NG
Sbjct: 49 FGAVN--RVIIYQEKQGEEEDAEIIVKI--------FVEFSIASETHKAIQALNG 93

>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 = 34.1 bits (79), Expect = 7e-04
 Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
          FG+  F++  S  +A+ ++N   +G +R++V +     
Sbjct: 63 FGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	81
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.72
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.72
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.72
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.72
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.72
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.72
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.71
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.7
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.69
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.69
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.69
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.69
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.69
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
2div_A	99	TRNA selenocysteine associated protein; structural	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.68
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.68
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.66
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.66
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.65
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.65
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.65
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.64
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.63
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.63
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.63
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.62
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.62
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.62
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.62
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.62
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.62
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.61
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.6
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.6
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.6
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.6
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.6
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.6
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.6
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.6
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.59
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.59
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.59
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.59
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.59
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.58
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.58
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.58
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.57
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.57
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.57
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.56
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.56
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.56
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.56
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.55
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.55
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.55
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.55
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.55
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.54
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.54
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.54
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.53
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.53
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.53
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.53
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.53
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.52
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.52
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.52
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.52
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.52
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.52
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.51
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.51
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.5
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.49
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.49
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.48
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.48
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.47
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.46
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.46
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.46
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.45
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.44
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.42
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.41
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.39
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.39
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.39
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.38
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.38
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.37
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.36
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.35
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.35
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.35
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.33
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.33
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.32
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.29
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.26
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.26
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.24
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.2
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.15
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.14
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.06
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.54
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	97.47
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.46
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	97.45
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.37
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.62
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	94.44
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.37
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	89.06
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	85.54

>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=99.82  E-value=3.9e-20  Score=106.38  Aligned_cols=60  Identities=33%  Similarity=0.612  Sum_probs=57.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++++++|+.+|.++|              ||||+|.++++|++|++.|||..+.|++|+|++|+|
T Consensus        39 ~F~~~G~I~~v~i~~d~~tg~~kG--------------~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           39 LFSSIGEVESAKLIRDKVAGHSLG--------------YGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             HHHTTSCEEEEEEEECSSSCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             HHHhcCCEEEeEeeecCCCCcccc--------------cEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            589999999999999999999999              999999999999999999999999999999999986

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.79  E-value=1.6e-19  Score=105.58  Aligned_cols=62  Identities=15%  Similarity=0.201  Sum_probs=59.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|++|+.|++++|              ||||+|.+.++|++|++.|||..++|+.|.|++|....
T Consensus        26 ~F~~~G~i~~v~i~~d~~tg~~rG--------------~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           26 MCRKYGEVEEVEILLHPRTRKHLG--------------LARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTTH
T ss_pred             HHHhcCCeeEEEEEECCCCCceee--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            589999999999999999999999              99999999999999999999999999999999997654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.8e-18  Score=99.14  Aligned_cols=66  Identities=33%  Similarity=0.565  Sum_probs=62.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|++||+|.+|.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.|
T Consensus        35 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~  100 (103)
T 2cq0_A           35 LFRPFGSISRIYLAKDKTTGQSKG--------------FAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGP  100 (103)
T ss_dssp             TSTTTCCEEEEEEEECSSSCSEEE--------------EEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCSCC
T ss_pred             HHHhCCCeEEEEEeecCCCCceee--------------EEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCCCC
Confidence            699999999999999998999999              999999999999999999999999999999999998876554

>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=99.77  E-value=1.9e-18  Score=95.27  Aligned_cols=62  Identities=27%  Similarity=0.485  Sum_probs=59.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.|||..++|+.|+|+++.++.
T Consensus        21 ~f~~~G~i~~~~i~~~~~~~~~~g--------------~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           21 AFKDFPSYLSGHVMWDMQTGSSRG--------------YGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             HHTTSTTEEEEEEEECTTTCCEEE--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             HHHhcCCeeEEEEEEcCCCCCccc--------------eEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            489999999999999988999999              99999999999999999999999999999999999875

>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=99.76  E-value=3.1e-18  Score=95.19  Aligned_cols=61  Identities=39%  Similarity=0.597  Sum_probs=56.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..++|+.|.|+++.++
T Consensus        26 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           26 AFAPFGRISDARVVKDMATGKSKG--------------YGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             HHHhcCCEeEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            489999999999999988999999              9999999999999999999999999999999999875

>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=99.75  E-value=2.2e-18  Score=100.55  Aligned_cols=66  Identities=74%  Similarity=1.218  Sum_probs=61.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|++||+|.+++|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++.++..+.+
T Consensus        45 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~  110 (115)
T 2cpz_A           45 MFMPFGNVVSAKVFIDKQTNLSKC--------------FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS  110 (115)
T ss_dssp             HHGGGSCCSEEEEEECSSSCSEEE--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCCC
T ss_pred             HHHhcCCeEEEEEEECCCCCCcCc--------------cEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcCCC
Confidence            489999999999999998999999              999999999999999999999999999999999998876553

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.75  E-value=3.2e-19  Score=102.37  Aligned_cols=62  Identities=26%  Similarity=0.400  Sum_probs=58.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC-EEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM-KRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g-~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|++++.||+++|              ||||+|.++++|++|++.|||..+.| +.|+|++|.++.
T Consensus        32 ~F~~~G~i~~v~i~~d~~tg~~kG--------------~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~~   94 (100)
T 3ns6_A           32 LFSKAGKVVNMEFPIDEATGKTKG--------------FLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVE   94 (100)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECS--------------EEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHHH
T ss_pred             HHHhcCCEeEEEEEEcCCCCccce--------------EEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchhh
Confidence            489999999999999999999999              99999999999999999999999999 999999997653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=3.3e-18  Score=96.52  Aligned_cols=65  Identities=26%  Similarity=0.548  Sum_probs=61.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..++|+.|+|+++.++..+.
T Consensus        25 ~f~~~G~v~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   89 (95)
T 2dnz_A           25 IFEPFGKIDNIVLMKDSDTGRSKG--------------YGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGG   89 (95)
T ss_dssp             HHTTTSCEEEEEEECCSSSCCCCS--------------EEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCCC
T ss_pred             HHHhcCCEeEEEEeecCCCCceee--------------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCCC
Confidence            489999999999999998999999              99999999999999999999999999999999998887654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=3.3e-19  Score=100.95  Aligned_cols=64  Identities=19%  Similarity=0.348  Sum_probs=58.1

Q ss_pred             CccCCc-eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh-CCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G-~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l-ng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++|| +|.+|+|++|+.++.++|              ||||+|.++++|++|++.+ |+..++|++|.|++|.|+...
T Consensus        21 ~F~~~G~~v~~v~i~~d~~t~~~rg--------------~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           21 QLQSHGVQAREVRLMRNKSSGQSRG--------------FAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             HHHHHTCCCSBCCSSSCSSSCCCSS--------------EEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCC
T ss_pred             HHHHhCCEeEEEEEEecCCCCCcCc--------------eEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCC
Confidence            488999 899999999999999999              9999999999999999987 466799999999999887654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.3e-18  Score=98.40  Aligned_cols=65  Identities=28%  Similarity=0.535  Sum_probs=60.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        32 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2cqb_A           32 AFIPFGDITDIQIPLDYETEKHRG--------------FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE   96 (102)
T ss_dssp             HHTTTSCCCCEECCCCSSSCCCSS--------------EEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             HhhccCCEEEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCC
Confidence            489999999999999998999999              99999999999999999999999999999999998876554

>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=99.74  E-value=4e-18  Score=96.92  Aligned_cols=65  Identities=28%  Similarity=0.345  Sum_probs=60.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++....
T Consensus        28 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (99)
T 1whw_A           28 LFSAYGPLSELHYPIDSLTKKPKG--------------FAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS   92 (99)
T ss_dssp             HHHTTSCEEEEECCCCTTTCCCCS--------------EEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTTC
T ss_pred             HHHhcCCEeEEEEEecCCCCCcCe--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcccc
Confidence            489999999999999998999999              99999999999999999999999999999999998877643

>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=99.74  E-value=2.6e-19  Score=100.75  Aligned_cols=66  Identities=20%  Similarity=0.267  Sum_probs=55.2

Q ss_pred             CccCCc--eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G--~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||  +|.+++++.++.+|+++|              ||||+|.+.++|++|++.|||..++|+.|+|.++.++...
T Consensus        21 ~F~~~G~~~v~~v~i~~~~~~g~~kG--------------~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~~   86 (90)
T 3p5t_L           21 AVHSLGVNDILEIKFFENRANGQSKG--------------FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH   86 (90)
T ss_dssp             HHHTTTCCCCCCEEEEECTTTCCEEE--------------EEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC------
T ss_pred             HHHHhCCCceEEEEEEecCCCCccCc--------------EEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCccc
Confidence            488999  999999999999999999              9999999999999999999999999999999999887665


Q ss_pred             CC
Q psy16913         79 RP   80 (81)
Q Consensus        79 ~~   80 (81)
                      .|
T Consensus        87 ~~   88 (90)
T 3p5t_L           87 HH   88 (90)
T ss_dssp             --
T ss_pred             cC
Confidence            43

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=9.5e-18  Score=97.72  Aligned_cols=64  Identities=39%  Similarity=0.580  Sum_probs=59.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++...
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           35 AFAPFGRISDARVVKDMATGKSKG--------------YGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             HHHhcCCeEEEEEEEcCCCCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            489999999999999988999999              9999999999999999999999999999999999877543

>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=99.74  E-value=6.2e-18  Score=95.86  Aligned_cols=63  Identities=30%  Similarity=0.534  Sum_probs=59.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++++.++.+|.++|              ||||+|.+.++|++|++.|||..++|+.|.|+++.++..
T Consensus        22 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           22 LCSNVGPVINLKMMFDPQTGRSKG--------------YAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             HHHTTSCEEEEECCBCTTTCCBCS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             HHHhcCCEEEEEEEeCCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            489999999999999998999999              999999999999999999999999999999999988764

>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=99.74  E-value=4.3e-18  Score=98.52  Aligned_cols=64  Identities=25%  Similarity=0.359  Sum_probs=60.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|+..|||..+.|+.|.|+++.++..+
T Consensus        46 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  109 (110)
T 1oo0_B           46 KFCDYGEIKNIHLNLDRRTGFSKG--------------YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  109 (110)
T ss_dssp             HHGGGSCEEEEECCBCTTTSSBCS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSCC
T ss_pred             HHHhcCCEEEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCCC
Confidence            489999999999999998999999              9999999999999999999999999999999999887654

>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=99.74  E-value=1.6e-17  Score=96.70  Aligned_cols=65  Identities=22%  Similarity=0.255  Sum_probs=57.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.|+.++.++.++.           ++|||||+|.++++|++|++.|||..++|+.|+|++|.++.
T Consensus        38 ~F~~~G~i~~v~i~~~~~~~~~~~-----------~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           38 YFGKFGKIHKVVINNSTSYAGSQG-----------PSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             TTTTTSCEEEEEEECCSSCCSSSC-----------CCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             HhhccCCEEEEEEecCCCcCccCC-----------CCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            699999999999999887654331           23399999999999999999999999999999999998876

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.2e-18  Score=96.75  Aligned_cols=65  Identities=29%  Similarity=0.483  Sum_probs=60.5

Q ss_pred             CccCCceeeEE-EEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v-~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++ +|+.++.++.++|              ||||+|.++++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        25 ~F~~~G~i~~~~~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   90 (96)
T 1x5t_A           25 TFSAFGVILQTPKIMRDPDTGNSKG--------------YAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG   90 (96)
T ss_dssp             HHHTTSCBSSCCEECCCTTTCSCCS--------------EEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCCC
T ss_pred             HHHhcCCeeEEEEEEEcCCCCCcCe--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCCC
Confidence            48999999999 9999988999999              99999999999999999999999999999999998876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=6.6e-18  Score=96.14  Aligned_cols=64  Identities=27%  Similarity=0.499  Sum_probs=59.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++ ||+..+.|+.|.|+++.++..+.
T Consensus        30 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           30 YFKKFGVVTEVVMIYDAEKQRPRG--------------FGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             HHSSSSCEEEEEECCCTTTCSCCS--------------EEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCCC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCCCc--------------eEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcccC
Confidence            489999999999999998999999              99999999999999999 99999999999999998876654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1e-17  Score=95.48  Aligned_cols=63  Identities=21%  Similarity=0.418  Sum_probs=59.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++ ++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++.++..+
T Consensus        37 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   99 (100)
T 2do4_A           37 ICKAHGTVKDLRLVTNR-AGKPKG--------------LAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS   99 (100)
T ss_dssp             HHTTTSCEEEEEEEECT-TSCEEE--------------EEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSCC
T ss_pred             HHHhCCCeEEEEEEECC-CCCEEe--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            48999999999999998 899999              9999999999999999999999999999999999987754

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.1e-18  Score=97.92  Aligned_cols=63  Identities=19%  Similarity=0.337  Sum_probs=59.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        43 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  105 (106)
T 1p27_B           43 KFAEYGEIKNIHLNLDRRTGYLKG--------------YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  105 (106)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEE--------------EEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESSC
T ss_pred             HHhccCCeEEEEEEecCCCCceee--------------EEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCCC
Confidence            489999999999999999999999              999999999999999999999999999999999988754

>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=99.73  E-value=8.5e-18  Score=95.58  Aligned_cols=63  Identities=21%  Similarity=0.292  Sum_probs=57.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|++||+|.+++|+.++.+   +|              ||||+|.++++|++|++.|||..++|+.|+|++|+++....|
T Consensus        33 ~F~~~G~v~~v~i~~~~~~---rg--------------~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~~   95 (96)
T 2dgx_A           33 AFARHGKVKSVELSPHTDY---QL--------------KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPSS   95 (96)
T ss_dssp             HHHHHSCEEEEEECSCCST---TC--------------CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSSCCCC
T ss_pred             hccccCcEEEEEEEeCCCC---Ce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCCCCC
Confidence            4889999999999999855   78              999999999999999999999999999999999988776543

>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=99.73  E-value=9e-18  Score=92.91  Aligned_cols=59  Identities=29%  Similarity=0.560  Sum_probs=56.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.|||..++|+.|+|++|+
T Consensus        27 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           27 AFIPFGDITDIQIPLDYETEKHRG--------------FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             HHGGGSCEEEEECCEETTTTEECS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHhccCCEEEEEEEECCCCCcccc--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            489999999999999988999999              99999999999999999999999999999999985

>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=99.73  E-value=7.7e-18  Score=93.62  Aligned_cols=64  Identities=23%  Similarity=0.411  Sum_probs=58.8

Q ss_pred             CccCCceeeEEEEEecCCCCC-cccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQ-SKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~-~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++.++. ++|              ||||+|.++++|++|++.|||..++|+.|.|+++.+...+
T Consensus        24 ~F~~~G~i~~~~i~~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~R   88 (88)
T 4a8x_A           24 IFSTYGKIKMIDMPVERMHPHLSKG--------------YAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR   88 (88)
T ss_dssp             HHHTTSCEEEEECCEETTEEEEECS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCCCC
T ss_pred             HHHhCCCEEEEEEEeCCCCCCCCCc--------------EEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCCCC
Confidence            489999999999999987766 888              9999999999999999999999999999999999887653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.8e-18  Score=97.32  Aligned_cols=64  Identities=27%  Similarity=0.396  Sum_probs=59.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+
T Consensus        33 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           33 VFEKYGRVGDVYIPREPHTKAPRG--------------FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD   96 (103)
T ss_dssp             HHTTTSCEEEEECCBCSSSCSBCS--------------CEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSC
T ss_pred             HHHhcCCEEEEEEEeCCCCCCCCe--------------EEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCC
Confidence            489999999999999998999999              9999999999999999999999999999999999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2e-17  Score=93.15  Aligned_cols=59  Identities=25%  Similarity=0.411  Sum_probs=56.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.|||..+.|+.|+|++|+
T Consensus        36 ~f~~~G~v~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           36 IFSKYGKVVKVTIMKDKDTRKSKG--------------VAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             HTTTTSCEEEEEECCCSSSCCCTT--------------CEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCccc--------------EEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            489999999999999998899999              99999999999999999999999999999999985

>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=99.72  E-value=1.3e-17  Score=97.68  Aligned_cols=62  Identities=35%  Similarity=0.602  Sum_probs=55.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|+|++++  +.++|              ||||+|.++++|++||+.|||..++|+.|.|+++.++..+
T Consensus        25 ~F~~~G~v~~v~i~~d~--~~~kg--------------~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~   86 (115)
T 4f25_A           25 TFSAFGNILSCKVVCDE--NGSKG--------------YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER   86 (115)
T ss_dssp             HHGGGSCEEEEEEEEET--TEEEE--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC-
T ss_pred             HHhccCCEEEEEEeecC--CCCCc--------------eEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcccc
Confidence            58999999999999986  34678              9999999999999999999999999999999999887643

>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=99.72  E-value=5.9e-18  Score=97.13  Aligned_cols=65  Identities=28%  Similarity=0.416  Sum_probs=60.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   99 (105)
T 1x5u_A           35 LFLQAGPVVNTHMPKDRVTGQHQG--------------YGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL   99 (105)
T ss_dssp             HHHTTSCEEEEECCBCSSSCSBCS--------------CEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCcCCc--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcCC
Confidence            489999999999999998999999              99999999999999999999999999999999998877643

>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=99.72  E-value=2.3e-17  Score=100.70  Aligned_cols=65  Identities=18%  Similarity=0.312  Sum_probs=60.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.+|.|+.++.++.++|              ||||+|.+.++|++||+.||+..|.|+.|.|++|.++...+
T Consensus        59 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  123 (156)
T 1h2v_Z           59 LFSKSGDIKKIIMGLDKMKKTACG--------------FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR  123 (156)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCTTC
T ss_pred             HHHhcCCeEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCcC
Confidence            589999999999999999999999              99999999999999999999999999999999998876544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=1.2e-17  Score=94.85  Aligned_cols=65  Identities=22%  Similarity=0.432  Sum_probs=59.0

Q ss_pred             CccCCceeeEEEEEecCC---CCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRA---TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~---~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++.   ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        25 ~F~~~G~i~~v~i~~~~~~~gt~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (98)
T 2cpf_A           25 VFSKVGAIKSCTISKKKNKAGVLLSMG--------------FGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK   90 (98)
T ss_dssp             HHHTTSCEEEEEEEEEECTTCCEEEEE--------------EEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSC
T ss_pred             HHHhcCCeEEEEEEecCCCCCCcCccc--------------EEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCC
Confidence            488999999999999886   568888              999999999999999999999999999999999988765


Q ss_pred             CC
Q psy16913         78 AR   79 (81)
Q Consensus        78 ~~   79 (81)
                      ..
T Consensus        91 ~~   92 (98)
T 2cpf_A           91 PA   92 (98)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.9e-17  Score=94.75  Aligned_cols=63  Identities=40%  Similarity=0.679  Sum_probs=58.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.+  ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        35 ~F~~~G~i~~v~i~~~--~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           35 AFSPFGTITSAKVMME--GGRSKG--------------FGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ   97 (103)
T ss_dssp             TTTTTSCEEEEEEEEC--SSSEEE--------------EEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCC
T ss_pred             HHHhcCCEEEEEEEcC--CCCcCE--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCC
Confidence            6999999999999998  788888              99999999999999999999999999999999998877654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=3.8e-18  Score=97.68  Aligned_cols=60  Identities=22%  Similarity=0.446  Sum_probs=55.6

Q ss_pred             CccCCce--eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc----EECCEEEEEEeeCC
Q psy16913          1 MFLPFGN--VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF----QIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~--i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~----~i~g~~i~V~~a~~   74 (81)
                      +|++||.  |.+|++++|+.||+++|              ||||+|.++++|++|++.|||.    .++||+|.|+||++
T Consensus        29 ~F~~~G~i~v~~v~i~~d~~tg~srG--------------~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           29 ALSPYASLAVNNIRLIKDKQTQQNRG--------------FAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             HSTTTCCCCGGGEECCCCSSSSSCSS--------------EEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             HHHhhCCccEEEEEEEecCCCCCCce--------------EeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            4899995  67999999999999999              9999999999999999999997    59999999999975

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.9e-17  Score=93.31  Aligned_cols=60  Identities=25%  Similarity=0.499  Sum_probs=57.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..++|+.|.|+++++
T Consensus        35 ~f~~~G~v~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           35 VFSKYGPIADVSIVYDQQSRRSRG--------------FAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             HHHTTSCEEEEEEEECSSSSSEEE--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             HHHhcCCeeEEEEEEcCCCCCccc--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            489999999999999998899999              999999999999999999999999999999999875

>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=99.72  E-value=1.4e-17  Score=96.31  Aligned_cols=65  Identities=26%  Similarity=0.455  Sum_probs=60.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC------CcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN------GFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln------g~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+|.|+.++.++.++|              ||||+|.+.++|++|++.||      |..++|+.|.|+++.+
T Consensus        35 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~  100 (111)
T 1x4h_A           35 VLQQFGDLKYVRVVLHPDTEHSKG--------------CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT  100 (111)
T ss_dssp             HHHTTSCEEEEECCBCSSSCCBCS--------------EEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCCcc--------------EEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCC
Confidence            489999999999999999999999              99999999999999999999      9999999999999988


Q ss_pred             CCCCC
Q psy16913         75 KDAAR   79 (81)
Q Consensus        75 ~~~~~   79 (81)
                      +..+.
T Consensus       101 ~~~~~  105 (111)
T 1x4h_A          101 RDEAA  105 (111)
T ss_dssp             CCCCC
T ss_pred             CccCC
Confidence            76643

>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=99.72  E-value=1.1e-17  Score=95.90  Aligned_cols=65  Identities=29%  Similarity=0.446  Sum_probs=60.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC---EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM---KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g---~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++ ++.++|              ||||+|.+.++|++|++.|||..+.|   +.|.|+++.++..
T Consensus        35 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~   99 (105)
T 2dnh_A           35 LFQPFGVIDECTVLRGP-DGSSKG--------------CAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE   99 (105)
T ss_dssp             HHTTTSCEEEEEEEECS-SSCEEE--------------EEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCC
T ss_pred             HHHhcCCeEEEEEEECC-CCCcCc--------------EEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcc
Confidence            58999999999999998 788899              99999999999999999999999998   9999999998877


Q ss_pred             CCC
Q psy16913         78 ARP   80 (81)
Q Consensus        78 ~~~   80 (81)
                      +.+
T Consensus       100 ~~~  102 (105)
T 2dnh_A          100 SGP  102 (105)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            654

>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=99.72  E-value=8e-18  Score=100.70  Aligned_cols=63  Identities=25%  Similarity=0.520  Sum_probs=60.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++|+.++.++.++|              ||||+|.+.++|++|++.|||..|+|+.|.|+++.++++
T Consensus        66 ~F~~~G~I~~v~i~~d~~tg~~~G--------------~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~p  128 (129)
T 2kxn_B           66 VFSKYGPIADVSIVYDQQSRRSRG--------------FAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP  128 (129)
T ss_dssp             HHTTTSCEEEEEEECCSSSSCCCC--------------EEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSSC
T ss_pred             HHHhcCCeEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            489999999999999998999999              999999999999999999999999999999999998765

>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=99.72  E-value=7.7e-18  Score=97.88  Aligned_cols=63  Identities=30%  Similarity=0.646  Sum_probs=59.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++.++.+
T Consensus        46 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~d  108 (108)
T 2jrs_A           46 IFEPFGRIESIQLMMDSETGRSKG--------------YGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD  108 (108)
T ss_dssp             HHTTTSCEEEEEEEEETTTTEEEE--------------EEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSCC
T ss_pred             HHHhcCCeEEEEEEEcCCCCccce--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCCC
Confidence            489999999999999998999999              999999999999999999999999999999999988753

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.3e-18  Score=97.27  Aligned_cols=65  Identities=32%  Similarity=0.553  Sum_probs=60.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.++++|++|++.|||..++|+.|+|+++.++...+
T Consensus        32 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   96 (102)
T 1x5s_A           32 VFSKYGQISEVVVVKDRETQRSRG--------------FGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR   96 (102)
T ss_dssp             HHHHHSCCCEEEECCCSSSCSCCS--------------EEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCCC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCccc--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            488999999999999998999999              99999999999999999999999999999999998876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=1.6e-17  Score=99.56  Aligned_cols=65  Identities=42%  Similarity=0.627  Sum_probs=60.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|+.||+|.+|+|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++.++..+.
T Consensus        62 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  126 (139)
T 1u6f_A           62 LFERYGPIESVKIVCDRETRQSRG--------------YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRP  126 (139)
T ss_dssp             HHHHHSCEEEEEEEEETTTTEEEE--------------EEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCCC
T ss_pred             HHHhcCCeEEEEEEEcCCCCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            488999999999999998999999              99999999999999999999999999999999998876654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.6e-17  Score=95.51  Aligned_cols=65  Identities=22%  Similarity=0.381  Sum_probs=60.3

Q ss_pred             CccCCceeeEEEEEec-CCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh-CCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFID-RATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~-~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l-ng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|+.+ +.++.++|              ||||+|.+.++|++|++.| ||..+.|+.|.|+++.++...
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           35 LFSTFGELKTVRLPKKMTGTGAHRG--------------FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV  100 (107)
T ss_dssp             HHHTTSCEEEEECCCCCSSSCSSCS--------------EEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCC
T ss_pred             HHHccCCeEEEEEecCCCCCCCcCc--------------eEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCC
Confidence            4899999999999999 78899999              9999999999999999999 999999999999999887654


Q ss_pred             C
Q psy16913         79 R   79 (81)
Q Consensus        79 ~   79 (81)
                      .
T Consensus       101 ~  101 (107)
T 2cph_A          101 Q  101 (107)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.71  E-value=3.6e-17  Score=91.17  Aligned_cols=61  Identities=23%  Similarity=0.401  Sum_probs=57.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|+ .|||..+.|+.|.|++++++.
T Consensus        26 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~~   86 (89)
T 3ucg_A           26 HFHGCGSVNRVTILCDKFSGHPKG--------------FAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTNR   86 (89)
T ss_dssp             HHGGGCCEEEEEEEESCSSSSCCE--------------EEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTTS
T ss_pred             HHHhCCCEEEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCCC
Confidence            489999999999999998999999              9999999999999999 899999999999999998754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=5.7e-17  Score=92.89  Aligned_cols=63  Identities=24%  Similarity=0.464  Sum_probs=58.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++|| |.+|.|+.++.++.++|              ||||+|.+.++|++|+ .|||..+.|+.|.|+++.++..+.
T Consensus        35 ~F~~~g-i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dng_A           35 IFKDLS-IRSVRLVRDKDTDKFKG--------------FCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDK   97 (103)
T ss_dssp             HTTTSC-EEEEEEEECSSSCSEEE--------------EEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCCC
T ss_pred             HHHhCC-ceEEEEeecCCCCccce--------------EEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCCC
Confidence            489997 99999999998999999              9999999999999999 899999999999999998876543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=6.1e-17  Score=94.12  Aligned_cols=60  Identities=20%  Similarity=0.223  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCC-CCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRAT-NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~-~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.|+.++.+ ++++|              ||||+|.++++|.+|++.|||..++||.|.|+++.+
T Consensus        33 ~f~~~G~V~~v~i~~~~~~~~~~~G--------------~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           33 ECEKYGKVGKCVIFEIPGAPDDEAV--------------RIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             HGGGGSCEEEEEEEECSSCCTTTSE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             HHHhcCCEEEEEEecCCCCCCCCcE--------------EEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            3899999999999998754 57888              999999999999999999999999999999999865

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.4e-17  Score=95.75  Aligned_cols=65  Identities=28%  Similarity=0.448  Sum_probs=60.3

Q ss_pred             CccCCceee--------EEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVI--------SSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~--------~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||.|.        .++|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus        35 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (113)
T 2cpe_A           35 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG--------------DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA  100 (113)
T ss_dssp             HHTTTSCBCBCSSSCCBSEECCBCTTTCSBCS--------------EEEEEBSSHHHHHHHHHHHTTCEETTEECEEECS
T ss_pred             HHHhcCCEeEccccCccCEEEEEeCCCCCeee--------------EEEEEECCHHHHHHHHHHcCCCccCCCEEEEEEC
Confidence            589999999        699999988999999              9999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q psy16913         73 RPKDAAR   79 (81)
Q Consensus        73 ~~~~~~~   79 (81)
                      .++..+.
T Consensus       101 ~~~~~~~  107 (113)
T 2cpe_A          101 RKKPPMN  107 (113)
T ss_dssp             SCCCCST
T ss_pred             CCCCCCC
Confidence            8876543

>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=99.70  E-value=1.7e-17  Score=101.19  Aligned_cols=65  Identities=31%  Similarity=0.466  Sum_probs=60.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.|+.+|.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        90 ~F~~~G~v~~~~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A           90 VFEKYGRVGDVYIPRDRYTKESRG--------------FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  154 (158)
T ss_dssp             HHHHHSCEEEEECCCCSSCTTSCC--------------EEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCCC
T ss_pred             HHHhcCCeEEEEEeecCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            488999999999999998999999              99999999999999999999999999999999998876543

>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=99.69  E-value=7.1e-17  Score=92.62  Aligned_cols=62  Identities=19%  Similarity=0.403  Sum_probs=57.9

Q ss_pred             CccCCceeeEEEEEecCCC-CCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRAT-NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~-~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++|| |.+|.|+.++.+ +.++|              ||||+|.+.++|++|+ .|||..+.|+.|.|+++.++..+
T Consensus        35 ~F~~~G-i~~v~i~~~~~~~g~~~g--------------~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           35 FFRGLN-ISAVRLPREPSNPERLKG--------------FGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             HTTTSC-EEEEECCBCSSCTTSBCS--------------CEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             HHHHCC-ceEEEEecCCCCCCCcCe--------------EEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence            589999 999999999987 89999              9999999999999999 89999999999999999887654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.69  E-value=4.2e-17  Score=95.33  Aligned_cols=59  Identities=78%  Similarity=1.237  Sum_probs=55.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.+++|+.++.++.++|              ||||+|.+.++|++|++.|||..++|+.|+|++++
T Consensus        60 ~F~~~G~i~~~~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           60 TFLPFGNVISAKVFIDKQTSLSKC--------------FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             HTTTSCEEEEEEECCCSSSSCCCC--------------EEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             HHHhcCCEEEEEEEeCCCCCCcCc--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            589999999999999998999999              99999999999999999999999999999999974

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=92.66  Aligned_cols=62  Identities=23%  Similarity=0.360  Sum_probs=57.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++ ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.+...
T Consensus        35 ~f~~~G~i~~~~i~~~~-~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   96 (114)
T 2do0_A           35 VFSMAGVVVRADILEDK-DGKSRG--------------IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP   96 (114)
T ss_dssp             HHTTTSCEEEEEEEECT-TCSEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCCC
T ss_pred             HHHhcCCeEEEEEEECC-CCCeee--------------EEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCCC
Confidence            58999999999999998 688888              999999999999999999999999999999999975443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.8e-17  Score=94.58  Aligned_cols=62  Identities=29%  Similarity=0.424  Sum_probs=57.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++|+.++.++.++|              ||||+|.+.++|++|++.+|+ .+.|+.|.|+++.++..
T Consensus        37 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           37 YFEGFGDIEEAVVITDRQTGKSRG--------------YGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAK   98 (116)
T ss_dssp             HHHTTSCEEEEEESCCSSSCCCCS--------------EEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCC
T ss_pred             HHHhCCCeeEEEEEEcCCCCccce--------------EEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCCC
Confidence            489999999999999998999999              999999999999999999998 89999999999966543

>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=99.69  E-value=1.5e-17  Score=95.56  Aligned_cols=65  Identities=22%  Similarity=0.296  Sum_probs=60.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE---CCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI---GMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i---~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+   .|+.|.|+++.++..
T Consensus        33 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           33 LFEEFGKIYELTVLKDRFTGMHKG--------------CAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             HHHHHSCCCEEECCCCSSSCSCCS--------------EEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSC
T ss_pred             HHHhcCCeeEEEEEecCCCCCcce--------------EEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCcccc
Confidence            488999999999999999999999              999999999999999999999998   899999999988765


Q ss_pred             CC
Q psy16913         78 AR   79 (81)
Q Consensus        78 ~~   79 (81)
                      +.
T Consensus        99 ~~  100 (106)
T 2dgp_A           99 GG  100 (106)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.69  E-value=9.6e-17  Score=91.84  Aligned_cols=63  Identities=27%  Similarity=0.396  Sum_probs=56.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.+|.|+.++.+  ++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..++
T Consensus        35 ~F~~~G~i~~v~i~~~~~~--~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2cqi_A           35 LFSQIGPCKSCKMITEHTS--NDP--------------YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK   97 (103)
T ss_dssp             HHHHHSCEEEEEEECCCCS--SCC--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCCC
T ss_pred             HHHhcCCEeEEEEEecCCC--CCC--------------EEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCcccc
Confidence            4889999999999998633  578              99999999999999999999999999999999998876544

>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=99.69  E-value=2.6e-17  Score=96.69  Aligned_cols=62  Identities=32%  Similarity=0.516  Sum_probs=58.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++ ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        27 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           27 VFGKHGPISEVLLIKDR-TSKSRG--------------FAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             HHHTSSCCSEEEEECST-TTTCCC--------------EEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             HHHhcCCEEEEEEEECC-CCCccc--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            48999999999999998 899999              999999999999999999999999999999999987653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=2.5e-17  Score=101.44  Aligned_cols=61  Identities=21%  Similarity=0.310  Sum_probs=58.1

Q ss_pred             CccCCc--eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G--~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||  .|.+|+|+.|+.+|+++|              ||||+|.+.++|++||+.|||..|+|+.|.|++|.++
T Consensus        75 ~F~~~G~i~v~~v~i~~d~~tg~skG--------------faFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           75 VIRSIGVYDVVELKFAENRANGQSKG--------------YAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             HHHHTTCCCEEEEEEEECTTTCCEEE--------------EEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             HHHHHCCccEEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            488999  999999999999999999              9999999999999999999999999999999999764

>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=99.69  E-value=1.8e-17  Score=97.85  Aligned_cols=64  Identities=19%  Similarity=0.333  Sum_probs=59.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++...
T Consensus        42 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           42 KFAEYGEIKNIHLNLDRRTGYLKG--------------YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             HHHTTSCEEEEECCBCTTTSSBCS--------------CEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             HHHhcCCeEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            489999999999999998999999              9999999999999999999999999999999999776543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=3.6e-17  Score=93.88  Aligned_cols=64  Identities=25%  Similarity=0.514  Sum_probs=59.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.+|.|+.++.++.++|              ||||+|.++++|++|+.. |+..++|+.|.|+++.++....
T Consensus        36 ~F~~~G~v~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~~   99 (105)
T 2dh8_A           36 YFSQYGEVVDCVIMKDKTTNQSRG--------------FGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQP   99 (105)
T ss_dssp             HHHTTSCEEEEEEEECSSSCCEEE--------------EEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSCCT
T ss_pred             HHHhcCCeEEEEEeeCCCCCCcce--------------EEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCCCC
Confidence            489999999999999998999999              999999999999999998 9999999999999998876543

>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=99.69  E-value=8.3e-17  Score=92.55  Aligned_cols=58  Identities=28%  Similarity=0.433  Sum_probs=55.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.|+.++ ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.
T Consensus        49 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           49 LFAEFGTLKKAAVHYDR-SGRSLG--------------TADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHTTSCEEEEEEEECT-TSCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHhcCCeEEEEEEECC-CCCcce--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            48899999999999998 899999              99999999999999999999999999999999986

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.69  E-value=1.2e-16  Score=94.14  Aligned_cols=62  Identities=21%  Similarity=0.362  Sum_probs=58.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|+ .|||..++|+.|.|+++++...
T Consensus        56 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~  117 (124)
T 2jwn_A           56 HFSSCGSINRITILCDKFSGHPKG--------------YAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMP  117 (124)
T ss_dssp             HHHTTSCEEEEEEEEECTTSSCEE--------------EEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCS
T ss_pred             HHHhcCCEEEEEEEecCCCCCccc--------------EEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCC
Confidence            489999999999999998999999              9999999999999999 7999999999999999987554

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.69  E-value=8.3e-17  Score=94.97  Aligned_cols=64  Identities=23%  Similarity=0.333  Sum_probs=59.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.+++|+.++ +|.++|              ||||+|.+.++|++|++.|||..+.|+.|+|++|.+.....
T Consensus        55 ~F~~~G~v~~v~i~~~~-~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  118 (124)
T 2kt5_A           55 LFAEFGTLKKAAVDYDR-SGRSLG--------------TADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE  118 (124)
T ss_dssp             HHHTTSCCSEEEEECCS-SSSCCS--------------EEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTCCC
T ss_pred             HHHhcCCeeEEEEEECC-CCCEee--------------EEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCCC
Confidence            48899999999999998 999999              99999999999999999999999999999999998876544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.9e-17  Score=94.00  Aligned_cols=64  Identities=22%  Similarity=0.391  Sum_probs=59.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++. |+..++|+.|.|+++.++....
T Consensus        47 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~~  110 (116)
T 1x4b_A           47 YYEQWGKLTDCVVMRDPASKRSRG--------------FGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG  110 (116)
T ss_dssp             HHTSSCCCSEEEEECCTTTSSCCS--------------EEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCCCC
T ss_pred             HHHhcCCEEEEEEEECCCCCCcCc--------------eEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCccCC
Confidence            589999999999999998999999              999999999999999997 9999999999999998887643

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.4e-17  Score=93.66  Aligned_cols=63  Identities=22%  Similarity=0.374  Sum_probs=59.2

Q ss_pred             CccCCceee-EEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEE----EEEEeeCCC
Q psy16913          1 MFLPFGNVI-SSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR----LKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~-~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~----i~V~~a~~~   75 (81)
                      +|++||+|. +++|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.    |+|++|.+.
T Consensus        29 ~F~~~G~i~~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           29 AFATMGETVMSVKIIRNRLTGIPAG--------------YCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             HHHHTTCCCCEEEEEECSSSCCEEE--------------EEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             HHHHhCCcceEEEEeecCCCCCcCC--------------EEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            488999999 999999999999999              9999999999999999999999999999    999999886


Q ss_pred             CC
Q psy16913         76 DA   77 (81)
Q Consensus        76 ~~   77 (81)
                      ..
T Consensus        95 ~~   96 (99)
T 2div_A           95 GP   96 (99)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=3.1e-17  Score=93.40  Aligned_cols=59  Identities=31%  Similarity=0.447  Sum_probs=56.3

Q ss_pred             CccCCceeeE--------EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVIS--------SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~--------v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||.|.+        ++++.++.+|.++|              ||||+|.+.++|++|++.|||..+.|+.|+|++|
T Consensus        33 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           33 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKG--------------EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             HHTTTSCBCEETTTTEESEEEEECTTTCSEEE--------------EEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             HHHHhCCEeeccccccccEEEEecCCCCCeee--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            4899999999        99999998999999              9999999999999999999999999999999998


Q ss_pred             C
Q psy16913         73 R   73 (81)
Q Consensus        73 ~   73 (81)
                      +
T Consensus        99 ~   99 (99)
T 2la6_A           99 T   99 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1.2e-16  Score=92.85  Aligned_cols=63  Identities=27%  Similarity=0.443  Sum_probs=58.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.++.+|.++|              ||||+|.+.++|++|+..+ +..++|+.|.|+++.++..+
T Consensus        45 ~F~~~G~i~~v~i~~~~~tg~~kg--------------~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           45 YFGQFGEVKECLVMRDPLTKRSRG--------------FGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             HHTTTSCEEEEEECCCTTTCCCTT--------------CEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCCC
T ss_pred             HHHccCCeEEEEEEECCCCCCcCc--------------EEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCCC
Confidence            489999999999999998999999              9999999999999999976 59999999999999987764

>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=99.68  E-value=2.3e-16  Score=90.20  Aligned_cols=62  Identities=27%  Similarity=0.533  Sum_probs=56.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.++.  .++|              ||||+|.+.++|++|+..|||..+.|+.|.|+++.++...
T Consensus        35 ~f~~~G~v~~v~i~~~~~--~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           35 MFGQFGKILDVEIIFNER--GSKG--------------FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             HGGGTSCEEEEEEECCTT--TTCC--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             HHHhcCCeEEEEEEecCC--CCcE--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            589999999999999863  3788              9999999999999999999999999999999999887654

>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=99.68  E-value=2e-17  Score=94.66  Aligned_cols=63  Identities=25%  Similarity=0.503  Sum_probs=59.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        28 ~f~~~G~i~~~~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           28 IFSEVGPVVSFRLVYDRETGKPKG--------------YGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             HHHTTSCCSEEEEEEETTTTEEEE--------------EEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTH
T ss_pred             HHHhcCCeeEEEEEeCCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccc
Confidence            488999999999999998999999              999999999999999999999999999999999988754

>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=99.68  E-value=9.5e-17  Score=90.48  Aligned_cols=59  Identities=31%  Similarity=0.528  Sum_probs=55.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.|+.++. +.++|              ||||+|.++++|++|++.|||..+.|+.|.|++++.
T Consensus        36 ~F~~~G~i~~v~i~~~~~-g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           36 LFLQAGPLTKVTICKDRE-GKPKS--------------FGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             HHGGGSCEEEEEEEECTT-SCEEE--------------EEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             HHHhcCCEEEEEEEECCC-CCCce--------------EEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            489999999999999984 88888              999999999999999999999999999999999864

>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=99.68  E-value=7.8e-17  Score=99.38  Aligned_cols=63  Identities=25%  Similarity=0.366  Sum_probs=58.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|..|.|+.++.+|.++|              ||||+|.+.++|+.||..|||..|.|+.|.|.|+.++..
T Consensus        92 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           92 KFCDYGEIKNIHLNLDRRTGFSKG--------------YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HhhcCCCEEEEEEEecCCCCcEee--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            589999999999999998999999              999999999999999999999999999999999977654

>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=99.68  E-value=1.1e-17  Score=93.66  Aligned_cols=63  Identities=29%  Similarity=0.524  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.+ |++|+..|||..++|+.|.|++|.++...
T Consensus        21 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           21 LFSQFGKVFNVKLIYDRETKKPKG--------------FGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKSL   83 (90)
T ss_dssp             THHHHTCCSEEEECCCSSSCCCCE--------------EEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC------
T ss_pred             HHHhcCCEEEEEEEEcCCCCCcce--------------EEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            589999999999999998999999              9999999999 99999999999999999999999876543

>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=99.68  E-value=4.1e-17  Score=92.57  Aligned_cols=62  Identities=18%  Similarity=0.261  Sum_probs=57.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.|||..+.|+.|+|+++..+.
T Consensus        35 ~F~~~G~v~~~~~~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (98)
T 2cqp_A           35 FFYGYQVIPGSVCLKYNEKGMPTG--------------EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS   96 (98)
T ss_dssp             HTTTSCCCTTTCEEEECSSSCEEE--------------EEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCSS
T ss_pred             HHHHcCCccceEEEEECCCCCeee--------------EEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCCC
Confidence            589999999999999998999999              99999999999999999999999999999999997654

>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=99.67  E-value=5e-17  Score=94.62  Aligned_cols=61  Identities=25%  Similarity=0.355  Sum_probs=57.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.|.+|.|+.++.++.++|              ||||+|.+.++|++|+ .|||..+.|+.|.|+++.++.
T Consensus        45 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           45 FFSAVGKVRDVRIISDRNSRRSKG--------------IAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEK  105 (114)
T ss_dssp             HHTTTSCEEEEEECCSCCSSSCCC--------------CEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHH
T ss_pred             HHHhCCCEeEEEEEecCCCCccCc--------------EEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCc
Confidence            589999999999999998999999              9999999999999999 899999999999999997654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.7e-17  Score=93.63  Aligned_cols=63  Identities=27%  Similarity=0.518  Sum_probs=58.6

Q ss_pred             CccC-CceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcE-ECCEEEEEEeeCCCCCC
Q psy16913          1 MFLP-FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ-IGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~-~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~-i~g~~i~V~~a~~~~~~   78 (81)
                      +|++ ||+|.++.|+.++ ++.++|              ||||+|.+.++|++|++.|||.. +.|+.|.|+++.++..+
T Consensus        29 ~F~~~~G~v~~v~i~~~~-~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           29 FFVKVYPSCRGGKVVLDQ-TGVSKG--------------YGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR   93 (104)
T ss_dssp             HHHHHCTTEEEEEEEECT-TCCEEE--------------EEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSC
T ss_pred             HHHHhCCCeEEEEEEECC-CCCccc--------------eEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcC
Confidence            4788 9999999999998 999999              99999999999999999999999 99999999999877654

>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=99.66  E-value=6e-17  Score=92.62  Aligned_cols=60  Identities=18%  Similarity=0.407  Sum_probs=56.4

Q ss_pred             CccCCceeeEEEEEecC-CCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDR-ATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~-~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++|| |.++.|+.++ .+|+++|              ||||+|.+.++|++|+ .|||..+.|+.|.|+++.++.
T Consensus        39 ~F~~~G-i~~v~i~~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           39 FFRGLN-ISAVRLPREPSNPERLKG--------------FGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             HSCSSC-EEEEECSCCTTTTCCCCS--------------CEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             HHHhcC-CeEEEEEecCCcCCccCe--------------EEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            489999 9999999998 6899999              9999999999999999 899999999999999998875

>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=99.66  E-value=8e-17  Score=90.79  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=56.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.|||..+.|+.|+|+++.+
T Consensus        35 ~F~~~G~i~~~~~~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           35 FFYGYQVIPGSVCLKYNEKGMPTG--------------EAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             HTTTSCBCTTCCEEEECTTSCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             HHHhcCCccceEEEEeCCCCCEee--------------EEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            489999999999999998999999              999999999999999999999999999999998864

>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=99.66  E-value=1.6e-16  Score=92.04  Aligned_cols=55  Identities=16%  Similarity=0.178  Sum_probs=51.8

Q ss_pred             cCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         3 ~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      ++||+|.++.|++++ +++++|              ||||+|.++++|++|+..|||..++||.|.|+++
T Consensus        49 ~~~G~V~~v~i~~~~-~~~~~G--------------~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           49 EKYGEVEEMNVCDNL-GDHLVG--------------NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHTCCEEEEEECCSS-SSSSEE--------------EEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             ccCCceEEEEEEeCC-CCCccE--------------EEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            899999999999886 477888              9999999999999999999999999999999986

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3e-17  Score=90.97  Aligned_cols=59  Identities=31%  Similarity=0.612  Sum_probs=55.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.++++|++|++.|||..++|+.|+++++.
T Consensus        25 ~f~~~G~i~~~~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           25 LCQPYGKIVSTKAILDKTTNKCKG--------------YGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             TSTTTSCEEEEEEECCSSSCSCCS--------------EEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCcCc--------------EEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            699999999999999998999999              99999999999999999999999999999887764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=9.1e-17  Score=92.67  Aligned_cols=61  Identities=21%  Similarity=0.445  Sum_probs=55.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCE-EEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK-RLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~-~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+  +.+|.++|              ||||+|.+.++|++|+..|||..+.|+ .|.|+++...+.
T Consensus        41 ~F~~~G~v~~v~i~--~~~g~~~G--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~k  102 (105)
T 2nlw_A           41 IFSKFGKITNDFYP--EEDGKTKG--------------YIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDK  102 (105)
T ss_dssp             HHGGGSCEEEEECC--CBTTBSCC--------------EEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCCC
T ss_pred             HHhcCCCEEEEEee--CCCCCeee--------------EEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHhh
Confidence            48999999999988  45889999              999999999999999999999999998 999999976543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.65  E-value=1.6e-16  Score=90.19  Aligned_cols=53  Identities=11%  Similarity=0.252  Sum_probs=49.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      ||++||+|.+++++.      ++|              ||||+|.++++|++|++.||+..+.|++|+|++|.
T Consensus        27 lF~q~G~V~~~~l~~------~kG--------------faFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           27 LCMQHGPLVSFHPYL------NQG--------------IALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             HHHHHSCEEEEEEET------TTT--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             HHHhhCCEEEEEEcC------CCc--------------EEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            589999999999865      578              99999999999999999999999999999999984

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.65  E-value=1.5e-16  Score=89.22  Aligned_cols=63  Identities=25%  Similarity=0.497  Sum_probs=57.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++.+  ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++....
T Consensus        28 ~f~~~G~v~~~~i~~~--~g~~~g--------------~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~~   90 (92)
T 2dgv_A           28 KFNECGHVLYADIKME--NGKSKG--------------CGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPS   90 (92)
T ss_dssp             HHHTTSCEEEEEEEES--SSCEEE--------------EEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSSCC
T ss_pred             HHHhcCCEEEEEEEcc--CCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCCCC
Confidence            4889999999999984  788888              99999999999999999999999999999999998876543

>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=99.65  E-value=3.5e-16  Score=90.84  Aligned_cols=60  Identities=17%  Similarity=0.132  Sum_probs=54.1

Q ss_pred             CccCCceeeEEEEEecCCCC--CcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATN--QSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~--~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      .|++||+|.++.|++++.++  +++|              |+||+|.++++|.+|++.|||..++||.|.|.++.+
T Consensus        35 ~f~k~G~V~~v~i~~~~~~~~~~~~G--------------~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           35 ECSKYGLVKSIEIPRPVDGVEVPGCG--------------KIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHHTTSCEEEEECCCCBTTBCCTTTT--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHHccCCEEEEEEeccCCCCCcCCcE--------------EEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCH
Confidence            37899999999999987553  5677              999999999999999999999999999999999854

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.65  E-value=1.9e-16  Score=94.49  Aligned_cols=58  Identities=29%  Similarity=0.555  Sum_probs=54.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+++++.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|+|++|
T Consensus        83 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           83 AFIPFGDITDIQIPLDYETEKHRG--------------FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHGGGSCEEEEECCCCTTTCCCCS--------------EEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             HHHhcCCEEEEEEeecCCCCCcCc--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            489999999999999998999999              9999999999999999999999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=4.4e-17  Score=98.02  Aligned_cols=64  Identities=31%  Similarity=0.474  Sum_probs=60.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|++++++..+
T Consensus        67 ~F~~~G~i~~v~i~~~~~~g~~~G--------------~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           67 VFEKYGRVGDVYIPRDRYTKESRG--------------FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             HHGGGSCCSEEECCCCSSSSSCCS--------------CCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             HHHhcCCEEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            489999999999999998999999              9999999999999999999999999999999999887654

>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=99.65  E-value=3.7e-16  Score=90.81  Aligned_cols=61  Identities=28%  Similarity=0.523  Sum_probs=56.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE--------CCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI--------GMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i--------~g~~i~V~~a   72 (81)
                      +|++||+|.+++|+.++ ++.++|              ||||+|.+.++|++|++.|||..+        .+++|.|.+|
T Consensus        45 ~F~~~G~i~~~~i~~~~-~g~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a  109 (114)
T 1x5o_A           45 MLKPFGQVISTRILRDS-SGTSRG--------------VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFS  109 (114)
T ss_dssp             TTTTTSCEEEEEEEECS-SSCEEE--------------EEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEEC
T ss_pred             HHHhcCCEEEEEEEECC-CCCcce--------------EEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEcc
Confidence            69999999999999998 899999              999999999999999999999999        5788999999


Q ss_pred             CCCC
Q psy16913         73 RPKD   76 (81)
Q Consensus        73 ~~~~   76 (81)
                      .|+.
T Consensus       110 ~p~~  113 (114)
T 1x5o_A          110 GPSS  113 (114)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8753

>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=99.65  E-value=4.8e-16  Score=86.39  Aligned_cols=57  Identities=23%  Similarity=0.476  Sum_probs=53.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|++|++ +++..++|+.|.|++|
T Consensus        31 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           31 YFTKFGEVVDCTIKMDPNTGRSRG--------------FGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             HHHhCCCEEEEEEeecCCCCcccc--------------EEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            489999999999999998999999              99999999999999996 5889999999999986

>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=99.65  E-value=7.1e-16  Score=88.16  Aligned_cols=62  Identities=27%  Similarity=0.393  Sum_probs=57.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.++.++.++|              ||||+|.+.++|++|+.  ++..++|+.|.|+++.++...
T Consensus        35 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           35 YFSTFGEVLMVQVKKDLKTGHSKG--------------FGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             HHGGGSCEEEEEEEECSSSCSEEE--------------EEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCccc--------------eEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            489999999999999998999999              99999999999999999  578999999999999887653

>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=99.65  E-value=1.1e-16  Score=92.33  Aligned_cols=63  Identities=16%  Similarity=0.250  Sum_probs=57.7

Q ss_pred             CccCCce-eeEEEEE-ecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC--CcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGN-VISSKVF-IDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN--GFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~-i~~v~i~-~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln--g~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+ |.++.++ .++.++.++|              ||||+|.+.++|+.|+..||  +..+.|+.|.|++|.++.
T Consensus        28 ~f~~~G~~v~~v~i~~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           28 EIAKVTEGVLDVIVYASAADKMKNRG--------------FAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             HHHHHSTTEEEEECCSSSCTTTTTCC--------------EEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             HHHHhcCCceEEEEEccCCCCCCcCc--------------EEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCC
Confidence            4789998 9999998 8888889999              99999999999999999996  589999999999998876


Q ss_pred             C
Q psy16913         77 A   77 (81)
Q Consensus        77 ~   77 (81)
                      .
T Consensus        94 ~   94 (109)
T 2dis_A           94 D   94 (109)
T ss_dssp             S
T ss_pred             C
Confidence            5

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=9.6e-17  Score=96.13  Aligned_cols=60  Identities=13%  Similarity=0.310  Sum_probs=54.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|.+..   +++++|              ||||+|.+.++|+.|+..|||..+.|++|+|+||.++..
T Consensus        53 ~F~~~G~I~~v~i~~---~~~~rG--------------~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           53 LASSQGDILDIVVDL---SDDNSG--------------KAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             HHHHHSCEEEEEECC---CCSSCC--------------CEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCH
T ss_pred             HhccCCCeEEEEecc---CCCcCC--------------EEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcch
Confidence            489999999987753   678888              999999999999999999999999999999999987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=3.6e-17  Score=88.77  Aligned_cols=57  Identities=25%  Similarity=0.465  Sum_probs=54.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++ |||..++|++|.|++|
T Consensus        19 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           19 YFEQFGKVDDAMLMFDKTTNRHRG--------------FGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHTTSCCSEECCCBCSSSTTSCB--------------EEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             HHHhcCCEEEEEEEecCCCCCcCc--------------EEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            488999999999999998999999              99999999999999998 9999999999999976

>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=99.64  E-value=8.9e-16  Score=88.64  Aligned_cols=62  Identities=23%  Similarity=0.452  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.+   +.++|              ||||+|.+.++|++|++.||+..++|+.|.|+++.++....
T Consensus        42 ~F~~~G~v~~~~i~~~---~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  103 (109)
T 1x4a_A           42 VFYKYGAIRDIDLKNR---RGGPP--------------FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG  103 (109)
T ss_dssp             HHGGGSCEEEEEECCS---SSSSC--------------CEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCCC
T ss_pred             HHHhcCCeEEEEEEEC---CCCCc--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCCC
Confidence            5899999999998654   45788              99999999999999999999999999999999998876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.64  E-value=7.5e-16  Score=93.00  Aligned_cols=60  Identities=28%  Similarity=0.498  Sum_probs=57.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|.+|+..|||..++|+.|.|+||++
T Consensus       107 ~f~~~G~i~~~~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          107 AFKDFPSYLSGHVMWDMQTGSSRG--------------YGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHTTSTTEEEEEEEECTTTCCEEE--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHhccCCeeEEEEEecCCCCCcce--------------EEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            489999999999999988999999              999999999999999999999999999999999864

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=9.2e-16  Score=85.97  Aligned_cols=60  Identities=17%  Similarity=0.331  Sum_probs=55.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++| .|.+++|+.+ .+|+++|              ||||+|.+.++|++|+. |||..+.|+.|.|.++.++..
T Consensus        30 ~F~~~-~i~~v~i~~~-~~g~~~g--------------~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~~   89 (91)
T 2dgw_A           30 FLAPL-KPVAIRIVRN-AHGNKTG--------------YIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGPS   89 (91)
T ss_dssp             HHTTS-CCSEEEEEEC-TTSCEEE--------------EEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCCC
T ss_pred             HHhhC-CceEEEEEEC-CCCCCce--------------EEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCCC
Confidence            48899 9999999999 6899999              99999999999999999 999999999999999988754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.63  E-value=2.7e-17  Score=98.15  Aligned_cols=62  Identities=19%  Similarity=0.389  Sum_probs=58.0

Q ss_pred             CccCCceeeE--EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc----EECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVIS--SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF----QIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~--v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~----~i~g~~i~V~~a~~   74 (81)
                      +|++||.|..  |+|++|+.+|+++|              ||||+|.+. +|.+|+..|||.    .++|+.|.|+++.+
T Consensus        43 ~F~~~G~v~~~~v~i~~d~~tg~~rG--------------~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~  107 (131)
T 2m2b_A           43 ALAPYAVLSSSNVRVIKDKQTQLNRG--------------FAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKG  107 (131)
T ss_dssp             HHGGGCCCCTTTEECCBCSSSSSBCS--------------CEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCC
T ss_pred             HHHHhCCcceeeEEEEEcCCCCCcce--------------EEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCC
Confidence            4899999977  99999999999999              999999999 999999999999    99999999999988


Q ss_pred             CCC
Q psy16913         75 KDA   77 (81)
Q Consensus        75 ~~~   77 (81)
                      +..
T Consensus       108 ~~~  110 (131)
T 2m2b_A          108 SKR  110 (131)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=2.4e-17  Score=96.31  Aligned_cols=64  Identities=28%  Similarity=0.406  Sum_probs=59.8

Q ss_pred             CccCCceeeE--------EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVIS--------SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~--------v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+        +.|+.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++
T Consensus        27 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   92 (116)
T 2lcw_A           27 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKG--------------EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   92 (116)
Confidence            5899999999        99999988999999              9999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy16913         73 RPKDAA   78 (81)
Q Consensus        73 ~~~~~~   78 (81)
                      .++..+
T Consensus        93 ~~~~~~   98 (116)
T 2lcw_A           93 TRRADF   98 (116)
Confidence            887654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2e-15  Score=85.63  Aligned_cols=59  Identities=31%  Similarity=0.520  Sum_probs=52.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|.      .++|              ||||+|.+.++|++|+..|||..+.|+.|.|+++.++....
T Consensus        33 ~F~~~G~i~~v~i~------~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~   91 (97)
T 1x5p_A           33 AFSPFGNIIDLSMD------PPRN--------------CAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD   91 (97)
T ss_dssp             HHTTTSCEEEEEEE------TTTT--------------EEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCCC
T ss_pred             HHhhCCCEEEEEec------CCCC--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCCC
Confidence            58999999999984      4577              99999999999999999999999999999999998876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=1.5e-16  Score=86.47  Aligned_cols=58  Identities=26%  Similarity=0.419  Sum_probs=54.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++.+| ..++|+.|.|++|.
T Consensus        20 ~F~~~G~v~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a~   77 (77)
T 1uaw_A           20 YFGQFGEVKECLVMRDPLTKRSRG--------------FGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAF   77 (77)
T ss_dssp             HHTTTSCCCCEEEECCCCSSSCSS--------------EEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEECC
T ss_pred             HHHhcCCEEEEEEecCCCCCCcCc--------------eEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEecC
Confidence            489999999999999998999999              99999999999999999999 99999999999873

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=5e-16  Score=90.11  Aligned_cols=60  Identities=28%  Similarity=0.556  Sum_probs=55.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++++.++  +.++|              ||||+|.+.++|++|++.|||..++|+.|.|+++.++.
T Consensus        49 ~F~~~G~i~~v~i~~~~--~~~kg--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  108 (109)
T 2err_A           49 MFGQFGKILDVEIIFNE--RGSKG--------------FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV  108 (109)
T ss_dssp             HGGGTCCCSCEEECCBT--TBCTT--------------EEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCSC
T ss_pred             HHHhcCCEEEEEEEECC--CCCce--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCc
Confidence            58999999999999886  34788              99999999999999999999999999999999998863

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.6e-16  Score=90.99  Aligned_cols=58  Identities=21%  Similarity=0.162  Sum_probs=54.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+|.|++++. +.++|              ||||+|.++++|++|+. +||..++|+.|.|.++..
T Consensus        31 ~F~~~G~v~~v~i~~d~~-g~~rG--------------~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           31 WLEDKGQVLNIQMRRTLH-KAFKG--------------SIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             HHHTSSCEEEEEEECCCT-TSCCC--------------EEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             HHhhcCCEEEEEEEECCC-CCCcc--------------EEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            489999999999999986 89999              99999999999999999 999999999999998743

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.62  E-value=8.3e-16  Score=96.59  Aligned_cols=64  Identities=27%  Similarity=0.490  Sum_probs=60.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.+.++|.+|++.|||..++|+.|.|+++.++...
T Consensus       145 ~f~~~G~v~~v~i~~~~~~g~~~g--------------~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          145 VFEAFGKIKSATLARDPTTGKHKG--------------YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             HHTTSSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             HHhccCCeeEEEEEecCCCCCcCc--------------eEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            489999999999999998999999              9999999999999999999999999999999999887543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.62  E-value=2.3e-16  Score=102.18  Aligned_cols=60  Identities=22%  Similarity=0.292  Sum_probs=57.4

Q ss_pred             CccCCc--eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFG--NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G--~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||  +|.+|+|++|+.+++++|              ||||+|.+.++|++||+.|||..|.|+.|+|++|.+
T Consensus        88 ~F~~~G~~~v~~v~i~~d~~tg~skG--------------faFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C           88 AVHSLGVNDILEIKFFENRANGQSKG--------------FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             HHHTTTCCCEEEEEEEECTTTCCEEE--------------EEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             HHHHHCCcceEEEEEEecCCCCccce--------------EEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            589999  999999999999999999              999999999999999999999999999999999864

>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=99.62  E-value=1.2e-15  Score=90.38  Aligned_cols=59  Identities=22%  Similarity=0.300  Sum_probs=53.3

Q ss_pred             ccCCceeeEEEEEecCC----CCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRA----TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~----~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |++||+|.+|.|++++.    ++.++|              |+||+|.++++|.+|++.|||..++||.|.|.++..
T Consensus        46 f~k~G~V~~v~I~~~~~~~~~~~~~~G--------------~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           46 CGKFGAVNRVIIYQEKQGEEEDAEIIV--------------KIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             HTTTSCEEEEEEEEEEESSSTTCEEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HhccCCEeEEEEeecCCCcccCCcceE--------------EEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCh
Confidence            78999999999999874    345667              999999999999999999999999999999999854

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.62  E-value=1.1e-15  Score=94.87  Aligned_cols=64  Identities=28%  Similarity=0.412  Sum_probs=60.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|.+|++.|||..++|+.|.|+++.++..+
T Consensus       134 ~f~~~G~v~~~~~~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  197 (198)
T 2yh0_A          134 LLTSFGPLKAFNLVKDSATGLSKG--------------YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN  197 (198)
T ss_dssp             HHHTBSCEEEEEEEECTTTCSEEE--------------EEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCCC
T ss_pred             HHHHcCCccEEEEeecCCCCCcce--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            488999999999999988999999              9999999999999999999999999999999999987653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.8e-15  Score=86.16  Aligned_cols=60  Identities=22%  Similarity=0.379  Sum_probs=53.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|   +++.+ .++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++...
T Consensus        35 ~F~~~g~v---~~~~~-~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           35 VFEKATFI---KVPQN-QNGKSKG--------------YAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             HCSSCSEE---ECCBC-SSSCBCS--------------EEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             HHHhCCEE---EEEEC-CCCCEee--------------EEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            48899987   56666 5788899              9999999999999999999999999999999999887654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4.3e-15  Score=84.64  Aligned_cols=62  Identities=29%  Similarity=0.471  Sum_probs=55.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|+.|   ..+.++.++.++.++|              ||||+|.+.++|++|++.|||..|.|+.|.|++++++..+.
T Consensus        35 ~F~~~---~~~~~~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2fc8_A           35 SFDGS---VRARIVTDRETGSSKG--------------FGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGG   96 (102)
T ss_dssp             TSTTC---SEEEEEECSSSCSEEE--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSSS
T ss_pred             HhcCC---eEEEEEecCCCCCcCc--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCCC
Confidence            46655   4678888988999999              99999999999999999999999999999999999887643

>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=99.61  E-value=1.4e-15  Score=88.08  Aligned_cols=56  Identities=16%  Similarity=0.241  Sum_probs=50.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc--EECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF--QIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~--~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+|.|+++      +|              ||||+|.+.++|+.|++.||+.  .+.|++|+|++|+++.
T Consensus        36 lF~~fG~V~~v~i~~~------kg--------------~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           36 LVEPFGVISNHLILNK------IN--------------EAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             TTGGGSCEEEEEECSS------SS--------------CEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             HHHhcCCEEEEEEEcC------CC--------------EEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            6999999999999865      47              9999999999999999999864  5999999999998654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.60  E-value=1.7e-16  Score=87.50  Aligned_cols=54  Identities=20%  Similarity=0.497  Sum_probs=49.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCE-EEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK-RLKVQ   70 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~-~i~V~   70 (81)
                      +|++||+|.++.|+  +.+|+++|              ||||+|.++++|++|++.|||..++|+ +|+|+
T Consensus        27 ~F~~~G~i~~v~i~--~~~g~~~g--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           27 IFSKFGKITNDFYP--EEDGKTKG--------------YIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             HHHTTCCEEEEECC--CBTTBCCC--------------EEEEEESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             HHhhcCCeEEEEec--CCCCcEeE--------------EEEEEECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            48999999999987  45889999              999999999999999999999999999 88763

>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=99.60  E-value=1.7e-15  Score=87.51  Aligned_cols=59  Identities=31%  Similarity=0.491  Sum_probs=53.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.|+.+      +|              ||||+|.+.++|++|+..|||..+.|+.|.|.++.++....
T Consensus        45 ~F~~~G~i~~v~i~~~------~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  103 (109)
T 1x4g_A           45 TFSPFGQIMEIRVFPE------KG--------------YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMT  103 (109)
T ss_dssp             HHHHHSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSSC
T ss_pred             HHHhcCCeEEEEEeCC------CC--------------EEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCCC
Confidence            4889999999999876      67              99999999999999999999999999999999998876543

>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=99.60  E-value=2.4e-15  Score=91.14  Aligned_cols=63  Identities=30%  Similarity=0.534  Sum_probs=59.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.++++|++|++.|||..+.|+.|.|.++.++..
T Consensus        23 ~f~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   85 (168)
T 1b7f_A           23 LFRAIGPINTCRIMRDYKTGYSYG--------------YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE   85 (168)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS
T ss_pred             HHHhcCCeeEEEEEEeCCCCccce--------------EEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc
Confidence            488999999999999998999999              999999999999999999999999999999999987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.60  E-value=7.9e-16  Score=92.89  Aligned_cols=60  Identities=17%  Similarity=0.258  Sum_probs=53.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcC----HHH----HHHHHH--hhCCcEECCEEEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDN----PAS----AHTAIQ--AMNGFQIGMKRLKVQ   70 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~----~~~----A~~Ai~--~lng~~i~g~~i~V~   70 (81)
                      +|++||+|.++.++.|+.||.++|              ||||+|.+    +++    |.+|+.  .+||..|+|+.|+|+
T Consensus        26 ~Fs~fGeV~~~~li~Dp~Tg~slG--------------fgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~   91 (136)
T 2j8a_A           26 YFKKYGEISHFEAFNDPNSALPLH--------------VYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVI   91 (136)
T ss_dssp             HHHTTSCCSEEEEEECTTTCCEEE--------------EEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEE
T ss_pred             HHHhcCCeEEEEEEecCCCCceee--------------EEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEE
Confidence            489999999999999999999999              99999996    444    788988  799999999999999


Q ss_pred             eeCC
Q psy16913         71 LKRP   74 (81)
Q Consensus        71 ~a~~   74 (81)
                      +.+.
T Consensus        92 ln~~   95 (136)
T 2j8a_A           92 LNKH   95 (136)
T ss_dssp             ECCT
T ss_pred             ECcc
Confidence            8754

>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=99.60  E-value=2.8e-15  Score=86.64  Aligned_cols=57  Identities=18%  Similarity=0.329  Sum_probs=52.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC-----EEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM-----KRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g-----~~i~V~~a~~~   75 (81)
                      +|++||+|.++.|+.+       |              ||||+|.+.++|++||+.|||..+.|     +.|+|++|.++
T Consensus        35 ~F~~~G~i~~~~i~~~-------g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~   93 (108)
T 1x4c_A           35 HMREAGDVCYADVYRD-------G--------------TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   93 (108)
T ss_dssp             HHGGGSCEEEEEEETT-------T--------------EEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCC
T ss_pred             HHHhcCCEeEEEEecC-------C--------------EEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCC
Confidence            5899999999999876       7              99999999999999999999999999     99999999887


Q ss_pred             CCC
Q psy16913         76 DAA   78 (81)
Q Consensus        76 ~~~   78 (81)
                      ...
T Consensus        94 ~~~   96 (108)
T 1x4c_A           94 SPS   96 (108)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.60  E-value=2.9e-15  Score=90.49  Aligned_cols=63  Identities=37%  Similarity=0.636  Sum_probs=59.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.++++|++|++.|||..+.|+.|.|.++.+...
T Consensus        22 ~f~~~G~i~~v~~~~~~~~~~~~g--------------~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   84 (167)
T 1fxl_A           22 LFGSIGEIESCKLVRDKITGQSLG--------------YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA   84 (167)
T ss_dssp             HHHTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG
T ss_pred             HHHhcCCeEEEEEEeCCCCCccee--------------EEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Confidence            488999999999999998999999              999999999999999999999999999999999987653

>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=99.60  E-value=3.1e-15  Score=87.14  Aligned_cols=59  Identities=24%  Similarity=0.337  Sum_probs=52.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|.| .++   .++|              ||||+|.+.++|++|+..|||..++|+.|.|+++.++..
T Consensus        46 ~f~~~G~v~~v~i-~~~---~~~G--------------~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           46 ECSKFGQIRKLLL-FDR---HPDG--------------VASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             HGGGTSCCSEEEE-ETT---CTTC--------------EEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             HHHccCCEeEEEE-ecC---CCCE--------------EEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            4899999999955 554   3688              999999999999999999999999999999999988654

>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=99.60  E-value=2e-15  Score=92.00  Aligned_cols=59  Identities=31%  Similarity=0.469  Sum_probs=56.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.++++|++|++.|||..++|+.|.|++|.
T Consensus       114 ~f~~~G~v~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          114 LLTSFGPLKAFNLVKDSATGLSKG--------------YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHTTSCEEEEEEEECTTTCSEEE--------------EEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHhcCCceEEEEEecCCCCCcce--------------EEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            488999999999999988999999              99999999999999999999999999999999973

>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=99.59  E-value=9e-15  Score=84.42  Aligned_cols=58  Identities=19%  Similarity=0.254  Sum_probs=51.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh--CCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l--ng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|.++.|+.+      +|              ||||+|.+.++|+.|++.|  ++..+.|++|.|+++.++...
T Consensus        35 ~F~~fG~v~~v~i~~~------kg--------------~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           35 LGLPFGKVTNILMLKG------KN--------------QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK   94 (101)
T ss_dssp             TTTTTSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCC
T ss_pred             HHHhcCCEEEEEEECC------CC--------------EEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCc
Confidence            6999999999988864      67              9999999999999999976  578899999999999887654

>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=99.59  E-value=1.5e-16  Score=92.54  Aligned_cols=65  Identities=20%  Similarity=0.333  Sum_probs=54.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||.|.++.+..+..++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        45 ~f~~~G~v~~~~~~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           45 LFARFQEKKGPPIQFRMMTGRMRG--------------QAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             HTHHHHHSSSSCCEEEEECSSSCS--------------EEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCCC
T ss_pred             HHHHhCCccceEEEEEcCCCccce--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCCC
Confidence            488999995443333333788889              99999999999999999999999999999999998877654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.59  E-value=6e-15  Score=88.86  Aligned_cols=58  Identities=22%  Similarity=0.446  Sum_probs=52.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceE-EEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCF-GFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~-~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|.|+.+.     +|              | |||+|.+.++|+.|++.|||..|.|  +.|+|++++++.-
T Consensus        48 lFs~yG~V~~V~i~~~~-----~g--------------fqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           48 IFSKFGTVLKIITFTKN-----NQ--------------FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             HHTTSSCEEEEEEEEET-----TE--------------EEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             HHhCcCCEEEEEEEcCC-----CC--------------cEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            59999999999887642     56              7 9999999999999999999999998  9999999988653

>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=99.59  E-value=5.9e-16  Score=87.47  Aligned_cols=60  Identities=25%  Similarity=0.427  Sum_probs=54.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.   ++.++|              ||||+|.+.++|+.|++.|||..+.|+.|.|+++.++..
T Consensus        32 ~f~~~G~i~~v~i~~---~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           32 IFSRFGQILDILVSR---SLKMRG--------------QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             HHGGGSCEEEEECCH---HHHHTT--------------CEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             HHHhCCCEEEEEEEc---CCCcCc--------------EEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCc
Confidence            489999999998873   567788              999999999999999999999999999999999988754

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.1e-15  Score=89.19  Aligned_cols=58  Identities=19%  Similarity=0.295  Sum_probs=51.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC--CcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN--GFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln--g~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|+++      +|              ||||+|.+.++|+.|++.|+  +..+.|++|+|++|.++...
T Consensus        36 lF~~fG~V~~v~i~~~------kG--------------faFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~   95 (105)
T 1sjq_A           36 LGLPFGKVTNLLMLKG------KN--------------QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK   95 (105)
T ss_dssp             HHHHHCCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCC
T ss_pred             HHHhcCCEEEEEEEcC------CC--------------EEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCC
Confidence            5899999999999875      57              99999999999999999886  47899999999999887654

>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=99.59  E-value=6e-16  Score=93.90  Aligned_cols=61  Identities=23%  Similarity=0.563  Sum_probs=57.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.+.++|.+|++ +||..+.|++|.|++|.|+.
T Consensus       107 ~F~~~G~i~~~~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          107 FFSQWGTIIDAQLMLDKDTGQSRG--------------FGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HHHTTSCCSEEECCCSSSSSTTSE--------------EEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCCC
T ss_pred             HHHhCccEEEEEEEEcCCCCccce--------------EEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCCC
Confidence            488999999999999988999999              99999999999999998 89999999999999999863

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.59  E-value=5.3e-17  Score=92.64  Aligned_cols=63  Identities=17%  Similarity=0.358  Sum_probs=57.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.. .++.++.++.++|              ||||+|.+.++|++|++ |||..+.|+.|.|+++.++..++
T Consensus        37 ~F~~~G~v~~-~~~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~~~   99 (101)
T 1fj7_A           37 AISELFAKND-LAVVDVRTGTNRK--------------FGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGTR   99 (101)
T ss_dssp             HHHHHHHHHT-CCCCEEEEETTTT--------------EEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCCSS
T ss_pred             HHHHhCCcce-EEEecCCCCCcCc--------------EEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCCCC
Confidence            4788999888 7777777888999              99999999999999999 99999999999999999987664

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=2.8e-15  Score=83.91  Aligned_cols=57  Identities=23%  Similarity=0.537  Sum_probs=52.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++        +|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        28 ~F~~~G~i~~v~~~--------~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   84 (90)
T 2dnq_A           28 LFEQYGKVLECDII--------KN--------------YGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKAS   84 (90)
T ss_dssp             HHHTSSCEEEEEEE--------TT--------------EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCCC
T ss_pred             HHHhCCCEEEEEEE--------CC--------------EEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCCC
Confidence            48899999999987        57              99999999999999999999999999999999998876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.59  E-value=1.1e-15  Score=87.24  Aligned_cols=60  Identities=32%  Similarity=0.487  Sum_probs=55.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.|+.++ ++.++|              ||||+|.+.++|++|+.  |+..++|+.|.|.++.++..
T Consensus        29 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           29 FFARYGSVKEVKIITDR-TGVSKG--------------YGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             HHGGGSCEEEEEEEECT-TSCEEE--------------EEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC-
T ss_pred             HHHhCCCeEEEEEEECC-CCCccc--------------eEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCcc
Confidence            48999999999999998 999999              99999999999999999  99999999999999976654

>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=99.58  E-value=7.5e-16  Score=89.92  Aligned_cols=60  Identities=15%  Similarity=0.146  Sum_probs=55.8

Q ss_pred             CccCCcee-eEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNV-ISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i-~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.| .+|+|+.|+ +++++|              ||||+|.+.++|++||+. |+..|.|+.|.|.++.++.
T Consensus        35 ~F~~~g~v~~~v~i~~d~-~g~~~G--------------~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           35 FLEGIPVDENAVHVLVDN-NGQGLG--------------QALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             HTTTSCCCSTTEEECCCT-TSSCSS--------------CEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHHH
T ss_pred             HHHhCCCcCCeEEEEECC-CCCcce--------------EEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHHH
Confidence            58999999 899999998 999999              999999999999999996 9999999999999997654

>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=99.58  E-value=4e-15  Score=92.24  Aligned_cols=64  Identities=19%  Similarity=0.360  Sum_probs=55.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|.+|+.. +|..++|+.|.|.+|.++....
T Consensus       124 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          124 YFEQYGKIEVIEIMTDRGSGKKRG--------------FAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC------
T ss_pred             HHhcCCCeEEEEEeecCCCCCccc--------------eEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhc
Confidence            489999999999999998999999              999999999999999986 8999999999999999887643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6.1e-15  Score=82.81  Aligned_cols=57  Identities=26%  Similarity=0.443  Sum_probs=51.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++        ++              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++....
T Consensus        30 ~F~~~G~v~~v~~~--------~~--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   86 (92)
T 2dgt_A           30 KFEEYGPVIECDIV--------KD--------------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA   86 (92)
T ss_dssp             HHHTTSCCCEEEEC--------SS--------------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSCC
T ss_pred             HHHhcCCeEEEEEE--------CC--------------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCCC
Confidence            48899999999887        44              99999999999999999999999999999999998876554

>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=99.58  E-value=3.5e-15  Score=104.22  Aligned_cols=63  Identities=16%  Similarity=0.422  Sum_probs=59.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|..|.|+.++.++.++|              ||||+|.+.++|..||..|||..|.|+.|.|+++.++..
T Consensus       122 ~F~~~G~I~~v~i~~d~~tg~~kG--------------~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          122 EFEVYGPIKRIHMVYSKRSGKPRG--------------YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             HHHHcCCeeEEEeeccCCCCCccc--------------eEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            589999999999999998999999              999999999999999999999999999999999987643

>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=99.58  E-value=2.7e-15  Score=86.40  Aligned_cols=60  Identities=13%  Similarity=0.187  Sum_probs=54.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||. .+|+|++++ +++++|              ||||+|.++++|++||+ +|+..+.|+.|.|.++.+...
T Consensus        35 ~F~~~G~-~~v~i~~d~-~g~~~G--------------~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           35 FFSPLNP-MRVHIEIGP-DGRVTG--------------EADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             SSCSCCC-SEEEEEESS-SSCEEE--------------EEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCC
T ss_pred             HHHHcCc-eEEEEEECC-CCCEee--------------EEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCC
Confidence            6999995 599999998 899999              99999999999999995 899999999999999977654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.58  E-value=1.4e-15  Score=96.62  Aligned_cols=60  Identities=37%  Similarity=0.625  Sum_probs=54.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.|.+++|++|+  +.++|              ||||+|.+.++|++|++.|||..|+|++|.|++|.++.
T Consensus       123 ~F~~~G~i~~~~i~~d~--~~~~g--------------~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          123 TFSAFGNILSCKVVCDE--NGSKG--------------YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             HHGGGSCEEEEEEEEET--TEEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             HHhhcCCeEEEEeeccC--CCCce--------------EEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            48999999999999985  34677              99999999999999999999999999999999998764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=5.9e-16  Score=88.22  Aligned_cols=58  Identities=24%  Similarity=0.425  Sum_probs=53.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.+     ++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        20 ~F~~~G~i~~v~i~~~-----~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A           20 AFSYYGPLRTVWIARN-----PPG--------------FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             HHHHHCCCSEEEEESS-----SSS--------------EEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             HHHhcCCeEEEEEeeC-----CCC--------------EEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            4889999999999987     678              999999999999999999999999999999999987654

>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=99.57  E-value=2.5e-15  Score=85.15  Aligned_cols=58  Identities=22%  Similarity=0.507  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC--CEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG--MKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~--g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.+      +|              ||||+|.+.++|++|++.|||..+.  |+.|.|++++++..+
T Consensus        37 ~F~~~G~v~~v~~~~~------~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~~~   96 (97)
T 1why_A           37 EFDRFGSIRTIDHVKG------DS--------------FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS   96 (97)
T ss_dssp             HHHTTSCEEEEEECSS------SC--------------CEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCCC
T ss_pred             HHHhcCCeeEEEEeCC------CC--------------EEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCCCC
Confidence            4899999999988754      67              9999999999999999999999999  999999999987653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.57  E-value=4e-15  Score=86.08  Aligned_cols=56  Identities=20%  Similarity=0.191  Sum_probs=50.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcE--ECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ--IGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~--i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.+++      +||              ||||+|.+.++|.+|++.||+..  +.|++|+|++++++.
T Consensus        41 lF~~fG~V~~v~i~~------~kg--------------~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           41 ALQEFGPISYVVVMP------KKR--------------QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             HHGGGSCEEEEEEET------TTT--------------EEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             HHhccCCEEEEEEEc------CCC--------------EEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            589999999999885      367              99999999999999999999875  789999999998864

>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=99.57  E-value=4.1e-15  Score=85.52  Aligned_cols=61  Identities=18%  Similarity=0.237  Sum_probs=55.7

Q ss_pred             CccCCceeeE-EEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVIS-SKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~-v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||.|.+ +.|+.+ .+|+++|              ||||+|.++++|++|++. |+..+.|+.|.|.++.++..
T Consensus        35 ~F~~~G~v~~~v~i~~~-~~g~~~G--------------~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~~   96 (104)
T 1wg5_A           35 FFSGLEIVPNGMTLPVD-FQGRSTG--------------EAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             HTTTCCEEEEEEECCBC-SSSCBCS--------------EEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTTS
T ss_pred             HHHhcCCcceeEEEEEC-CCCCcce--------------EEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHHH
Confidence            4899999998 888888 6899999              999999999999999997 99999999999999977653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=2.8e-15  Score=84.63  Aligned_cols=60  Identities=17%  Similarity=0.267  Sum_probs=52.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||.|..+     ..++.++|              ||||+|.+.++|++|+..|||..+.|+.|.|+++.++..++
T Consensus        36 ~F~~~g~v~~~-----~~~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   95 (96)
T 1fjc_A           36 VFEDALEIRLV-----SQDGKSKG--------------IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR   95 (96)
T ss_dssp             HHCSEEEECCE-----EETTEEEE--------------EEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCCCC
T ss_pred             HHhhCCcEEEe-----CCCCCcce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCCCC
Confidence            47889988765     34678888              99999999999999999999999999999999998877654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.56  E-value=9.4e-15  Score=92.78  Aligned_cols=62  Identities=29%  Similarity=0.413  Sum_probs=58.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+|+|++|+.+++++|              ||||+|.+.++|++|++.+|+..+.|+.|++.++.+..
T Consensus        35 ~F~~~G~I~~v~i~~d~~tg~~~G--------------~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~   96 (213)
T 4f02_A           35 KFSPAGPILSIRVCRDMITRRSLG--------------YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDP   96 (213)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCT
T ss_pred             HHHhhCCEEEEEEecccCCCCccc--------------cccceeCCHHHHHHHHHHhhhhhcCCcccccccccccc
Confidence            589999999999999999999999              99999999999999999999999999999999987653

>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=99.56  E-value=2.4e-15  Score=87.19  Aligned_cols=59  Identities=19%  Similarity=0.187  Sum_probs=51.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc--EECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF--QIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~--~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.+      +|              ||||+|.+.++|++|++.||+.  .+.|++|.|+++.++...
T Consensus        35 ~F~~fG~V~~v~i~~~------kg--------------~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           35 ALEKFGTICYVMMMPF------KR--------------QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             HHTTTSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             HHHhCCCEEEEEEECC------CC--------------EEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            5899999999998864      67              9999999999999999988764  489999999999887654


Q ss_pred             C
Q psy16913         79 R   79 (81)
Q Consensus        79 ~   79 (81)
                      +
T Consensus        95 ~   95 (104)
T 1wex_A           95 R   95 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.56  E-value=3.6e-16  Score=84.69  Aligned_cols=57  Identities=21%  Similarity=0.452  Sum_probs=53.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.++++|++|++ +++..+.|+.|.|++|
T Consensus        19 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           19 YFGGFGEVESIELPMDNKTNKRRG--------------FCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHSCCSEECCCCSCCCSSSCC--------------CEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             HHHhcCCeEEEEEEecCCCCCcCC--------------EEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            488999999999999998999999              99999999999999999 4899999999999875

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=7.9e-15  Score=82.04  Aligned_cols=57  Identities=32%  Similarity=0.487  Sum_probs=51.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.++        ++              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+.
T Consensus        29 ~F~~~G~v~~~~~~--------~~--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   85 (90)
T 2dnp_A           29 LFERRGRVIECDVV--------KD--------------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKS   85 (90)
T ss_dssp             HHHHHSCEEEEEEC--------SS--------------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCCCC
T ss_pred             HHHcCCCEEEEEEE--------CC--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCCCC
Confidence            48899999999987        34              99999999999999999999999999999999998876543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=1.9e-15  Score=94.57  Aligned_cols=62  Identities=24%  Similarity=0.348  Sum_probs=58.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|.|+.++ ++.++|              ||||+|.+.++|++|++.|||..++|+.|.|++|.+...
T Consensus       108 ~F~~~G~I~~v~i~~d~-~g~~kG--------------~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~~  169 (177)
T 2f3j_A          108 LFAEFGTLKKAAVDYDR-SGRSLG--------------TADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID  169 (177)
T ss_dssp             HHHHTSCCSEEEECCCT-TSSCSC--------------CEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGGG
T ss_pred             HHHhcCCeEEEEEEECC-CCCEee--------------EEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            58899999999999998 899999              999999999999999999999999999999999977543

>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=99.56  E-value=5.2e-15  Score=85.57  Aligned_cols=57  Identities=25%  Similarity=0.453  Sum_probs=51.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.++.+        ++|              ||||+|.+.++|++|++.|||..++|+.|.|+++.++...+
T Consensus        48 ~F~~~G~v~~v~i--------~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  104 (110)
T 1wf1_A           48 IFSKYGRVAGCSV--------HKG--------------YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDR  104 (110)
T ss_dssp             HHGGGSCCSEEEE--------ETT--------------EEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCSCC
T ss_pred             HHHhCCCeEEEEE--------eCC--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCCCC
Confidence            4899999999988        467              99999999999999999999999999999999998655443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.56  E-value=2.5e-15  Score=88.40  Aligned_cols=59  Identities=12%  Similarity=0.171  Sum_probs=54.5

Q ss_pred             CccCCce---eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGN---VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~---i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||.   |.+|+|+.++. |+++|              ||||+|.+.++|++|++ |||..|.|+.|+|.++.++
T Consensus        37 ~F~~~G~~~~v~~v~i~~~~~-g~~~G--------------~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           37 FLSDCTIHDGVAGVHFIYTRE-GRQSG--------------EAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             HTTTSCBTTGGGGEEEEECSS-SCEEE--------------EEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHH
T ss_pred             HHHHcCCccCceeEEEEECCC-CCCCe--------------EEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHH
Confidence            4899999   89999999985 88899              99999999999999999 9999999999999998654

>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=99.55  E-value=3.8e-16  Score=92.29  Aligned_cols=61  Identities=21%  Similarity=0.216  Sum_probs=55.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.|.++.++.++.+|+++|              ||||+|.+.++|++||. |||..|.|+.|.|.++.++.
T Consensus        45 ~F~~~G~v~~~~~~~~~~~g~~~G--------------~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~  105 (124)
T 1wel_A           45 FFKKLDIVEDSIYIAYGPNGKATG--------------EGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKG  105 (124)
T ss_dssp             HSCSSCBCTTTCEEEECTTSSEEE--------------EEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHH
T ss_pred             HHHhcCCccceEEEEECCCCCCCe--------------EEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCHHH
Confidence            589999999877777777999999              99999999999999999 99999999999999997643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.55  E-value=8e-15  Score=85.08  Aligned_cols=56  Identities=29%  Similarity=0.501  Sum_probs=50.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++        +|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..+
T Consensus        51 ~F~~~G~i~~v~i~--------kg--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           51 IFGPFGPMKEVKIL--------NG--------------FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR  106 (108)
T ss_dssp             HHTTTSCCCEEEEE--------TT--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC--
T ss_pred             HHHhcCCEEEEEEE--------CC--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCCC
Confidence            48999999999988        67              9999999999999999999999999999999999887654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.55  E-value=3.3e-15  Score=85.09  Aligned_cols=55  Identities=22%  Similarity=0.430  Sum_probs=50.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+++++      .++|              ||||+|.+.++|++|+..|||..++|+.|+|++++++
T Consensus        47 ~f~~~G~i~~~~~~------~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           47 LFQNFGFILDFKHY------PEKG--------------CCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             HHHTTSCCSEEEEE------TTTT--------------EEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             HHHhCCCEEEEEEe------cCCC--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            48899999999987      3467              9999999999999999999999999999999999875

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.55  E-value=9.5e-15  Score=83.60  Aligned_cols=56  Identities=27%  Similarity=0.522  Sum_probs=50.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++        ++              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++...
T Consensus        31 ~F~~~G~i~~v~~~--------~~--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           31 AFSQFGKLERVKKL--------KD--------------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             HHHHHSCEEEEEEC--------SS--------------CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHHhcCCEEEEEEE--------CC--------------EEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            48899999999876        45              9999999999999999999999999999999999877653

>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=99.55  E-value=2e-15  Score=87.75  Aligned_cols=59  Identities=17%  Similarity=0.336  Sum_probs=53.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.+   +.++|              ||||+|.+.++|.+|++.|||..+.|+.|.|+++.++.
T Consensus        28 ~F~~~G~v~~v~i~~~---~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A           28 IFGKYGPIRQIRVGNT---PETRG--------------TAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             HHHTTSCEEEEEEECS---TTTTT--------------CEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             HHHhcCCeEEEEEeeC---CCCCc--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            4899999999999865   34578              99999999999999999999999999999999998643

>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=99.55  E-value=6.5e-15  Score=83.67  Aligned_cols=57  Identities=21%  Similarity=0.382  Sum_probs=52.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.+      +|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        35 ~F~~~G~i~~v~~~~~------kg--------------~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           35 LFEKYGKAGEVFIHKD------KG--------------FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             HTSTTCCCSEEEEETT------TT--------------EEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             HHhhcCCeEEEEEecC------CC--------------EEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            5899999999998854      57              999999999999999999999999999999999988764

>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=99.55  E-value=5.4e-15  Score=87.82  Aligned_cols=59  Identities=19%  Similarity=0.298  Sum_probs=52.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCC--cEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG--FQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng--~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|+.+      +|              ||||+|.+.++|++|++.|++  ..+.|++|+|++|.++...
T Consensus        51 lF~~fG~V~~v~i~~~------kG--------------~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~  110 (119)
T 2ad9_A           51 LGLPFGKVTNLLMLKG------KN--------------QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK  110 (119)
T ss_dssp             HHTTTSCCCEEEEEGG------GT--------------EEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCC
T ss_pred             HHHhcCCEEEEEEeCC------CC--------------EEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCC
Confidence            5899999999999875      57              999999999999999999884  6899999999999887654


Q ss_pred             C
Q psy16913         79 R   79 (81)
Q Consensus        79 ~   79 (81)
                      .
T Consensus       111 ~  111 (119)
T 2ad9_A          111 T  111 (119)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.54  E-value=2.3e-14  Score=81.56  Aligned_cols=54  Identities=28%  Similarity=0.534  Sum_probs=49.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.+.        +|              ||||+|.+.++|++|++.|||..+.|+.|.|++++++.
T Consensus        43 ~F~~~G~v~~v~i~--------~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           43 IFSPYGHIMQINIK--------NA--------------FGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             HHGGGSCEEEEEEC--------SS--------------EEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             HHHhcCCEEEEEEe--------CC--------------EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            48999999999883        67              99999999999999999999999999999999998764

>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=99.54  E-value=8.2e-15  Score=91.26  Aligned_cols=58  Identities=21%  Similarity=0.417  Sum_probs=51.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~~   76 (81)
                      +|++||+|.+|.|..++    ++|              ||||+|.+.++|++|++.|||..|.|  +.|+|+|++++.
T Consensus        66 ~Fs~fG~V~~V~i~~k~----~rg--------------fAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           66 IFSKFGTVLKIITFTKN----NQF--------------QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             HHHHHSCEEEEEEEESS----SCE--------------EEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             HHHhcCCEEEEEEEeCC----CCC--------------EEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            58999999999986432    467              99999999999999999999999976  999999998874

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.54  E-value=3e-14  Score=85.90  Aligned_cols=62  Identities=26%  Similarity=0.425  Sum_probs=55.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++ ++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|.++.++..
T Consensus        20 ~f~~~G~i~~v~i~~~~-~~~~~g--------------~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~   81 (166)
T 3md3_A           20 YFQVGGPIANIKIMIDK-NNKNVN--------------YAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ   81 (166)
T ss_dssp             HHGGGSCEEEEEEECCC-C-CCEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC
T ss_pred             HHHhcCCeEEEEEEECC-CCCCCC--------------EEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC
Confidence            48999999999999997 567888              999999999999999999999999999999999977653

>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=99.54  E-value=9.5e-15  Score=88.52  Aligned_cols=58  Identities=24%  Similarity=0.466  Sum_probs=55.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a   72 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|.+|++.|||..+.|  ++|.|++|
T Consensus       109 ~f~~~G~i~~~~i~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          109 IFGKYGSIVQKNILRDKLTGRPRG--------------VAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHTSSSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             hhhcCCcEEEEEEEEcCCCCCcce--------------EEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            489999999999999998899999              99999999999999999999999988  99999986

>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=99.54  E-value=1.8e-15  Score=91.51  Aligned_cols=59  Identities=10%  Similarity=0.142  Sum_probs=54.9

Q ss_pred             CccCCce---eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGN---VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~---i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||.   |.+|+|++|+. |+++|              ||||+|.++++|++|++ |||..+.|+.|.|.++.++
T Consensus        64 ~F~~~G~v~~v~~v~i~~d~~-g~srG--------------~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           64 FLSDCTIHDGAAGVHFIYTRE-GRQSG--------------EAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             HTTTCCCSSSSTTEEEEECSS-SCEEE--------------EEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHH
T ss_pred             HHHHhCCcCceeEEEEEECCC-CCCCe--------------EEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChH
Confidence            4899999   89999999986 89999              99999999999999999 9999999999999998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=3.9e-15  Score=84.41  Aligned_cols=58  Identities=21%  Similarity=0.437  Sum_probs=51.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|. +.++.+    .++|              ||||+|.+.++|++|++.|||..+.|+.|.|+++.++..
T Consensus        39 ~F~~~G~v~-~~~~~~----~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   96 (97)
T 2e5j_A           39 ALRELGSVP-LRLTWQ----GPRR--------------RAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD   96 (97)
T ss_dssp             HHHHTTCCC-SEEEEE----TTTT--------------EEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCCC
T ss_pred             HHHhcCCEE-EEEEcC----CCCc--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            488999997 676654    5678              999999999999999999999999999999999988764

>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=99.53  E-value=5e-15  Score=89.73  Aligned_cols=57  Identities=26%  Similarity=0.429  Sum_probs=53.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++++.+     ++|              ||||+|.+.++|++|+..|||..+.|++|+|+++.++.
T Consensus        93 ~F~~~G~i~~v~i~~~-----~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           93 AFGYYGPLRSVWVARN-----PPG--------------FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHSCEEEEEECSS-----SCS--------------EEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHhhCCEEEEEEeeC-----CCc--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            4889999999999876     478              99999999999999999999999999999999998864

>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=99.53  E-value=8.4e-15  Score=86.48  Aligned_cols=60  Identities=15%  Similarity=0.197  Sum_probs=51.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE-----CCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI-----GMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i-----~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+|.|+.+      +|              ||||+|.+.++|++|++.|||..+     .|++|.|.++...
T Consensus        47 ~F~~fG~v~~v~i~~~------rg--------------faFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           47 VLEKCGLVDALLMPPN------KP--------------YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             HHHHHSCEEEEECCTT------CS--------------CEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCC
T ss_pred             HHHhcCCeEEEEEeCC------CC--------------EEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccC
Confidence            4899999999987642      67              999999999999999999999998     6899999999765


Q ss_pred             CCCCC
Q psy16913         76 DAARP   80 (81)
Q Consensus        76 ~~~~~   80 (81)
                      ....|
T Consensus       107 p~~~~  111 (114)
T 2cq2_A          107 QWSGP  111 (114)
T ss_dssp             CCSSC
T ss_pred             cccCC
Confidence            54443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.53  E-value=6e-15  Score=86.50  Aligned_cols=58  Identities=12%  Similarity=0.066  Sum_probs=50.1

Q ss_pred             CccCCc-eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G-~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++|| +|..+.++.+    .++|              ||||+|.+.++|++||+.|||..++|+.|+|+++..+.
T Consensus        48 ~F~~~G~~v~~v~i~~~----~~rG--------------faFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           48 LARENSLETTFSSVNTR----DFDG--------------TGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             HHHHHTCCCSEEECSSC----SSSC--------------CEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             HHHHhCCeeEEEEEEcC----CCCC--------------EEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            488999 8999887532    4678              99999999999999999999999999999999997654

>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=99.53  E-value=1.2e-14  Score=95.09  Aligned_cols=63  Identities=17%  Similarity=0.280  Sum_probs=58.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|+.||.|.++.++.++ +|.++|              ||||+|.+.++|.+|+..|||..+.|+.|.|.++.++..+
T Consensus       205 ~f~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  267 (284)
T 3smz_A          205 ALSAVHSPTFCQLACGQ-DGQLKG--------------FAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG  267 (284)
T ss_dssp             HTCSSSCCSEEEEEECS-SCCEEE--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCH
T ss_pred             HhhCCCCeEEEEEEECC-CCCccc--------------EEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcc
Confidence            58999999999999987 788888              9999999999999999999999999999999999887653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=2.9e-14  Score=85.16  Aligned_cols=56  Identities=30%  Similarity=0.445  Sum_probs=50.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceE-EEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCF-GFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~-~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~~   76 (81)
                      +|++||.|.+|.|+. +     .|              | |||+|.+.++|..|++.|||..|.|  +.|+|++|+++.
T Consensus        45 ~Fs~yG~V~~v~i~~-~-----~G--------------f~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           45 VCNPVGKVQRIVIFK-R-----NG--------------IQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             HHTTTSCEEEEEEEE-S-----SS--------------EEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             HHHhcCCEEEEEEEe-C-----CC--------------CEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            599999999999864 2     27              7 9999999999999999999999988  699999998875

>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=99.52  E-value=8.3e-15  Score=85.31  Aligned_cols=55  Identities=16%  Similarity=0.115  Sum_probs=50.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++.|+.      ++|              ||||+|.+.++|++|++.|||..+.|++|.|+||...
T Consensus        30 ~F~~~G~i~~v~i~~------~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           30 TFSRFGSLGRVLLPE------GGI--------------TAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             HHHTTSCEEEEECCS------SSS--------------CEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             HHHhcCCEEEEEEeC------CCC--------------EEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            589999999998774      467              9999999999999999999999999999999999664

>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=99.52  E-value=1.6e-15  Score=91.30  Aligned_cols=63  Identities=21%  Similarity=0.274  Sum_probs=52.1

Q ss_pred             CccCCceeeEEE--E---EecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSK--V---FIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~--i---~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||.|.++.  +   +....++.++|              ||||+|.+.++|.+|+..|||..+.|+.|.|++|++.
T Consensus        65 ~F~~~G~i~~~~~~~~~di~~~~~g~~~g--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A           65 IFGRYVDFSSETQRIMFDIRLMKEGRMKG--------------QAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             HHGGGCCTTCHHHHHHCEEEEEEETTTEE--------------EEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             HHHHhCCcccccccceeeEEeccCCCccc--------------EEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            489999987741  1   11123678888              9999999999999999999999999999999999775


Q ss_pred             CC
Q psy16913         76 DA   77 (81)
Q Consensus        76 ~~   77 (81)
                      ..
T Consensus       131 ~~  132 (143)
T 3egn_A          131 RP  132 (143)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.52  E-value=1.7e-14  Score=84.96  Aligned_cols=56  Identities=20%  Similarity=0.105  Sum_probs=50.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      .|++||+|.++.|+++.    ++|              |+||+|.+.++|++|++.|||..++||.|.|+++..
T Consensus        37 ~f~kfG~V~~v~i~~~~----~~G--------------~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           37 ECNKHGGVIHIYVDKNS----AQG--------------NVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL   92 (114)
T ss_dssp             HHTTTTCCSEEEECTTC----TTC--------------CEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHhccCCEEEEEEecCC----CcE--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcH
Confidence            37899999999987653    478              999999999999999999999999999999999853

>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=99.52  E-value=2.1e-14  Score=91.41  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=51.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||.|.+|+++.++     +|              ||||+|.++++|+.||+.|||..+.|+.|+|.+++.
T Consensus        25 ~F~~~G~v~~v~i~~~~-----~g--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A           25 VFCLYGNVEKVKFMKSK-----PG--------------AAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             HHTTTSCEEEEEECTTS-----TT--------------CEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             HHHhcCCeEEEEEecCC-----CC--------------EEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            58999999999998753     68              999999999999999999999999999999999864

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.8e-14  Score=83.17  Aligned_cols=57  Identities=18%  Similarity=0.239  Sum_probs=49.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|+     ++++|              ||||+|.+.++|+.|++.+++  +.|++|+|+|+.++...
T Consensus        37 ~F~~~G~V~~v~i~-----~~~rG--------------faFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           37 LLQKYGEVLNLVLS-----SKKPG--------------TAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             HHHTTSCEEEEEEE-----SSSSS--------------EEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             HHHhcCCEEEEEEc-----cCCCC--------------EEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            58999999999988     36688              999999999999999998554  68999999999876543

>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=99.52  E-value=1e-14  Score=85.79  Aligned_cols=58  Identities=14%  Similarity=0.213  Sum_probs=50.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCC--cEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG--FQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng--~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|.|++      ++|              ||||+|.+.++|+.|++.||+  ..+.|++|+|++|.++...
T Consensus        46 lF~~fG~V~~v~i~~------~kg--------------~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           46 LAEPYGKIKNYILMR------MKS--------------QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKL  105 (112)
T ss_dssp             TTTTTSCCSEEEEET------TTT--------------EEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSS
T ss_pred             HHHhcCCEEEEEEec------CCC--------------EEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccccc
Confidence            699999999999874      367              999999999999999998864  5699999999999876543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=1.7e-14  Score=84.21  Aligned_cols=58  Identities=17%  Similarity=0.273  Sum_probs=52.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++| .|.+|.|+.|+. |+++|              ||||+|.++++|++|+ .+|+..+.||.|.|..+.++
T Consensus        36 ~F~~~-~v~~v~i~~d~~-g~~~G--------------~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           36 FFHGL-RVDAVHLLKDHV-GRNNG--------------NGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HTTTS-CCCEEEECCCTT-CCCCS--------------EEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             HhccC-CeeEEEEEECCC-CCCCe--------------EEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            48899 899999999984 89999              9999999999999999 59999999999999988653

>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=99.52  E-value=2.2e-14  Score=79.15  Aligned_cols=53  Identities=25%  Similarity=0.411  Sum_probs=48.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh-CCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l-ng~~i~g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.+      +|              ||||+|.+.++|++|++.| ||..+.|+.|+|+||+
T Consensus        32 ~f~~~G~i~~~~~~~~------kg--------------~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           32 HFYQFGEIRTITVVQR------QQ--------------CAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             HHHTTSCEEEEEEEGG------GT--------------EEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             HHHhCCCEeEEEEECC------CC--------------EEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            4889999999999864      57              9999999999999999999 9999999999999985

>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=99.52  E-value=1.9e-14  Score=94.44  Aligned_cols=61  Identities=26%  Similarity=0.441  Sum_probs=55.2

Q ss_pred             CccCCceeeEEEEEecCC-CCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRA-TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~-~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++++.+.. ||.++|              ||||+|.+.++|.+|+ .|||..+.|+.|.|.||.++.
T Consensus       231 ~F~~~G~v~~v~i~~~~~~tg~~~g--------------~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          231 SFEGFGSIEKINIPAGQKEHSFNNC--------------CAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             HHGGGSCEEEEECCSCCC---CCCE--------------EEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             HHhccCCeeEEEEEecCCcCCCCce--------------EEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            489999999999999875 588888              9999999999999999 999999999999999999863

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.1e-14  Score=79.93  Aligned_cols=56  Identities=30%  Similarity=0.455  Sum_probs=50.1

Q ss_pred             CccCC--ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPF--GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~--G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++|  |.|.+++++        +|              ||||+|.+.++|++|+..|||..+.|+.|.|++++++...
T Consensus        35 ~F~~~g~g~v~~~~~~--------~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   92 (99)
T 2cpd_A           35 EFNNIKPGAVERVKKI--------RD--------------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD   92 (99)
T ss_dssp             HHHTTSTTCEEEEEEC--------SS--------------EEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCCC
T ss_pred             HHHhcCCcceEEEEEe--------CC--------------eEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCC
Confidence            48899  899988764        56              9999999999999999999999999999999999887653

>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=99.51  E-value=1.5e-14  Score=87.29  Aligned_cols=58  Identities=29%  Similarity=0.608  Sum_probs=53.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEE--EEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR--LKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~--i~V~~a   72 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.+.++|.+|++.|||..+.|+.  |.|+||
T Consensus       108 ~f~~~G~i~~~~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          108 LFSQYGRIITSRILVDQVTGVSRG--------------VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHhcCCEeEEEEEecCCCCCccc--------------eEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            489999999999999998899999              9999999999999999999999999965  888876

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.51  E-value=9.2e-15  Score=82.81  Aligned_cols=55  Identities=27%  Similarity=0.527  Sum_probs=50.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.+.        +|              ||||+|.+.++|+.|++.|||..+.|+.|.|+++.++..
T Consensus        31 ~F~~~G~v~~v~i~--------~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           31 IFSPYGHIMQINIK--------NA--------------FGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             HHTTTCCCCEEEEE--------TT--------------EEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             HHHhcCCEEEEEEe--------CC--------------EEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            48999999999884        67              999999999999999999999999999999999977654

>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=99.50  E-value=5e-14  Score=87.26  Aligned_cols=61  Identities=20%  Similarity=0.384  Sum_probs=55.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.++++|++|++. ++..+.|+.|.|.++.++.
T Consensus        33 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~   93 (196)
T 1l3k_A           33 HFEQWGTLTDCVVMRDPNTKRSRG--------------FGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSRE   93 (196)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC--
T ss_pred             HHHhCCCEEEEEEEEcCCCCCccc--------------eEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCcc
Confidence            589999999999999998999999              999999999999999985 9999999999999997654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.49  E-value=2.8e-14  Score=89.55  Aligned_cols=62  Identities=31%  Similarity=0.496  Sum_probs=55.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++++.++.++.++|              ||||+|.+.++|++|++.|||..+.|+.|.|.++.+..
T Consensus        48 ~f~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  109 (216)
T 2qfj_A           48 AFAPFGPIKSIDMSWDSVTMKHKG--------------FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG  109 (216)
T ss_dssp             HHGGGSCEEEEEECCC-CC-CCCS--------------EEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCG
T ss_pred             HHHhCCCEEEEEEeecCCCCccCc--------------eEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCcc
Confidence            489999999999999998999999              99999999999999999999999999999999887654

>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=99.49  E-value=1.7e-14  Score=81.01  Aligned_cols=58  Identities=17%  Similarity=0.269  Sum_probs=48.9

Q ss_pred             CccCCce-eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCC-cEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGN-VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-FQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~-i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng-~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||. |..+.+.       ++|              ||||+|.+.++|++|++.||| ..++|+.|+|+++.++..+
T Consensus        28 ~F~~~G~vv~~~~~~-------~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           28 LFGDRKLPLAGQVLL-------KSG--------------YAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             HHHHTTCCCSSCEEE-------ETT--------------EEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             HHHHcCCceEEEEEc-------CCC--------------EEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence            4788998 5555442       367              999999999999999999999 9999999999999887654


Q ss_pred             C
Q psy16913         79 R   79 (81)
Q Consensus        79 ~   79 (81)
                      .
T Consensus        87 ~   87 (93)
T 2cqh_A           87 S   87 (93)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.49  E-value=1.8e-15  Score=87.44  Aligned_cols=59  Identities=8%  Similarity=0.184  Sum_probs=54.5

Q ss_pred             CccCCce---eeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGN---VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~---i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||.   |.+|+|+.++. |+++|              ||||+|.+.++|++|++ +|+..+.|+.|.|.++.++
T Consensus        31 ~F~~~g~~~~v~~v~i~~~~~-g~~~G--------------~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           31 FFSDCRIRNGENGIHFLLNRD-GKRRG--------------DALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             HTTTSCBTTTTTTEECCCCTT-STTCS--------------EEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHH
T ss_pred             HHHhcCCcCCcceEEEEECCC-CCEee--------------EEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHH
Confidence            4889888   89999999986 99999              99999999999999999 9999999999999998764

>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=99.49  E-value=9.3e-14  Score=84.93  Aligned_cols=57  Identities=16%  Similarity=0.247  Sum_probs=51.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.|..+     ..++.++|              ||||+|.+.++|.+|+..|||..+.|+.|.|++|.++.
T Consensus       119 ~F~~~g~v~~~-----~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          119 VFEDALEIRLV-----SQDGKSKG--------------IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             HCTTCSEEEEE-----CSSSSCCS--------------EEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             HHHhcCeEEEe-----cCCCCCce--------------EEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            48889988765     45788899              99999999999999999999999999999999998863

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.7e-14  Score=82.74  Aligned_cols=53  Identities=25%  Similarity=0.276  Sum_probs=48.0

Q ss_pred             CccCC-ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPF-GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~-G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++| |+|.+|       ++   |              +|||+|.+.++|++|++.|||..+.||+|+|++|+.+.+
T Consensus        33 lF~~yGG~Vl~V-------tg---G--------------~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd   86 (96)
T 2diu_A           33 LSDNCGGKVLSI-------TG---C--------------SAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRE   86 (96)
T ss_dssp             HHHTTTCCEEEC-------CT---T--------------CEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCC
T ss_pred             HHHHcCCeeEEE-------ec---C--------------EEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcc
Confidence            58999 599987       33   7              999999999999999999999999999999999988764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=7e-14  Score=78.76  Aligned_cols=58  Identities=24%  Similarity=0.469  Sum_probs=49.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+|  +.++.++.                 ||||+|.++++|++|++ |||..++|+.|.|+++.++...
T Consensus        28 ~F~~~G~v~~v--~~~~~~g~-----------------~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           28 YFLAFGPVASV--VMDKDKGV-----------------FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             HGGGTSCEEEE--EECSSSCC-----------------EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCCC
T ss_pred             HHHhcCCeEEE--EEcCCCCc-----------------EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCCC
Confidence            48999999987  56654332                 89999999999999999 9999999999999999776543

>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=99.47  E-value=5.1e-14  Score=85.62  Aligned_cols=58  Identities=29%  Similarity=0.417  Sum_probs=52.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC---CEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG---MKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~---g~~i~V~~a~   73 (81)
                      +|++||+|.++.++.++ +|.++|              ||||+|.+.++|.+|++.|||..+.   +++|.|+||.
T Consensus       115 ~F~~~G~i~~v~~~~~~-~g~~~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          115 MFSSFGQIEECRILRGP-DGLSRG--------------CAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHGGGSCEEEEEEEECT-TSCEEE--------------EEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHhCCCEEEEEEEECC-CCCEEE--------------EEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            48999999999999997 688888              9999999999999999999998877   4999999973

>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=99.47  E-value=1.3e-13  Score=90.10  Aligned_cols=59  Identities=25%  Similarity=0.440  Sum_probs=54.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+|++++   +++++|              ||||+|.+.++|++|++.|||..+.|+.|+|+++.++.
T Consensus        33 ~F~~~G~i~~v~~~~---~~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   91 (282)
T 3pgw_A           33 IFSQFGQILDILVSR---SLKMRG--------------QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   91 (282)
T ss_pred             HHhccCCeEEEEEcC---CCCcce--------------EEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCc
Confidence            589999999998875   677888              99999999999999999999999999999999997654

>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=99.46  E-value=1.4e-13  Score=89.91  Aligned_cols=62  Identities=26%  Similarity=0.388  Sum_probs=58.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++.+|.++|              ||||+|.+.++|.+|+..|||..+.|+.|.|.++.++.
T Consensus       115 ~f~~~G~i~~~~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          115 LVRPFGSLERCFLVYSERTGQSKG--------------YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             HHHhcCCeeEEEEEeeCCCCccce--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            488999999999999998999999              99999999999999999999999999999999997754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=3.8e-14  Score=79.86  Aligned_cols=59  Identities=27%  Similarity=0.367  Sum_probs=52.0

Q ss_pred             CccCCceeeEE-EEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v-~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++ .++.++.    .|              .|||+|.+.++|++|+..|||..+.|+.|.|+++.+++.
T Consensus        35 ~F~~~G~v~~~~~i~~~~~----~~--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~~   94 (96)
T 2e44_A           35 LLVQYGVVESCEQVNTDSE----TA--------------VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMA   94 (96)
T ss_dssp             HHHHHSCEEEEEEECCSSS----SE--------------EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCCS
T ss_pred             HHHhcCCeEEEEEeecCCC----CC--------------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcccc
Confidence            48899999999 4777753    24              589999999999999999999999999999999999854

>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=99.46  E-value=5.5e-14  Score=82.16  Aligned_cols=56  Identities=18%  Similarity=0.347  Sum_probs=47.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEE-----EEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR-----LKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~-----i~V~~a~~~   75 (81)
                      +|++||+|.++.|+.+       |              ||||+|.+.++|++||+.|||..|+|+.     |+|..+.++
T Consensus        36 ~F~~~G~v~~~~i~~~-------g--------------~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           36 HMREAGDVCYADVYRD-------G--------------TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             HHGGGSCEEEEEECTT-------S--------------EEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC--
T ss_pred             HHHhcCCeEEEEEecC-------C--------------EEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCC
Confidence            5899999999998866       7              9999999999999999999999999988     888887665


Q ss_pred             CC
Q psy16913         76 DA   77 (81)
Q Consensus        76 ~~   77 (81)
                      ..
T Consensus        95 ~~   96 (115)
T 3beg_B           95 SP   96 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.45  E-value=1.6e-13  Score=76.48  Aligned_cols=54  Identities=26%  Similarity=0.311  Sum_probs=48.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++| +|.++++.      +++|              ||||+|.++++|++|++.|||..+.|++|+|+++..+
T Consensus        25 ~F~~~-~v~~~~i~------~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           25 LLKDY-DLKYCYVD------RNKR--------------TAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             HTCSS-CCCCEEEE------GGGT--------------EEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             HHhhC-CeEEEEEe------CCCc--------------EEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            48899 99999884      5678              9999999999999999999999999999999999664

>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=99.44  E-value=9.5e-15  Score=88.66  Aligned_cols=60  Identities=15%  Similarity=0.208  Sum_probs=54.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++|| |.+|.|++|+. ++++|              ||||+|.++++|++|| .+|+..+.|+.|.|.++.++..
T Consensus        66 ~F~~~G-i~~v~i~~d~~-g~srG--------------faFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           66 FFSPLN-PVRVHIEIGPD-GRVTG--------------EADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             HHCSCC-CSEEECCCSSS-SCSSC--------------CCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             HHHhcC-CeEEEEEECCC-CCCce--------------EEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            489999 77999999985 89999              9999999999999999 6999999999999999987654

>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=99.42  E-value=4.1e-13  Score=84.87  Aligned_cols=59  Identities=19%  Similarity=0.113  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+|+|+++. ++.++|              ||||+|.+.++|++|+..++ ..++|+.|.|.++..-
T Consensus       129 ~F~~~G~v~~v~i~~~~-~~~~kG--------------~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          129 WLEDKGQVLNIQMRRTL-HKAFKG--------------SIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDY  187 (193)
T ss_dssp             HHTTSCCEEEEEEEECT-TCCEEE--------------EEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC
T ss_pred             HHhcCCCEEEEEEEECC-CCCccc--------------EEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHH
Confidence            48999999999999987 588888              99999999999999998665 5999999999998653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=4e-13  Score=76.38  Aligned_cols=53  Identities=28%  Similarity=0.490  Sum_probs=48.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      |++||.|..++++.|+                      +||+|.+.++|.+||+ |||..+.||.|+|+++.|.-.
T Consensus        36 F~~~G~Vi~vr~~~d~----------------------~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           36 FASFGEVILIRFVEDK----------------------MWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPSGP   88 (91)
T ss_dssp             HHTTCCEEEEEECSSS----------------------EEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCSSC
T ss_pred             HHhCCCeEEEEEecCC----------------------EEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCCcc
Confidence            7899999999999873                      6999999999999998 999999999999999988643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.39  E-value=2.7e-13  Score=88.74  Aligned_cols=56  Identities=25%  Similarity=0.305  Sum_probs=49.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE------------CCEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI------------GMKRLK   68 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i------------~g~~i~   68 (81)
                      +|++||+|.+|+|+.+      +|              ||||+|.+.++|+.|++.|||..|            .|+.|.
T Consensus       163 ~F~~fG~I~~v~v~~~------kG--------------~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~  222 (240)
T 3u1l_A          163 VFSRLGDIDRIRYVES------KN--------------CGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLL  222 (240)
T ss_dssp             HHHTTSCEEEEEEEGG------GT--------------EEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCE
T ss_pred             HHHccCCEEEEEEECC------CC--------------EEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEE
Confidence            4899999999999853      67              999999999999999999999999            899999


Q ss_pred             EEeeCCCC
Q psy16913         69 VQLKRPKD   76 (81)
Q Consensus        69 V~~a~~~~   76 (81)
                      |+||.++.
T Consensus       223 V~wA~~~p  230 (240)
T 3u1l_A          223 VKWANEDP  230 (240)
T ss_dssp             EEECC---
T ss_pred             EEEccCCC
Confidence            99997654

>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=99.39  E-value=6.1e-13  Score=74.69  Aligned_cols=55  Identities=22%  Similarity=0.397  Sum_probs=43.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcE--ECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ--IGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~--i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|+++     ++|              ||||+|.++++|++    ++|..  +.|+.|.|.+|.++..+
T Consensus        31 ~F~~~G~i~~v~i~~~-----srG--------------faFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~~   87 (89)
T 3d2w_A           31 FFCQYGEVVDVFIPKP-----FRA--------------FAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHNK   87 (89)
T ss_dssp             HHTTTSCEEEEECCSS-----CCS--------------EEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC-----
T ss_pred             HHhccCCEEEEEEeeC-----CCC--------------EEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCcC
Confidence            4899999999999874     688              99999999999883    56655  45999999999988754

>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=99.39  E-value=3.5e-13  Score=81.87  Aligned_cols=62  Identities=26%  Similarity=0.389  Sum_probs=54.9

Q ss_pred             CccCCceeeEEEEEecCCCC--CcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC---CEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATN--QSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG---MKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~--~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~---g~~i~V~~a~~~   75 (81)
                      +|++||+|.++++++++.++  .++|              ||||+|.++++|++|++.|||..+.   ++.+.+.++.++
T Consensus        23 ~F~~~G~i~~v~i~~~~~~~~~~~~g--------------~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~   88 (175)
T 3nmr_A           23 LFEQYGAVYEINVLRDRSQNPPQSKG--------------CCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE   88 (175)
T ss_dssp             HHHTTSCEEEEEEEEECSSSSCEEEE--------------EEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGG
T ss_pred             HHHhCCCEEEEEEEecCCCCCCCcce--------------EEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccc
Confidence            48999999999999999776  7888              9999999999999999999998876   678888887655


Q ss_pred             C
Q psy16913         76 D   76 (81)
Q Consensus        76 ~   76 (81)
                      .
T Consensus        89 ~   89 (175)
T 3nmr_A           89 K   89 (175)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=5e-14  Score=83.87  Aligned_cols=59  Identities=12%  Similarity=0.088  Sum_probs=52.7

Q ss_pred             CccCCcee----eEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNV----ISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i----~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|    .+|.|+.++ +|+++|              ||||+|.++++|++|++. |+..+.||.|.|..+.++
T Consensus        43 ~F~~~g~v~g~v~~v~i~~d~-~gr~~G--------------~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~~  105 (123)
T 2dha_A           43 FFGQHCPITGGKEGILFVTYP-DGRPTG--------------DAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAA  105 (123)
T ss_dssp             HHHTTSCCTTGGGGEEEEECT-TSCEEE--------------EEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECHH
T ss_pred             HHHhhCCccCCcceEEEEECC-CCCEee--------------EEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCHH
Confidence            48899875    689999985 899999              999999999999999995 999999999999988654

>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=99.38  E-value=4.3e-13  Score=81.19  Aligned_cols=59  Identities=29%  Similarity=0.521  Sum_probs=54.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++++++++.+|.++|              ||||+|.++++|++|++.  +..+.|+.|.|.++.++
T Consensus        23 ~F~~~G~i~~v~i~~~~~~g~~~g--------------~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A           23 YFGKYGTVTDLKIMKDPATGRSRG--------------FGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             HHTTTCCEEEEECCCCTTTSSCCS--------------CEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCH
T ss_pred             HHHhCCCEEEEEEEECCCCCCccc--------------eEEEEEccHHHHHHHHhc--ccccCCeEcccccccch
Confidence            489999999999999998999999              999999999999999994  67999999999988764

>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=99.37  E-value=9.8e-14  Score=83.00  Aligned_cols=59  Identities=17%  Similarity=0.274  Sum_probs=52.3

Q ss_pred             CccCCceee--EEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVI--SSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~--~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++| .|.  +|+|++|+. |+++|              ||||+|.++++|++||+ +++..|.||.|.|..+.+++
T Consensus        62 ~F~~~-~i~~~~v~i~~d~~-GrsrG--------------faFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a~~~e  122 (126)
T 2hgm_A           62 FFSGL-EIVPNGITLPVDPE-GKITG--------------EAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE  122 (126)
T ss_dssp             HTTTS-CEEEEEEECCCCSS-SSSCS--------------EEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEECHHH
T ss_pred             HHhcC-CceeeEEEEEECCC-CCCce--------------EEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCHHH
Confidence            48999 566  899999986 99999              99999999999999998 57899999999999987643

>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=99.36  E-value=1.5e-12  Score=85.03  Aligned_cols=54  Identities=28%  Similarity=0.490  Sum_probs=50.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~   73 (81)
                      +|++||.|.+++++.++     +|              ||||+|.+.++|.+|++.|||..+. |+.|+|+|++
T Consensus       227 ~F~~~G~i~~v~~~~~~-----~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          227 LFNQFPGFKEVRLVPGR-----HD--------------IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             HHHhcCCeEEEEEecCC-----Cc--------------EEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            58999999999999654     57              9999999999999999999999999 9999999986

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=7e-13  Score=77.18  Aligned_cols=55  Identities=18%  Similarity=0.182  Sum_probs=45.0

Q ss_pred             CccCCceeeEEEEEecCCC---CCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRAT---NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~---~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|. +.++.++.+   |+++|              ||||+|.++++|++|++.|+  .++|+.+.+..+
T Consensus        28 ~F~~~G~i~-~~~~~~~~~~~~g~~~G--------------~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~   85 (114)
T 2dnl_A           28 SFRRFGPLV-VDWPHKAESKSYFPPKG--------------YAFLLFQEESSVQALIDACL--EEDGKLYLCVSS   85 (114)
T ss_dssp             HTTTTCCCC-EECTTSSSSCCCSCTTS--------------EEEECCSSHHHHHHHHHHSE--EETTEEEEEECC
T ss_pred             HHHhcCCEE-EEEeecCCCCCCCCccc--------------EEEEEECCHHHHHHHHHhhh--hcCCcEEEeccC
Confidence            589999999 888888877   68888              99999999999999999983  355555555444

>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=99.35  E-value=6.2e-13  Score=85.15  Aligned_cols=56  Identities=21%  Similarity=0.443  Sum_probs=52.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+++++.++     +|              ||||+|.+.++|++|++.|||..+.|+.|.|.++.++
T Consensus        55 ~F~~~G~i~~v~i~~~~-----~g--------------~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           55 LFGVYGDVQRVKILFNK-----KE--------------NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             HHHHHTCEEEEEECCTT-----SC--------------CEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             HHHhCCCeEEEEEEECC-----CC--------------EEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            48899999999999876     77              9999999999999999999999999999999999765

>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=99.35  E-value=1.3e-12  Score=83.35  Aligned_cols=58  Identities=22%  Similarity=0.307  Sum_probs=51.9

Q ss_pred             ccCCceeeEEEEEecCCCC----CcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          2 FLPFGNVISSKVFIDRATN----QSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~----~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      |++||+|.++.|+++..++    +++|              ++||+|.+.++|++|++.|||..+.||.|.|.+..
T Consensus       150 ~~~~G~v~~~~v~~~~~~~~~~~~~~G--------------~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          150 CGKFGAVNRVIIYQEKQGEEEDAEIIV--------------KIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HTTTSCEEEEEEEEEECCSSTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHccCCeEEEEEecCCCCcccCcCcee--------------EEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            7899999999999765443    6666              99999999999999999999999999999999874

>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=99.33  E-value=9.9e-13  Score=86.22  Aligned_cols=62  Identities=18%  Similarity=0.323  Sum_probs=50.4

Q ss_pred             CccCCc-eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G-~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++|| +|.++.++.++. +.++|              ||||+|.+.++|.+|+..|||..+.|+.|.|.++.++..
T Consensus       137 ~f~~~G~~i~~v~i~~~~~-~~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          137 LLQDINVVALSIRLPSLRF-NTSRR--------------FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             HHHHTTCCCCEEECC--------CC--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             HHHHhCCCeEEEEEEeCCC-CCcce--------------EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            488999 999999999874 77888              999999999999999999999999999999999987653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.33  E-value=4.4e-13  Score=83.54  Aligned_cols=56  Identities=21%  Similarity=0.443  Sum_probs=51.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+++++.++     +|              ||||+|.++++|++|++.|||..+.|+.|.|.++.++
T Consensus        24 ~F~~~G~i~~v~i~~~~-----~g--------------~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A           24 LFGVYGDVQRVKILFNK-----KE--------------NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             HHHTTCCCSEEECSTTC-----SS--------------CCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             HHHhcCCEEEEEEEeCC-----CC--------------EEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            48899999999998875     67              9999999999999999999999999999999999765

>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=99.32  E-value=1.9e-12  Score=84.32  Aligned_cols=62  Identities=24%  Similarity=0.324  Sum_probs=54.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC-CcEEC---CEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN-GFQIG---MKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln-g~~i~---g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.++ +|.++|              ||||+|.+.++|.+|+..|| |..+.   +++|.|.++.+..
T Consensus       116 ~F~~~G~i~~v~i~~~~-~g~~~g--------------~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          116 AFSQFGPVEKAVVVVDD-RGRATG--------------KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHGGGSCEEEEEEEEET-TSCEEE--------------EEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHhcCCeEEEEeeeCC-CCCcCc--------------EEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            48999999999999995 889999              99999999999999999994 55555   9999999997764


Q ss_pred             C
Q psy16913         77 A   77 (81)
Q Consensus        77 ~   77 (81)
                      +
T Consensus       181 ~  181 (261)
T 3sde_A          181 D  181 (261)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.29  E-value=1.3e-12  Score=72.58  Aligned_cols=57  Identities=19%  Similarity=0.344  Sum_probs=46.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|+.+     ++|              ||||+|.+.++|++|+..  ...+.|+.|.|.++.++...
T Consensus        25 ~F~~~G~i~~v~i~~~-----~~g--------------~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           25 FFSQYGDVMDVFIPKP-----FRA--------------FAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             HSTTTSCCCEEECCSS-----CCS--------------CCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCCC
T ss_pred             HHHHcCCeeEEEEecC-----CCC--------------EEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCCC
Confidence            5899999999998865     578              999999999999765331  34568999999999887654

>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=99.28  E-value=3.7e-12  Score=70.27  Aligned_cols=44  Identities=25%  Similarity=0.439  Sum_probs=40.1

Q ss_pred             eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913          7 NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus         7 ~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      +|.++.++.+      +|              ||||+|.++++|++|+ .|||..+.|+.|+|+.
T Consensus        43 ~v~~~~~~~~------kg--------------~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           43 PVLAVQINQD------KN--------------FAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SEEEEEECSS------SS--------------EEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             cceEEEecCC------Cc--------------EEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            8999988754      57              9999999999999999 9999999999999974

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.26  E-value=5.3e-13  Score=81.54  Aligned_cols=60  Identities=17%  Similarity=0.354  Sum_probs=49.7

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      |++||.+.. .++.+..++.++|              ||||+|.++++|++|++ |||..+.|+.|.|.++.++..
T Consensus        34 f~~~g~~~~-~~~~~~~~~~~~g--------------~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~   93 (175)
T 1fje_B           34 ISELFAKND-LAVVDVRTGTNRK--------------FGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDS   93 (175)
T ss_dssp             HHHHHHHHT-CCCCEEEEETTTT--------------EEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSC
T ss_pred             HHHhCCcce-EEEEECCCCcccc--------------EEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCccc
Confidence            567777665 3445555778888              99999999999999995 999999999999999987654

>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=99.26  E-value=4.8e-12  Score=80.99  Aligned_cols=56  Identities=18%  Similarity=0.350  Sum_probs=50.6

Q ss_pred             CccCCc-eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeCCC
Q psy16913          1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G-~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~~~   75 (81)
                      +|++|| +|.+++++.+     ++|              ||||+|.+.++|.+|++.|||..+. |+.|+|+|++++
T Consensus       171 ~f~~~G~~i~~v~i~~~-----~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          171 LFSSNGGVVKGFKFFQK-----DRK--------------MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHTTSCCEEEEEECSS-----STT--------------CEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHcCCCeeEEEEEEC-----CCc--------------EEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            488999 9999998653     267              9999999999999999999999999 999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.24  E-value=2.1e-12  Score=80.43  Aligned_cols=56  Identities=18%  Similarity=0.345  Sum_probs=50.6

Q ss_pred             CccCCc-eeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeCCC
Q psy16913          1 MFLPFG-NVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G-~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~~~   75 (81)
                      +|++|| +|.+++++.+.     +|              ||||+|.+.++|.+|+..|||..+. |+.|.|.|++++
T Consensus       140 ~f~~~G~~v~~v~i~~~~-----~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          140 LFSSNGGVVKGFKFFQKD-----RK--------------MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHTTSCCCEEEESSTT-----SS--------------CEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHcCCCceEEEEEeCC-----Cc--------------EEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            478999 99999986542     67              9999999999999999999999999 999999999875

>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=99.20  E-value=7.3e-12  Score=79.63  Aligned_cols=56  Identities=20%  Similarity=0.320  Sum_probs=48.5

Q ss_pred             CccCCcee--eEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCE----EEEEEee
Q psy16913          1 MFLPFGNV--ISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK----RLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i--~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~----~i~V~~a   72 (81)
                      +|++||.|  .+++++.++  +.++|              ||||+|.+.++|.+||..|||..+.|+    ++.|++|
T Consensus       143 ~F~~~G~v~~~~v~~~~~~--~~~~g--------------~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          143 ICDELGVKRPTSVKVFSGK--SERSS--------------SGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHHHHTCCCCSEEEECSCC--SSSSE--------------EEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             HHHhcCCcceEEEEEEcCC--CCCce--------------EEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            58899999  899988775  45568              999999999999999999999999986    6777765

>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=99.18  E-value=3.6e-11  Score=78.28  Aligned_cols=55  Identities=18%  Similarity=0.384  Sum_probs=50.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++.+.++      +|              ||||+|.+.++|++|+..|||..+.|+.|.|.++.+.
T Consensus        42 ~F~~~G~i~~v~i~~~------kg--------------~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~   96 (261)
T 3sde_A           42 LFERYGEPSEVFINRD------RG--------------FGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG   96 (261)
T ss_dssp             HTGGGCCCSEEEEETT------TT--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             HHHhcCCEEEEEEeCC------Cc--------------EEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccC
Confidence            4899999999998643      57              9999999999999999999999999999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.15  E-value=4e-12  Score=78.70  Aligned_cols=36  Identities=22%  Similarity=0.408  Sum_probs=34.3

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      ||||+|.++++|++|+ .|||..+.|+.|.|+++.+.
T Consensus        53 ~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           53 FAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             EEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             EEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            9999999999999999 79999999999999998765

>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=99.14  E-value=4e-11  Score=68.54  Aligned_cols=50  Identities=14%  Similarity=0.356  Sum_probs=45.8

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |++||.|..++++.|+                      +||+|.+.++|.+||+ |||..+.||.|+|++..+
T Consensus        45 F~~~G~Vilvr~v~d~----------------------~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           45 LGSYGTIVLVRINQGQ----------------------MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHSCCSEEEEETTE----------------------EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHCCCEEEEEEecCc----------------------EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccCC
Confidence            7889999999999884                      6999999999999999 999999999999998654

>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=99.09  E-value=1e-10  Score=79.88  Aligned_cols=53  Identities=15%  Similarity=0.192  Sum_probs=44.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC---CE--EEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG---MK--RLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~---g~--~i~V~~a~   73 (81)
                      +|++||+|.+|.|+.      +||              ||||+|.+.++|++||+.|||..+.   |+  .|.|+++.
T Consensus        40 ~F~~~G~V~~v~~~~------~kg--------------faFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           40 VLEKCGLVDALLMPP------NKP--------------YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             HHHTTSCEEEEECCT------TCS--------------EEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             HHHhcCCeEEEEEeC------CCC--------------EEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            489999999987653      467              9999999999999999999999983   44  67888773

>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=99.06  E-value=2.6e-10  Score=69.05  Aligned_cols=38  Identities=21%  Similarity=0.397  Sum_probs=35.1

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      ||||+|.++++|++|+ .|||..+.|+.|.|.++.+...
T Consensus        53 ~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~   90 (172)
T 2g4b_A           53 FAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQP   90 (172)
T ss_dssp             EEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCC
T ss_pred             EEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCC
Confidence            9999999999999999 8999999999999999876543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.54  E-value=8.3e-08  Score=56.94  Aligned_cols=52  Identities=15%  Similarity=0.208  Sum_probs=44.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcC-HHHHHHHHHhhC--CcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDN-PASAHTAIQAMN--GFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~-~~~A~~Ai~~ln--g~~i~g~~i~V~~a   72 (81)
                      +|++||+|..|.++.++.                    .|||.|.+ +++|..|+..||  +..|.|..++++..
T Consensus        39 ~F~~~G~V~~Vd~~~g~~--------------------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           39 LFSNHGEIKWIDFVRGAK--------------------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             HTCSSCCEEEEECCTTCS--------------------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             HHHhcCCEEEEEEecCCC--------------------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            489999999999988764                    68999999 799999999995  77888988777654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.78  E-value=2.3e-05  Score=45.86  Aligned_cols=46  Identities=15%  Similarity=0.140  Sum_probs=39.1

Q ss_pred             ceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEe
Q psy16913          6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL   71 (81)
Q Consensus         6 G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~   71 (81)
                      |.|..+.+..|-     .               =|+|+|.+...|.+|.-.|||.++.||.|++.-
T Consensus        51 g~i~KI~L~pDH-----~---------------GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           51 KDIRKILLVSDF-----N---------------GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTCSEEEEETTT-----T---------------EEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             cceeEEEEecCC-----C---------------ceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            777777766664     2               599999999999999999999999999999753

>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=97.47  E-value=0.0001  Score=44.08  Aligned_cols=35  Identities=11%  Similarity=0.021  Sum_probs=28.7

Q ss_pred             EEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc
Q psy16913         10 SSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF   60 (81)
Q Consensus        10 ~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~   60 (81)
                      +++|+++..  .++|              ||||+|.++++|++|++.+++.
T Consensus         2 ~~kl~ln~~--~~~G--------------~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGK--TLKG--------------ETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECS--SCEE--------------EEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecCc--cccc--------------hhHHHHHHHHhHHHHHHhhccc
Confidence            467777753  5777              9999999999999999888753

>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=97.46  E-value=0.00032  Score=40.45  Aligned_cols=37  Identities=22%  Similarity=0.213  Sum_probs=33.9

Q ss_pred             EEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913         40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus        40 ~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      ..|.|.++++|.+|...|++..+.|+.|+|-++++-.
T Consensus        49 irv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~~   85 (104)
T 1wey_A           49 VRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             EEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             EEEEeCChHHHHHHHHHhccceecCceeEEEecCCCC
Confidence            5799999999999999999999999999999987654

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=97.45  E-value=6.7e-05  Score=44.72  Aligned_cols=35  Identities=9%  Similarity=-0.062  Sum_probs=33.2

Q ss_pred             EEEEEEcCHHHHHHHHHhh-CCcEECCEEEEEEeeCC
Q psy16913         39 FGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKRP   74 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~l-ng~~i~g~~i~V~~a~~   74 (81)
                      +++|+|.++++|++|++.| ||..++| .|.++++.+
T Consensus        15 ~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           15 ETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             EEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            9999999999999999999 9999999 999998865

>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=97.37  E-value=0.00039  Score=40.99  Aligned_cols=50  Identities=16%  Similarity=0.282  Sum_probs=39.2

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC-EEEEEEee
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM-KRLKVQLK   72 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g-~~i~V~~a   72 (81)
                      |++||.|.+.....      ...              +-.|.|.++.+|++|+. .||..+.| -.|-|...
T Consensus        44 F~~~G~Iv~~~~~~------~~N--------------WihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           44 FAQYGNILKHVMSN------TGN--------------WMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             HHTTSCEEEEEECS------SSS--------------EEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             HHhhCcEEEeccCC------CCC--------------eEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            78999999877511      112              89999999999999999 69999985 55666653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.62  E-value=0.00096  Score=39.93  Aligned_cols=36  Identities=31%  Similarity=0.306  Sum_probs=31.3

Q ss_pred             ceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913         37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus        37 ~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      .++-.|+|+++.+|++|+. .||..+.|..|-|....
T Consensus        62 ~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             CcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            4588999999999999998 79999999977777653

>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=95.05  E-value=0.027  Score=32.14  Aligned_cols=36  Identities=31%  Similarity=0.506  Sum_probs=30.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN   58 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln   58 (81)
                      +|+.||. ..|+.+.|.                     -|||.|.+++.|..|+..+.
T Consensus        25 lFs~fgg-v~I~WidDT---------------------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           25 LFSAFGN-IQISWIDDT---------------------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             HTTTSEE-EEEEEEETT---------------------EEEEEEEEECHHHHHHHHHT
T ss_pred             HHhccCC-EEEEEEcCC---------------------eEEEEecCHHHHHHHHHhcc
Confidence            5899994 457778775                     89999999999999999764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.44  E-value=0.17  Score=28.97  Aligned_cols=39  Identities=21%  Similarity=0.385  Sum_probs=31.7

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      -|+|+|.+++.|++.++. ..+.+++.+|.|....++..+
T Consensus        49 ~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~~~~~   87 (104)
T 2dhx_A           49 GGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPPRAPA   87 (104)
T ss_dssp             EEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCCCCCC
T ss_pred             cEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCCCCcc
Confidence            689999999999999883 357888999999877666544

>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=94.37  E-value=0.031  Score=31.86  Aligned_cols=36  Identities=28%  Similarity=0.504  Sum_probs=29.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN   58 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln   58 (81)
                      +|+.||.| .|+.+.|.                     -|||.|.+++.|..|+..++
T Consensus        35 lFs~fggv-~I~WidDT---------------------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           35 LFSAFGNI-QISWIDDT---------------------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             HHTTTCSC-CCEEEETT---------------------EEEEECSCHHHHHHHHHHHH
T ss_pred             HhhccCCE-EEEEEcCC---------------------eEEEEecCHHHHHHHHHhcc
Confidence            58889844 56777775                     89999999999999998763

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=89.06  E-value=0.13  Score=36.37  Aligned_cols=36  Identities=14%  Similarity=0.202  Sum_probs=25.1

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHh
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA   56 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~   56 (81)
                      |++||+|.++.+-.++  |   -              |+.|+|.+.++++.++..
T Consensus        73 ~~~~g~i~~~~~~~~~--g---~--------------~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           73 LSQFGPINNHFFYESF--G---L--------------YAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HGGGSCCCCEEEECSS--S---E--------------EEEEECC---CCHHHHSS
T ss_pred             HHhcCCcceEEEEccC--C---e--------------EEEEEeCCHHHHHHHHhc
Confidence            6899999998765443  2   3              999999999998877553

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=85.54  E-value=0.49  Score=24.71  Aligned_cols=34  Identities=21%  Similarity=0.270  Sum_probs=26.1

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      |.||+-.. +.|..+++.|++..+.|+.+.|+.+.
T Consensus        42 ~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           42 ASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             CEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             cEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            78998876 45888999999999999999988764

---

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	81
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-05
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:) 9e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	9e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.001
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.001
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.002
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.002
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.003
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.003
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003

>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 = 49.2 bits (117), Expect = 6e-10
 Identities = 8/53 (15%), Positives = 20/53 (37%)

Query: 27 ECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
          +     +   +   +V +++   A  A   ++GF +  + L V       A +
Sbjct: 36 QIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 48.3 bits (115), Expect = 1e-09
 Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 8/80 (10%)

Query: 9  ISSKVFI-----DRATNQS--KCFGECNRKVSVNQKC-FGFVSFDNPASAHTAIQAMNGF 60
          ++S+VFI                F +  + V  +    F FV + N  +A  A+   +G 
Sbjct: 14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGR 73

Query: 61 QIGMKRLKVQLKRPKDAARP 80
           I  + L + L       R 
Sbjct: 74 MIAGQVLDINLAAEPKVNRS 93

>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 = 47.3 bits (112), Expect = 2e-09
 Identities = 12/59 (20%), Positives = 23/59 (38%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY 81
          K       K+      F FV + + A A  A++ +NG ++  + ++          R Y
Sbjct: 35 KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQY 93

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 8e-09
 Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 5/58 (8%)

Query: 23 KCFGECNRKVSV-----NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
              +  +   +     +      VSF +P  A   IQ ++G   G +++  Q     
Sbjct: 38 VECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT 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 = 45.1 bits (106), Expect = 2e-08
 Identities = 32/42 (76%), Positives = 37/42 (88%)

Query: 38  CFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
           CFGFVS+DNP SA  AIQ+MNGFQIGMKRLKVQLKR K+ ++
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 44.2 bits (104), Expect = 3e-08
 Identities = 13/53 (24%), Positives = 20/53 (37%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
           F       +   K + F  + +      AI  +NG Q+G K+L VQ      
Sbjct: 30 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 82

>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 = 43.0 bits (101), Expect = 9e-08
 Identities = 10/51 (19%), Positives = 20/51 (39%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          +G+         K FGF+  +    A  A   ++   +  K+L+V+     
Sbjct: 32 YGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 82

>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 = 43.1 bits (101), Expect = 9e-08
 Identities = 13/40 (32%), Positives = 22/40 (55%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
          + + FV F N   A  A++A+NG  +    ++V L +P D
Sbjct: 44 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 83

>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 = 43.0 bits (101), Expect = 1e-07
 Identities = 14/51 (27%), Positives = 21/51 (41%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          FG+        +K + FV F    SA  AI ++NG  I    +K    +  
Sbjct: 42 FGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 42.7 bits (100), Expect = 1e-07
 Identities = 11/53 (20%), Positives = 23/53 (43%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
             + N+   +    FGFV +  P  A  A++ + G  +   +L+V++     
Sbjct: 30 ISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT 82

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.7 bits (100), Expect = 1e-07
 Identities = 8/58 (13%), Positives = 17/58 (29%)

Query: 22 SKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
                         K   ++ F + A A   ++   G +I  + + +     K   R
Sbjct: 38 EDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 42.1 bits (98), Expect = 3e-07
 Identities = 11/59 (18%), Positives = 24/59 (40%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY 81
                  K+  N+K    V   +   A  A+  +NG ++  K +++ L + ++   P 
Sbjct: 26 VYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR 84

>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 = 41.6 bits (97), Expect = 3e-07
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 20 NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          ++     +     S+  +   FV F   +SA  A+++M GF    K +++Q  +  
Sbjct: 29 SRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 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 = 41.2 bits (96), Expect = 4e-07
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 14/72 (19%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
          PFG++   ++ +D  T + + F               FV F+    A  AI  MN  ++ 
Sbjct: 28 PFGDITDIQIPLDYETEKHRGFA--------------FVEFELAEDAAAAIDNMNESELF 73

Query: 64 MKRLKVQLKRPK 75
           + ++V L +P 
Sbjct: 74 GRTIRVNLAKPM 85

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 4e-07
 Identities = 13/56 (23%), Positives = 19/56 (33%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
                  ++   K F FV+F  P  A  A   ++G     + L V     K  A 
Sbjct: 37 ELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 41.2 bits (96), Expect = 5e-07
 Identities = 15/51 (29%), Positives = 25/51 (49%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
                 K++     +GFV++ +P  A  AI  +NG ++  K +KV   RP
Sbjct: 31 SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81

>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 = 41.3 bits (96), Expect = 5e-07
 Identities = 14/56 (25%), Positives = 25/56 (44%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
                 + +   + FGFV+F+N   A  A+ AMNG  +  ++++V         R
Sbjct: 34 EVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 40.7 bits (95), Expect = 6e-07
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 14/73 (19%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F P G ++S +V  D  T +S  +               +V+F  PA A  A+  MN  
Sbjct: 20 KFSPAGPILSIRVCRDMITRRSLGYA--------------YVNFQQPADAERALDTMNFD 65

Query: 61 QIGMKRLKVQLKR 73
           I  K +++   +
Sbjct: 66 VIKGKPVRIMWSQ 78

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 6e-07
 Identities = 14/48 (29%), Positives = 20/48 (41%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
             K +   K F F+SF     A  AI  ++GF      L V+  +P 
Sbjct: 41 AKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 88

>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 = 41.2 bits (96), Expect = 8e-07
 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 2/55 (3%)

Query: 29 NRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI--GMKRLKVQLKRPKDAARPY 81
              + N +    + + +P SA  A  +++G  I      L++   +       Y
Sbjct: 37 IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 91

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.3 bits (94), Expect = 9e-07
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 2/51 (3%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI--GMKRLKVQL 71
                  K++   +   FV ++    A  AI A+N      G + L V+L
Sbjct: 34 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 84

>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 = 40.3 bits (94), Expect = 1e-06
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 30 RKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
             S        V F+  A A  A++  NG  +  + + +QL
Sbjct: 34 YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 75

>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 = 40.5 bits (94), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 26/84 (30%), Gaps = 10/84 (11%)

Query: 6  GNVISSKVFI---------DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
          G+  SS + +             +  K +      V  N++        N   A  AIQ 
Sbjct: 1  GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVT-LLNGEQAQNAIQM 59

Query: 57 MNGFQIGMKRLKVQLKRPKDAARP 80
           + +    K L VQL+        
Sbjct: 60 FHQYSFRGKDLIVQLQPTDALLCS 83

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (94), Expect = 1e-06
 Identities = 8/57 (14%), Positives = 19/57 (33%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARPY 81
          + +              ++F NP SA  A   ++  +   K +K+   +       +
Sbjct: 34 YDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 39.6 bits (92), Expect = 2e-06
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 14/74 (18%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F   G + + ++  D  T  S  +   +              F +   +  AI+ +NG 
Sbjct: 22 LFRAIGPINTCRIMRDYKTGYSYGYAFVD--------------FTSEMDSQRAIKVLNGI 67

Query: 61 QIGMKRLKVQLKRP 74
           +  KRLKV   RP
Sbjct: 68 TVRNKRLKVSYARP 81

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 2e-06
 Identities = 11/49 (22%), Positives = 23/49 (46%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
             +V+   + +GFV F +   A  AI+ M+  ++  K ++V      +
Sbjct: 42 PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 90

>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 = 39.7 bits (92), Expect = 2e-06
 Identities = 13/48 (27%), Positives = 21/48 (43%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
           + K       F FV F++P  A  A+   +G+     RL+V+  R  
Sbjct: 44 IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (92), Expect = 2e-06
 Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 2/63 (3%)

Query: 20 NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKDA 77
             + FG     + +  K    V F+N  SA   +         I  ++        K  
Sbjct: 34 EALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI 93

Query: 78 ARP 80
           RP
Sbjct: 94 TRP 96

>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 = 39.3 bits (91), Expect = 2e-06
 Identities = 13/45 (28%), Positives = 20/45 (44%)

Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
          +   + FV F     A  A+ AMNG +I  K +KV       + +
Sbjct: 46 SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 39.8 bits (92), Expect = 2e-06
 Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F   G V  +K                  K +   K    VS+++P +A  A++  +G 
Sbjct: 28 FFKQCGVVKMNKR------TGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK 81

Query: 61 QIGMKRLKVQLKRPK 75
               +LKV L R K
Sbjct: 82 DFQGSKLKVSLARKK 96

>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 = 39.5 bits (92), Expect = 3e-06
 Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKRPKDAAR 79
               +   + FGFV F     A  A  A+ +   +  +RL ++    +   +
Sbjct: 42 KKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 39.7 bits (92), Expect = 3e-06
 Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 24  CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
                    S   + FGFV+F + A    A+ A     I  + ++ +    ++
Sbjct: 49  DCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVARE 100

>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 = 38.9 bits (90), Expect = 4e-06
 Identities = 12/39 (30%), Positives = 23/39 (58%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
          K FGFV+F+N A A  A + ++G  +  ++++V     +
Sbjct: 51 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 89

>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 = 38.9 bits (90), Expect = 4e-06
 Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 12/85 (14%)

Query: 6  GNVISSKVFI---------DRATNQSKCFGECNR-KVSVNQKCFGFVSFDNPASAHTAIQ 55
          G+  SS VF+         D        +G+     +    + F FV+F +   A +   
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC- 59

Query: 56 AMNGFQIGMKRLKVQLKRPKDAARP 80
                I    + +    PK  +  
Sbjct: 60 -GEDLIIKGISVHISNAEPKHNSNS 83

>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 = 38.9 bits (90), Expect = 4e-06
 Identities = 10/52 (19%), Positives = 21/52 (40%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
                 + +   K +  V ++    A  A +A+NG +I  + ++V     K
Sbjct: 36 NIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 38.1 bits (88), Expect = 5e-06
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
            FG          +   FV+++   SA  A+  +NG Q+   +LKV + R +
Sbjct: 25 SPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 77

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.1 bits (90), Expect = 7e-06
 Identities = 18/53 (33%), Positives = 25/53 (47%)

Query: 24  CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
                  + +   + +GFV F + +SA  AI  +NGF I  KRLKV L     
Sbjct: 71  SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>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 = 38.1 bits (88), Expect = 8e-06
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 38 CFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
           +GFV F+   +A  AI+ MNG  +  +++ V   + +
Sbjct: 49 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.8 bits (87), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 12 KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
          +   +   +  K      +K      C  F+ F+N  SA  A+Q MN   +G + + V L
Sbjct: 23 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL 81

Query: 72 KRPK 75
             K
Sbjct: 82 ADKK 85

>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 = 37.0 bits (85), Expect = 2e-05
 Identities = 13/49 (26%), Positives = 24/49 (48%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
               + N K + F++F +  ++  AI+AMNG  +  + + V     KD
Sbjct: 32 MRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD 80

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 2e-05
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 14/69 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
          +F  +G +    +  D+ + +S+ F               FV F+N   A  A +  NG 
Sbjct: 29 VFSKYGPIADVSIVYDQQSRRSRGFA--------------FVYFENVDDAKEAKERANGM 74

Query: 61 QIGMKRLKV 69
          ++  +R++V
Sbjct: 75 ELDGRRIRV 83

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 2e-05
 Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 2/49 (4%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
               + + K FGFV F    +    +   +   I  +    +L   K 
Sbjct: 41 KKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQ 87

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 2e-05
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
           F     + +   K +GF  + +  +A +A++ +NG +   + L+V     +
Sbjct: 37 SFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE 88

>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 = 36.6 bits (84), Expect = 2e-05
 Identities = 9/54 (16%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-FQIGMKRLKVQLKRPK 75
                     + +  + FV + +   A  AI+ ++G  ++  K ++V     K
Sbjct: 23 GDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK 76

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 2e-05
 Identities = 8/42 (19%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNG--FQIGMKRLKVQLKRPKD 76
          + F FV +++  +A  A + +     Q+   ++ V    P+ 
Sbjct: 45 RGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 37.3 bits (86), Expect = 2e-05
 Identities = 9/45 (20%), Positives = 16/45 (35%)

Query: 32 VSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
          V V      FV F +      A+Q + G +   + +  +   P  
Sbjct: 53 VEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>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 = 36.7 bits (84), Expect = 3e-05
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 6/57 (10%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMN------GFQIGMKRLKVQLKRPKDAA 78
               + + K   F  F    +A   + A +      G ++  ++LKV L   +D A
Sbjct: 41 VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 36.3 bits (83), Expect = 5e-05
 Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 1/61 (1%)

Query: 20 NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR 79
             +       + +   + +GFV+  + A+A  A +  N   I  ++  V L       R
Sbjct: 35 GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAYLGAKPR 93

Query: 80 P 80
           
Sbjct: 94 S 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 = 36.3 bits (83), Expect = 5e-05
 Identities = 5/53 (9%), Positives = 13/53 (24%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP 80
                V +   G V +        A++ ++  +      +    R       
Sbjct: 41 DVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSS 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 = 35.9 bits (82), Expect = 7e-05
 Identities = 6/38 (15%), Positives = 14/38 (36%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
           G  +  +    K + F  +     +  A   +NG ++
Sbjct: 44 CGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 81

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 9e-05
 Identities = 6/44 (13%), Positives = 14/44 (31%)

Query: 28  CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
               +  +     +V F     A  A+  +N      + +  +L
Sbjct: 59  VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 34.6 bits (79), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK 72
                  +V+   +  GF+ FD    A  AI+ +NG +       + +K
Sbjct: 34 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 83

>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 = 34.3 bits (78), Expect = 2e-04
 Identities = 9/35 (25%), Positives = 18/35 (51%)

Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
               V+F++   A  A+  +N   IG +++K+ L
Sbjct: 51 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL 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 = 34.0 bits (77), Expect = 2e-04
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK 68
             K +   K +GFV FD+P++A  A+ A+    +  +  K
Sbjct: 31 ILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK 71

>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 = 34.3 bits (78), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIG--MKRLKVQLKRPKDAA 78
              F ++ +++  +A  A   M GF +G   +RL+V   +   ++
Sbjct: 51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 33.9 bits (77), Expect = 3e-04
 Identities = 5/51 (9%), Positives = 16/51 (31%), Gaps = 1/51 (1%)

Query: 20 NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
                       +   + FGFV++        A+      ++  + ++ +
Sbjct: 31 GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPK 80

>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 = 34.0 bits (77), Expect = 3e-04
 Identities = 9/55 (16%), Positives = 12/55 (21%)

Query: 20 NQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
                    R  S   +  GF   ++       I   NG  I           P
Sbjct: 42 FGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 33.2 bits (75), Expect = 4e-04
 Identities = 7/52 (13%), Positives = 17/52 (32%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
                        + F ++   +   A   ++ +NG +I    L  ++  P
Sbjct: 29 ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>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 = 33.6 bits (76), Expect = 5e-04
 Identities = 11/49 (22%), Positives = 24/49 (48%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
            R ++   +   F++F N   A  A+  +NG+++  K L ++  + K 
Sbjct: 51 QFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 99

>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 = 34.2 bits (77), Expect = 7e-04
 Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 36  QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
           ++ F FV+FD+  S    +       +     +V+    K
Sbjct: 138 KRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSK 176

>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 = 33.0 bits (75), Expect = 7e-04
 Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
          +G   + V  N   +  + + +   A  A+   +G   G + + + +K   D
Sbjct: 27 YGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFG-ESIMIGVKPCID 76

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.1 bits (75), Expect = 7e-04
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 15/75 (20%)

Query: 1  MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
           F   G V   ++  DR + +SK                 +V F    S       + G 
Sbjct: 38 FFSAVGKVRDVRIISDRNSRRSKGIA--------------YVEFCEIQSVP-LAIGLTGQ 82

Query: 61 QIGMKRLKVQLKRPK 75
          ++    + VQ  + +
Sbjct: 83 RLLGVPIIVQASQAE 97

>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 = 32.9 bits (74), Expect = 9e-04
 Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 11/66 (16%)

Query: 4  PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
           FG +    +    +   S+                 +V++     A  AIQ +N   + 
Sbjct: 34 KFGKIHKVVINNSTSYAGSQGPS-----------ASAYVTYIRSEDALRAIQCVNNVVVD 82

Query: 64 MKRLKV 69
           + LK 
Sbjct: 83 GRTLKA 88

>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 = 32.5 bits (73), Expect = 0.001
 Identities = 9/69 (13%), Positives = 21/69 (30%), Gaps = 2/69 (2%)

Query: 9  ISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKR 66
          +  +V           FG+    + +  K   F+      +A T +         +  + 
Sbjct: 16 LPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQP 75

Query: 67 LKVQLKRPK 75
          + +Q    K
Sbjct: 76 IYIQYSNHK 84

>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 = 31.9 bits (72), Expect = 0.001
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
          K        ++   + FGFV+F + A     + A +  ++  K +  ++
Sbjct: 28 KECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKV 75

>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 = 31.9 bits (72), Expect = 0.002
 Identities = 4/48 (8%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
                   +  ++ F F++F         ++      +G+ + ++++
Sbjct: 28 SIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKV 74

>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 = 31.5 bits (71), Expect = 0.002
 Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 1/43 (2%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
              ++   + FGFV F    S    +      ++  K +  +
Sbjct: 32 KLDPITGRSRGFGFVLFKESESVDKVM-DQKEHKLNGKVIDPK 73

>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 = 31.2 bits (70), Expect = 0.002
 Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 24 CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
                 + S  ++ F FV+FD+   +   I       +     +V+
Sbjct: 31 VIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQKYHTVNGHNCEVR 76

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 31.2 bits (70), Expect = 0.003
 Identities = 8/49 (16%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
                  K +   + FGFV+F++        + ++  +I  K ++ + 
Sbjct: 27 DDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK 74

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 31.5 bits (70), Expect = 0.003
 Identities = 7/48 (14%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 28 CNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
               +   + FG+V F++      A++ + G ++    +K++  + +
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 31.5 bits (70), Expect = 0.003
 Identities = 9/72 (12%), Positives = 17/72 (23%)

Query: 9  ISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK 68
          + +             FG   R +         V F  P  A  A + +   +     L 
Sbjct: 18 LPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY 77

Query: 69 VQLKRPKDAARP 80
          ++          
Sbjct: 78 LEWAPIGVFGAA 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.73
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.73
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.68
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.64
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.63
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.62
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.6
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.6
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.58
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.58
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.55
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.53
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.52
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.52
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.51
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.51
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.5
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.49
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.47
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.45
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.45
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.43
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.33
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.29
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.16
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.15
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.09
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.99
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.75

>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=99.82  E-value=1.9e-20  Score=105.46  Aligned_cols=67  Identities=19%  Similarity=0.340  Sum_probs=63.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAARP   80 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~~   80 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|+.|++.|||..++|++|+|+||.+....+.
T Consensus        27 ~F~~~G~i~~v~i~~~~~~~~~kg--------------~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~~grq   92 (93)
T d1h2vz_          27 LFSKSGDIKKIIMGLDKMKKTACG--------------FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ   92 (93)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCTTCC
T ss_pred             HHHHHCCcceeccccccccccccc--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCCCC
Confidence            589999999999999999999999              999999999999999999999999999999999998888777


Q ss_pred             C
Q psy16913         81 Y   81 (81)
Q Consensus        81 ~   81 (81)
                      |
T Consensus        93 y   93 (93)
T d1h2vz_          93 Y   93 (93)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.82  E-value=2.9e-20  Score=103.99  Aligned_cols=62  Identities=34%  Similarity=0.562  Sum_probs=59.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|+.|+.+|.++|              ||||+|.+.++|++|++.|||..++|+.|+|+||+|+.
T Consensus        28 ~f~~~G~v~~v~i~~d~~t~~~rg--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          28 LFRPFGSISRIYLAKDKTTGQSKG--------------FAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             TSTTTCCEEEEEEEECSSSCSEEE--------------EEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             HHHHhccccccccccccccccccc--------------ceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            699999999999999998999999              99999999999999999999999999999999999875

>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=99.81  E-value=3e-20  Score=103.64  Aligned_cols=61  Identities=26%  Similarity=0.376  Sum_probs=58.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++++++|+.+|.++|              ||||+|.+.++|++|++.|||..++|+.|+|+||.++
T Consensus        27 ~F~~~G~i~~v~i~~d~~tg~~~g--------------~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          27 KFCDYGEIKNIHLNLDRRTGFSKG--------------YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             HHHHcCCccccccccccccccccc--------------ceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            589999999999999999999999              9999999999999999999999999999999999876

>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=99.81  E-value=2.8e-20  Score=102.20  Aligned_cols=60  Identities=32%  Similarity=0.566  Sum_probs=57.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++++++++.+|.++|              ||||+|.++++|++|++.|||..+.|+.|+|++|+|
T Consensus        22 ~F~~~G~v~~~~i~~~~~~g~~~g--------------~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          22 LFRAIGPINTCRIMRDYKTGYSYG--------------YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECS--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCCcceeeeeeecccCCccc--------------cceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            589999999999999999999999              999999999999999999999999999999999987

>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=99.80  E-value=2.2e-20  Score=104.29  Aligned_cols=64  Identities=28%  Similarity=0.541  Sum_probs=60.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.++.|+.+|.++|              ||||+|.++++|+.|++.|||..++|+.|.|++|+|++.+
T Consensus        25 ~F~~~G~i~~v~i~~d~~~~~~kg--------------~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~~k   88 (89)
T d2cqba1          25 AFIPFGDITDIQIPLDYETEKHRG--------------FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   88 (89)
T ss_dssp             HHTTTSCCCCEECCCCSSSCCCSS--------------EEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHhhCCeEEecccccccccccccc--------------eeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCC
Confidence            489999999999999999999999              9999999999999999999999999999999999987654

>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=99.80  E-value=4.7e-20  Score=105.32  Aligned_cols=65  Identities=75%  Similarity=1.235  Sum_probs=61.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|.+++++.++.+|.++|              ||||+|.++++|+.||+.|||..+.|+.|+|+||+++++++
T Consensus        38 ~F~~~G~i~~~~~~~~~~~g~~kG--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~~k  102 (102)
T d2cpza1          38 MFMPFGNVVSAKVFIDKQTNLSKC--------------FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK  102 (102)
T ss_dssp             HHGGGSCCSEEEEEECSSSCSEEE--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCC
T ss_pred             HHHhhccccccceeeecccCCCcc--------------ceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCCCC
Confidence            589999999999999999999999              99999999999999999999999999999999999998764

>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=99.80  E-value=8.6e-20  Score=100.09  Aligned_cols=60  Identities=30%  Similarity=0.428  Sum_probs=57.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+++|++|+.+|.++|              ||||+|.++++|..|++.|||..+.|++|+|+||+.
T Consensus        20 ~F~~~G~i~~v~i~~d~~tg~~~g--------------~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1          20 KFSPAGPILSIRVCRDMITRRSLG--------------YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             HHHHhCCEeEEEEEecccccCCCC--------------ceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            489999999999999999999999              999999999999999999999999999999999954

>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=99.79  E-value=5.9e-20  Score=101.89  Aligned_cols=63  Identities=29%  Similarity=0.420  Sum_probs=59.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++|++|+.||.++|              ||||+|.++++|+.|++.|||..+.|++|.|++|.+...
T Consensus        21 ~F~~~G~v~~v~i~~d~~tg~~rg--------------~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~~   83 (85)
T d2u2fa_          21 LLTSFGPLKAFNLVKDSATGLSKG--------------YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK   83 (85)
T ss_dssp             HHTSSSCEEEEEEECCCSSSCCCC--------------EEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCCC
T ss_pred             HHHhcCccceEEeeccccccccce--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            589999999999999999999999              999999999999999999999999999999999987654

>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=99.79  E-value=1.3e-19  Score=99.37  Aligned_cols=60  Identities=37%  Similarity=0.651  Sum_probs=57.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++++++++.++.++|              ||||+|.++++|+.|++.|||..++|+.|+|++|+|
T Consensus        22 ~f~~~G~v~~v~i~~~~~~~~~~g--------------~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          22 LFGSIGEIESCKLVRDKITGQSLG--------------YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             HHHTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCCcccccceeeccCCCcee--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            489999999999999998899999              999999999999999999999999999999999987

>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=99.78  E-value=7.3e-20  Score=103.01  Aligned_cols=63  Identities=29%  Similarity=0.443  Sum_probs=60.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++++++++.+|.++|              ||||+|.+.++|++|++.|||..+.|+.|+|++|.+++.
T Consensus        29 ~F~~~G~v~~v~~~~d~~tg~~kg--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          29 LFLQAGPVVNTHMPKDRVTGQHQG--------------YGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             HHHTTSCEEEEECCBCSSSCSBCS--------------CEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             HHHHhCCccccceeeccccccccc--------------ceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            589999999999999999999999              999999999999999999999999999999999998764

>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=99.78  E-value=2.9e-19  Score=101.32  Aligned_cols=64  Identities=28%  Similarity=0.352  Sum_probs=60.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|+.|+.+++++|              ||||+|.+.++|+.|++.|||..++|+.|+|++|.++.+.
T Consensus        28 ~F~~~g~v~~v~i~~d~~tg~~~g--------------~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          28 LFSAYGPLSELHYPIDSLTKKPKG--------------FAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             HHHTTSCEEEEECCCCTTTCCCCS--------------EEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             HHHhcCCceeeeecccccccccCc--------------ceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            489999999999999999999999              9999999999999999999999999999999999887643

>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=99.77  E-value=1.5e-19  Score=99.54  Aligned_cols=64  Identities=30%  Similarity=0.496  Sum_probs=59.1

Q ss_pred             CccCCceeeEE-EEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v-~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++ ++++++.+|+++|              ||||+|.++++|++|++.|||..++|++|+|++|.+++.+
T Consensus        18 ~F~~~G~i~~~~~i~~~~~~g~~~g--------------~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          18 TFSAFGVILQTPKIMRDPDTGNSKG--------------YAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             HHHTTSCBSSCCEECCCTTTCSCCS--------------EEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             HHHHhCceeeeEEEEeeccccccCc--------------eEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCcC
Confidence            58999999765 7899999999999              9999999999999999999999999999999999988754

>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=99.77  E-value=2.9e-19  Score=106.51  Aligned_cols=64  Identities=42%  Similarity=0.642  Sum_probs=60.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|+.++.|++++|              ||||+|.+.++|..||+.|||..|+|+.|+|++|.++..+
T Consensus        62 ~F~~~G~i~~v~i~~d~~t~~~rg--------------~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          62 LFERYGPIESVKIVCDRETRQSRG--------------YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             HHHHHSCEEEEEEEEETTTTEEEE--------------EEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             HHHhhccccccccccccccccccc--------------eeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            589999999999999999999999              9999999999999999999999999999999999877654

>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=99.76  E-value=7.4e-19  Score=95.91  Aligned_cols=59  Identities=27%  Similarity=0.428  Sum_probs=55.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+++|+.++ +++++|              ||||+|.++++|++|++.|||..++|++|+|++|.+
T Consensus        20 ~F~~~G~v~~~~i~~~~-~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_          20 LFAEFGTLKKAAVHYDR-SGRSLG--------------TADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             HHHHHSCEEEEEESCSS-CCCSCC--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             HHHHhCCCeEEEEEEee-ccccce--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            48899999999999987 888999              999999999999999999999999999999999863

>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=99.75  E-value=3.7e-18  Score=95.26  Aligned_cols=59  Identities=20%  Similarity=0.263  Sum_probs=52.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ   70 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~   70 (81)
                      +|++||+|.++.|++++.++.+++           +.|||||+|.++++|.+|++.|||..++|++|+|+
T Consensus        31 ~F~~~G~I~~v~i~~~~~~~~~~~-----------~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          31 YFGKFGKIHKVVINNSTSYAGSQG-----------PSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             TTTTTSCEEEEEEECCSSCCSSSC-----------CCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             HhcccCCceEEEEeeccCcCCCCC-----------cceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            599999999999999987776553           34599999999999999999999999999999985

>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=99.75  E-value=1.1e-18  Score=96.38  Aligned_cols=62  Identities=23%  Similarity=0.471  Sum_probs=55.4

Q ss_pred             CccCCceeeEEEEEecCCCC---CcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATN---QSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~---~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|++++.++   .++|              ||||+|.++++|++|++.|||..++|+.|.|++|.++.
T Consensus        18 ~F~~~G~v~~v~i~~~~~~~~~~~~kG--------------~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~~   82 (85)
T d2cpfa1          18 VFSKVGAIKSCTISKKKNKAGVLLSMG--------------FGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT   82 (85)
T ss_dssp             HHHTTSCEEEEEEEEEECTTCCEEEEE--------------EEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             HHHHhCCccccceecccccccccccce--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            58999999999999987665   3456              99999999999999999999999999999999997654

>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=99.75  E-value=7.2e-19  Score=99.01  Aligned_cols=63  Identities=22%  Similarity=0.377  Sum_probs=57.7

Q ss_pred             CccCCceeeEEEEEecCC-CCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh-CCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRA-TNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM-NGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~-~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l-ng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++|++++. +|.++|              ||||+|.++++|++|++.| ||..++|++|.|+||.++..
T Consensus        28 ~F~~~G~i~~v~i~~~~~~~g~~rg--------------~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          28 LFSTFGELKTVRLPKKMTGTGAHRG--------------FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             HHHTTSCEEEEECCCCCSSSCSSCS--------------EEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             HHHHhCCceEEEEEeccccCCCccc--------------EEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            589999999999998854 788999              9999999999999999998 99999999999999988754

>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=99.74  E-value=2e-18  Score=98.62  Aligned_cols=61  Identities=30%  Similarity=0.433  Sum_probs=56.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|+.++.+|+++|              ||||+|.+.++|++||+.+|+ .++|+.|.|++|.++.
T Consensus        30 ~F~~~G~i~~v~i~~d~~tg~~kg--------------~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          30 YFEGFGDIEEAVVITDRQTGKSRG--------------YGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   90 (103)
T ss_dssp             HHHTTSCEEEEEESCCSSSCCCCS--------------EEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             HHhhcccccceeccccccccccCC--------------eEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCC
Confidence            489999999999999999999999              999999999999999999886 7999999999986543

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.3e-19  Score=98.90  Aligned_cols=65  Identities=32%  Similarity=0.553  Sum_probs=61.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|..+.++.++.++.++|              ||||+|.++++|+.|++.|||..+.|+.|.|++|.++.+.+
T Consensus        25 ~F~~~G~i~~~~~~~~~~~~~~~g--------------~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~~r   89 (90)
T d1x5sa1          25 VFSKYGQISEVVVVKDRETQRSRG--------------FGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR   89 (90)
T ss_dssp             HHHHHSCCCEEEECCCSSSCSCCS--------------EEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCCC
T ss_pred             hhhccccccceeeccccccccccc--------------eEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCCC
Confidence            488999999999999998999999              99999999999999999999999999999999998887654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=1.1e-18  Score=96.50  Aligned_cols=58  Identities=24%  Similarity=0.466  Sum_probs=55.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a   72 (81)
                      +|++||+|.++++++++.+|.++|              ||||+|.++++|.+|++.|||..+.|  ++|.|+||
T Consensus        26 ~F~~~G~i~~~~~~~d~~~g~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          26 IFGKYGSIVQKNILRDKLTGRPRG--------------VAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHTSSSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHhhCCEeeeeeecccccccCce--------------eEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            589999999999999999999999              99999999999999999999999987  88999987

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=9.7e-19  Score=96.81  Aligned_cols=58  Identities=29%  Similarity=0.613  Sum_probs=54.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a   72 (81)
                      +|++||+|.++++++|+.+|.++|              ||||+|.++++|++|++.|||..+.|  ++|.|+||
T Consensus        26 ~F~~~G~v~~v~i~~d~~~g~~kg--------------~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          26 LFSQYGRIITSRILVDQVTGVSRG--------------VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhCCccccccccccccccCCC--------------eeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            589999999999999998999999              99999999999999999999999998  56999986

>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=99.74  E-value=3.4e-18  Score=95.41  Aligned_cols=62  Identities=29%  Similarity=0.403  Sum_probs=56.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++++.++.++  +|              ||||+|.+.++|..|++.|||..+.|+.|+|+||.++..+
T Consensus        28 ~F~~~G~i~~v~i~~d~~~~--~~--------------~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~   89 (90)
T d2cqia1          28 LFSQIGPCKSCKMITEHTSN--DP--------------YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   89 (90)
T ss_dssp             HHHHHSCEEEEEEECCCCSS--CC--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             HHHhcCCceeeeeecccCcc--ce--------------eeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            58899999999999987543  67              9999999999999999999999999999999999887654

>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=99.74  E-value=1.4e-18  Score=96.81  Aligned_cols=62  Identities=35%  Similarity=0.602  Sum_probs=56.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|+.++  +.++|              ||||+|.+.++|++|++.|||..++|+.|.|++|.++++|
T Consensus        28 ~F~~~G~v~~~~i~~~~--~~~kg--------------~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~R   89 (89)
T d1cvja2          28 TFSAFGNILSCKVVCDE--NGSKG--------------YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER   89 (89)
T ss_dssp             HHHTTSCEEEEEECCBT--TBCCS--------------CEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTTC
T ss_pred             HHHhcCCceEEEEEeec--CCCcc--------------eeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            58999999999999986  34678              9999999999999999999999999999999999988764

>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=99.73  E-value=3e-18  Score=95.95  Aligned_cols=62  Identities=27%  Similarity=0.388  Sum_probs=56.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|++|+.+|.++|              ||||+|.++++|++|++.  +..++|+.|.|++|.++..+
T Consensus        28 ~F~~~G~i~~v~i~~d~~tg~srG--------------~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~~~   89 (90)
T d2cqga1          28 YFSTFGEVLMVQVKKDLKTGHSKG--------------FGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQSQ   89 (90)
T ss_dssp             HHGGGSCEEEEEEEECSSSCSEEE--------------EEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTCCC
T ss_pred             HHHhhcccceeeeccCCCCcccCC--------------EEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCCCC
Confidence            489999999999999999999999              999999999999999984  45899999999999987653

>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=99.73  E-value=5.2e-19  Score=100.98  Aligned_cols=61  Identities=25%  Similarity=0.347  Sum_probs=57.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|+.||+|.+++|++++.+|+++|              ||||+|.++++|++|+. |||..+.|+.|.|+++.+++
T Consensus        38 ~F~~~G~V~~v~i~~d~~tg~~kG--------------~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~~   98 (101)
T d2cq4a1          38 FFSAVGKVRDVRIISDRNSRRSKG--------------IAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEK   98 (101)
T ss_dssp             HHTTTSCEEEEEECCSCCSSSCCC--------------CEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHHH
T ss_pred             HHcCCCeEEEEEeeecCCCccccc--------------eEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCCC
Confidence            589999999999999999999999              99999999999999995 99999999999999987643

>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=99.73  E-value=7.8e-19  Score=100.20  Aligned_cols=62  Identities=26%  Similarity=0.513  Sum_probs=58.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|+.++.+|+++|              ||||+|.+.++|+.|++.|||..+.|+.|+|++|.++.
T Consensus        28 ~f~~~G~i~~v~i~~~~~tg~~~g--------------~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          28 IFSEVGPVVSFRLVYDRETGKPKG--------------YGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             HHHTTSCCSEEEEEEETTTTEEEE--------------EEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             hhhccccccccccccccceeccCC--------------ceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            589999999999999999999999              99999999999999999999999999999999998764

>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=99.73  E-value=3.7e-18  Score=97.69  Aligned_cols=63  Identities=21%  Similarity=0.386  Sum_probs=59.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.|++|+.++.++|              ||||+|.+.++|++|++ ++|..|+|+.|.|++|.++.++
T Consensus        40 ~F~~~G~i~~~~i~~d~~~~~~kg--------------~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          40 YYEQWGKLTDCVVMRDPASKRSRG--------------FGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             HHTSSCCCSEEEEECCTTTSSCCS--------------EEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCCC
T ss_pred             HHHhhCcccceeecccccCCCccC--------------eEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCCC
Confidence            489999999999999999999999              99999999999999996 7999999999999999998764

>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=99.73  E-value=1.3e-18  Score=95.22  Aligned_cols=60  Identities=18%  Similarity=0.293  Sum_probs=50.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|..+.++.++.+|.++|              ||||+|.++++|++|++.|||..++|++|.|++|+|
T Consensus        21 ~f~~~G~v~~~~~~~~~~~~~~~g--------------~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          21 LLQDINVVALSIRLPSLRFNTSRR--------------FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             HHHHTTCCCCEEECC-------CC--------------EEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCcEEeeeeecccccccccc--------------eeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            488999999999888888899999              999999999999999999999999999999999987

>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=99.73  E-value=1.1e-17  Score=93.81  Aligned_cols=61  Identities=28%  Similarity=0.538  Sum_probs=55.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+|+++.++.  .++|              ||||+|.++++|.+|++.|||..++|+.|+|++|+++..
T Consensus        31 ~F~~~G~v~~v~~~~~~~--~~kg--------------~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          31 MFGQFGKILDVEIIFNER--GSKG--------------FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             HGGGTSCEEEEEEECCTT--TTCC--------------EEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             HHhhcceeeecccccccc--CCcc--------------eeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            589999999999998863  3678              999999999999999999999999999999999998754

>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=99.73  E-value=3.5e-18  Score=94.72  Aligned_cols=60  Identities=28%  Similarity=0.477  Sum_probs=52.4

Q ss_pred             CccCCceeeEEEEEec-CCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFID-RATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~-~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+++|+.+ +.+++++|              ||||+|.+.++|++|++ |||..++|+.|+|++|.++
T Consensus        25 ~F~~~G~i~~v~i~~~~~~~~~~kg--------------~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          25 SFEGFGSIEKINIPAGQKEHSFNNC--------------CAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             HHGGGSCEEEEECCSCCC---CCCE--------------EEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             HHHhhhhccceeeecccCCccccce--------------eeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            4899999999998764 46788888              99999999999999996 9999999999999999875

>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=99.72  E-value=6.2e-18  Score=92.92  Aligned_cols=55  Identities=27%  Similarity=0.571  Sum_probs=52.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV   69 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V   69 (81)
                      +|++||+|.+++|+.++.+++++|              ||||+|.+.++|+.|++.|||..++|++|+|
T Consensus        29 ~F~~~G~i~~v~i~~~~~~~~~~g--------------~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          29 VFSKYGPIADVSIVYDQQSRRSRG--------------FAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             HHHTTSCEEEEEEEECSSSSSEEE--------------EEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             HHHHhCCCcccccccccccccccc--------------ceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            489999999999999998999999              9999999999999999999999999999987

>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=99.71  E-value=1.6e-18  Score=94.55  Aligned_cols=57  Identities=26%  Similarity=0.446  Sum_probs=54.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+++|++|+.||+++|              ||||+|.++++|++|++ +|+..++|+.|.|+.|
T Consensus        20 ~F~~~G~i~~v~i~~d~~tg~~kG--------------~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          20 YFGQFGEVKECLVMRDPLTKRSRG--------------FGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             HHTTTSCCCCEEEECCCCSSSCSS--------------EEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             HHHHhCCcceeeeecccCCCCccc--------------eEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            489999999999999999999999              99999999999999997 7999999999999987

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.7e-17  Score=91.65  Aligned_cols=59  Identities=19%  Similarity=0.349  Sum_probs=55.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.+++|++|+.+|.++|              ||||+|.++++|++|++ +++..|+|+.|+|+.|.+
T Consensus        26 ~F~~~G~i~~v~i~~d~~tg~~kG--------------~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1          26 HFEQWGTLTDCVVMRDPNTKRSRG--------------FGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (84)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             HHHhhccccceeecccccCCCccc--------------EEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeeeC
Confidence            489999999999999999999999              99999999999999997 699999999999998853

>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=99.71  E-value=2.5e-17  Score=93.33  Aligned_cols=56  Identities=25%  Similarity=0.462  Sum_probs=51.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|        ++|              ||||+|.+.++|++||+.|||..+.|+.|+|+++.++...
T Consensus        36 ~F~~~G~i~~~~i--------~rg--------------~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          36 IFSKYGKIVGCSV--------HKG--------------FAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN   91 (98)
T ss_dssp             SSTTSSCEEEEEE--------ETE--------------EEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCCC
T ss_pred             HHhhcCCEEEEEE--------eCC--------------eEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            6999999999988        367              9999999999999999999999999999999999775543

>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=99.70  E-value=1.4e-17  Score=94.13  Aligned_cols=65  Identities=28%  Similarity=0.448  Sum_probs=57.6

Q ss_pred             CccCCceee--------EEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVI--------SSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~--------~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.        .+.+..++.+++++|              ||||+|.++++|++|++.|||..++|++|+|++|
T Consensus        28 ~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g--------------~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a   93 (101)
T d2cpea1          28 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG--------------DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA   93 (101)
T ss_dssp             HHTTTSCBCBCSSSCCBSEECCBCTTTCSBCS--------------EEEEEBSSHHHHHHHHHHHTTCEETTEECEEECS
T ss_pred             HHHHCceEEEeeecccceeEEeeccccccccc--------------eeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            488999874        566778888888888              9999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q psy16913         73 RPKDAAR   79 (81)
Q Consensus        73 ~~~~~~~   79 (81)
                      +++.++.
T Consensus        94 ~~~~p~~  100 (101)
T d2cpea1          94 RKKPPMN  100 (101)
T ss_dssp             SCCCCST
T ss_pred             CCCCCCC
Confidence            9876653

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9.9e-18  Score=96.07  Aligned_cols=57  Identities=18%  Similarity=0.175  Sum_probs=53.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+++|+++. +++++|              ||||+|.+.++|.+|++.|||..++||+|.|++.
T Consensus        47 ~f~k~G~I~~v~I~~~~-~~~~~G--------------~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          47 MEEKYGEVEEMNVCDNL-GDHLVG--------------NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHTCCEEEEEECCSS-SSSSEE--------------EEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HhccCCCEEEEEeecCC-CCCEee--------------EEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            47899999999998775 888999              9999999999999999999999999999999985

>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=99.69  E-value=1.2e-18  Score=98.87  Aligned_cols=64  Identities=20%  Similarity=0.339  Sum_probs=60.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|..+.++.+..+|.++|              ||||+|.++++|+.|++.|||..+.|+.|+|+||++++++
T Consensus        38 ~f~~~G~v~~~~~~~~~~~g~~~g--------------~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~r  101 (102)
T d2cpxa1          38 LFARFQEKKGPPIQFRMMTGRMRG--------------QAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  101 (102)
T ss_dssp             HTHHHHHSSSSCCEEEEECSSSCS--------------EEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             HHhhccceeeEEeecccccccccc--------------cceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcccC
Confidence            588999999999998888899999              9999999999999999999999999999999999998875

>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=99.69  E-value=9e-18  Score=90.97  Aligned_cols=57  Identities=25%  Similarity=0.446  Sum_probs=53.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.++.|++++.+++++|              ||||+|.++++|++|++ +++..|+|+.|.|+.|
T Consensus        19 ~F~~~G~i~~~~i~~d~~t~~~kg--------------~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          19 YFSKFGEVVDCTLKLDPITGRSRG--------------FGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             HHHTTSCEEEEECCCBTTTTBCCS--------------EEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             HHHhhccccccccccCCCCCCcCc--------------eEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            489999999999999999999999              99999999999999997 7999999999999754

>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=99.68  E-value=3.7e-17  Score=91.83  Aligned_cols=64  Identities=27%  Similarity=0.465  Sum_probs=58.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhC------CcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN------GFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~ln------g~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|.++.++.++.++.++|              ||||+|.+.++|.+|++.||      |..++|+.|+|++|.+
T Consensus        28 ~f~~~G~v~~~~~~~~~~~~~~~g--------------~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~   93 (98)
T d1x4ha1          28 VLQQFGDLKYVRVVLHPDTEHSKG--------------CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT   93 (98)
T ss_dssp             HHHTTSCEEEEECCBCSSSCCBCS--------------EEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCC
T ss_pred             HHhccccceeeeeccccccccccc--------------eEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCC
Confidence            488999999999999998999999              99999999999999999886      6789999999999998


Q ss_pred             CCCC
Q psy16913         75 KDAA   78 (81)
Q Consensus        75 ~~~~   78 (81)
                      +.+.
T Consensus        94 k~~a   97 (98)
T d1x4ha1          94 RDEA   97 (98)
T ss_dssp             CCCC
T ss_pred             CCcC
Confidence            8754

>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=99.66  E-value=6.2e-17  Score=91.34  Aligned_cols=57  Identities=32%  Similarity=0.513  Sum_probs=52.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.+++++.+      +|              ||||+|.+.++|+.|+..|||..+.|+.|+|.|++++..
T Consensus        38 ~F~~fG~i~~v~i~~~------kg--------------~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p~   94 (96)
T d1x4ga1          38 TFSPFGQIMEIRVFPE------KG--------------YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD   94 (96)
T ss_dssp             HHHHHSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             HHHHhCCceEEEEEec------ce--------------EEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            5889999999999976      57              999999999999999999999999999999999987643

>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=99.66  E-value=1.4e-16  Score=86.56  Aligned_cols=57  Identities=19%  Similarity=0.394  Sum_probs=53.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|..+.++.++.++.++|              ||||+|.++++|++|++ +||..|+|++|.|+.|
T Consensus        22 ~F~~~G~i~~~~~~~~~~~~~~~g--------------~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          22 YFEQYGKIEVIEIMTDRGSGKKRG--------------FAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             HHHHhccccccccccCCCCccccc--------------EEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            489999999999999999999999              99999999999999986 8999999999999987

>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=99.65  E-value=1.4e-17  Score=90.46  Aligned_cols=57  Identities=21%  Similarity=0.452  Sum_probs=52.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+++|+.|+.+++++|              ||||+|.++++|++||+ +++..++|+.|.|+.|
T Consensus        19 ~F~~~G~I~~v~i~~d~~t~~~rG--------------~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          19 YFGGFGEVESIELPMDNKTNKRRG--------------FCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHSCEEEEECCCCTTTCCTTC--------------CEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             HHHHhCCccccccccccccccccc--------------EEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            489999999999999999999999              99999999999999997 5778999999999875

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=5.1e-17  Score=92.89  Aligned_cols=57  Identities=21%  Similarity=0.448  Sum_probs=52.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++|++++     +|              ||||+|.+.++|++|++.|||..+.|+.|+|++++.+.
T Consensus        23 ~F~~fG~I~~v~i~~~~-----kg--------------~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          23 LFGVYGDVQRVKILFNK-----KE--------------NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             HHHHHTCEEEEEECCTT-----SC--------------CEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             HHhhccccceEEEEecc-----cc--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            58999999999999875     67              99999999999999999999999999999999997554

>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=99.64  E-value=5.9e-17  Score=92.02  Aligned_cols=59  Identities=27%  Similarity=0.454  Sum_probs=54.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|++||+|..+.++.+. ++.++|              ||||+|.+.++|++|++.|||..|.|+++.|.++.|
T Consensus        38 ~F~~~G~i~~~~~~~~~-~~~~~g--------------~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          38 MLKPFGQVISTRILRDS-SGTSRG--------------VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             TTTTTSCEEEEEEEECS-SSCEEE--------------EEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             HHhhcccccceeeeccc-cccccc--------------ceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            69999999999998885 788888              999999999999999999999999999999887765

>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=99.64  E-value=4.7e-17  Score=87.52  Aligned_cols=57  Identities=25%  Similarity=0.465  Sum_probs=53.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|..+.++.++.++.++|              ||||+|.++++|++|++ +||..++|++|+|++|
T Consensus        19 ~F~~~G~i~~~~~~~~~~~~~~~~--------------~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          19 YFEQFGKVDDAMLMFDKTTNRHRG--------------FGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHTTSCCSEECCBCCTTCTTSCC--------------EEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             HHHHhCCcceeeeeeeccccccCc--------------eeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            489999999999999998999999              99999999999999997 9999999999999986

>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=99.63  E-value=2.6e-16  Score=90.65  Aligned_cols=58  Identities=17%  Similarity=0.306  Sum_probs=52.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+|++..+   +.++|              ||||+|.+.++|..|++.|||..|+|+.|.|.++.+.
T Consensus        27 ~F~~~G~v~~i~~~~~---~~~kG--------------~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          27 IFGKYGPIRQIRVGNT---PETRG--------------TAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             HHHTTSCEEEEEEECS---TTTTT--------------EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             HHhhcCCeEeeccccc---CCcCC--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            5899999999998754   46688              9999999999999999999999999999999998653

>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=99.63  E-value=5.9e-17  Score=86.73  Aligned_cols=54  Identities=33%  Similarity=0.708  Sum_probs=51.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK   68 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~   68 (81)
                      +|++||+|.++++++++.++.++|              ||||+|.++++|++|++.|||..++|+.|+
T Consensus        18 ~F~~~G~v~~~~~~~~~~~~~~~g--------------~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          18 LCQPYGKIVSTKAILDKTTNKCKG--------------YGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             TSTTTSCEEEEEEECCSSSCSCCS--------------EEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             HHhhhccccccccccccccccccc--------------eeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            699999999999999999999999              999999999999999999999999998763

>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=99.63  E-value=9.9e-17  Score=87.46  Aligned_cols=56  Identities=32%  Similarity=0.540  Sum_probs=50.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.+..+      +|              ||||+|.+.++|..|++.|||..++|++|+|+||+++.
T Consensus        23 ~F~~~G~I~~v~~~~~------~~--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          23 AFSPFGNIIDLSMDPP------RN--------------CAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             HHSTTCCCSCEEEETT------TT--------------EEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             HHhccCccceeeeccC------CC--------------EEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            5899999999998754      56              99999999999999999999999999999999998753

>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=99.62  E-value=1.2e-16  Score=89.20  Aligned_cols=60  Identities=25%  Similarity=0.427  Sum_probs=53.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++++..   +++++|              ||||+|.+.++|.+|++.|||..++|+.|.|.||+++.+
T Consensus        27 ~f~~~G~i~~i~~~~---~~~~~g--------------~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~~   86 (91)
T d1nu4a_          27 IFSRFGQILDILVSR---SLKMRG--------------QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   86 (91)
T ss_dssp             HHGGGSCEEEEECCH---HHHHTT--------------CEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             HhcccccccceEEee---eccCCC--------------ceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCch
Confidence            389999999988654   466788              999999999999999999999999999999999988754

>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=99.61  E-value=4.1e-16  Score=89.19  Aligned_cols=57  Identities=19%  Similarity=0.176  Sum_probs=51.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++++++      +++              ||||+|.+.++|.+|++.|||..++|+.|+|.||+++..
T Consensus        30 lF~~~G~i~~~~~~k------~~~--------------~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          30 LFRTYDKDTTFQYFK------SFK--------------RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             HHHTTCSSCEEEEET------TTT--------------EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             HhcccccceEEEEec------CCC--------------EEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            589999999999874      356              999999999999999999999999999999999977654

>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=99.61  E-value=3.5e-16  Score=86.57  Aligned_cols=56  Identities=21%  Similarity=0.382  Sum_probs=51.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+++++.+      +|              ||||+|.+.++|++|++.|||..++|+.|+|+||.++.
T Consensus        28 ~F~~~G~i~~i~~~~~------k~--------------~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          28 LFEKYGKAGEVFIHKD------KG--------------FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             HTSTTCCCSEEEEETT------TT--------------EEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             HHHHhCCceEeeeecc------cc--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            5899999999999865      46              99999999999999999999999999999999998764

>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=99.60  E-value=1.1e-15  Score=85.74  Aligned_cols=60  Identities=23%  Similarity=0.469  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|..+.+..+   +.++|              ||||+|.++++|+.||+.|||..+.|++|+|+||++...
T Consensus        34 ~F~~~G~v~~~~~~~~---~~~~g--------------~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~r~   93 (95)
T d1x4aa1          34 VFYKYGAIRDIDLKNR---RGGPP--------------FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG   93 (95)
T ss_dssp             HHGGGSCEEEEEECCS---SSSSC--------------CEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCC
T ss_pred             HHhcCCceEEEEeccc---ccccc--------------eEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCCCC
Confidence            5899999999887543   35677              999999999999999999999999999999999987543

>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=99.60  E-value=2.7e-17  Score=92.05  Aligned_cols=59  Identities=15%  Similarity=0.269  Sum_probs=53.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.++.++.+ .+|+++|              ||||+|.+.++|++|++ |||..+.|++|+|++|++|
T Consensus        33 ~F~~~G~i~~~~v~~~-~~g~~kg--------------~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          33 AISELFAKNDLAVVDV-RTGTNRK--------------FGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             HHHHHHHHHTCCCCEE-EEETTTT--------------EEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             HHhcCCcEEEeeeeec-CCCCccE--------------EeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            4889999999988765 4889999              99999999999999996 9999999999999999875

>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=99.60  E-value=3.6e-16  Score=87.85  Aligned_cols=64  Identities=16%  Similarity=0.253  Sum_probs=54.8

Q ss_pred             CccCCce-eeEEEEEecC-CCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCC--cEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGN-VISSKVFIDR-ATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG--FQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~-i~~v~i~~~~-~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng--~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+ |.++.++.+. .+++++|              ||||+|.++++|..|++.|++  ..+.|+.|.|+||.|+.
T Consensus        21 ~f~~~g~~i~~v~~~~~~~~~~~~rg--------------~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          21 EIAKVTEGVLDVIVYASAADKMKNRG--------------FAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             HHHHHSTTEEEEECCSSSCTTTTTCC--------------EEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             HHHHhCCcceEEEEeeeccccccCCC--------------eEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCC
Confidence            4889996 8999999875 4578888              999999999999999999964  45679999999999876


Q ss_pred             CC
Q psy16913         77 AA   78 (81)
Q Consensus        77 ~~   78 (81)
                      +.
T Consensus        87 ~~   88 (96)
T d2disa1          87 DV   88 (96)
T ss_dssp             ST
T ss_pred             CC
Confidence            54

>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=99.59  E-value=1.5e-15  Score=83.76  Aligned_cols=57  Identities=21%  Similarity=0.172  Sum_probs=52.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~   73 (81)
                      +|+.||+|.+++|+.++ ++.++|              ||||+|.++++|++|++ ++|..+.|+.|.|.++.
T Consensus        26 ~F~~~G~v~~v~l~~~~-~~~~kG--------------~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          26 WLEDKGQVLNIQMRRTL-HKAFKG--------------SIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHTTSCCEEEEEEEECT-TCCEEE--------------EEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             HHHHhcccccceeeeec-cCCcce--------------EEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            48999999999998876 888899              99999999999999996 79999999999999853

>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=99.58  E-value=2.7e-15  Score=85.11  Aligned_cols=62  Identities=19%  Similarity=0.393  Sum_probs=52.5

Q ss_pred             CccCCceeeEEEEEecC-CCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDR-ATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~-~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++|| |.++.++.++ .++.++|              ||||+|.++++|++|+ .||+..|+|+.|+|++|.++...
T Consensus        35 ~f~~~g-~~~~~~~~~~~~~g~~~g--------------~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          35 FFRGLN-ISAVRLPREPSNPERLKG--------------FGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             HTTTSC-EEEEECCBCSSCTTSBCS--------------CEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             HHHHhc-cccceeeeeeccCCCcce--------------eeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCCC
Confidence            589999 6777777665 4678888              9999999999998776 59999999999999999887654

>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=99.58  E-value=1.5e-15  Score=85.36  Aligned_cols=60  Identities=17%  Similarity=0.268  Sum_probs=52.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAAR   79 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~~   79 (81)
                      +|++||+|..+.     .++.++|              ||||+|.+.++|++|++.|||..++|++|+|+|+.++..++
T Consensus        36 ~F~~~g~v~~~~-----~~~~~~~--------------~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~~r   95 (96)
T d1fjca_          36 VFEDALEIRLVS-----QDGKSKG--------------IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR   95 (96)
T ss_dssp             HHCSEEEECCEE-----ETTEEEE--------------EEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCCCC
T ss_pred             HHHhcccceeee-----ecCcccc--------------EEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCCC
Confidence            488999886653     2567778              99999999999999999999999999999999999987754

>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=99.58  E-value=1.5e-15  Score=83.63  Aligned_cols=58  Identities=26%  Similarity=0.367  Sum_probs=50.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|..+.+.      .++|              ||||+|.++++|..|+..|||..|.|+.|.|+||+|++..
T Consensus        28 ~F~~~g~i~~~~~~------~~rg--------------~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~~   85 (86)
T d2cpda1          28 EFNNIKPGAVERVK------KIRD--------------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD   85 (86)
T ss_dssp             HHHTTSTTCEEEEE------ECSS--------------EEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCCC
T ss_pred             hhcccceeeeEEEc------cccE--------------EEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCCC
Confidence            48899998877653      3467              9999999999999999999999999999999999987653

>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=99.58  E-value=4.5e-16  Score=85.04  Aligned_cols=58  Identities=19%  Similarity=0.302  Sum_probs=50.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCc-EECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF-QIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~-~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||.|.++.++..      +|              ||||+|.++++|++|++.|||. .++|++|+|++|.|+..+
T Consensus        21 ~F~~~G~i~~~~~~~~------rg--------------~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1          21 LFGDRKLPLAGQVLLK------SG--------------YAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             HHHHTTCCCSSCEEEE------TT--------------EEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             HHHHhCcEEEeEEecc------cc--------------eEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            4889999877666543      57              9999999999999999999996 699999999999998765

>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=99.57  E-value=8.3e-16  Score=84.64  Aligned_cols=58  Identities=19%  Similarity=0.289  Sum_probs=50.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|+.||.+....++.+..++.++|              +|||+|.+.++|++|++.|||..+.||+|+|.++
T Consensus        29 ~F~~~~~~~~~~~~~~~~~g~~~G--------------~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          29 FFYGYQVIPGSVCLKYNEKGMPTG--------------EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             HTTTSCCCTTTCEEEECSSSCEEE--------------EEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             HHhhcccceeEEEEEeCCCCCcce--------------EEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            488999987754444455889999              9999999999999999999999999999999985

>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=99.55  E-value=3.5e-15  Score=85.35  Aligned_cols=59  Identities=20%  Similarity=0.435  Sum_probs=52.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE--CCEEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI--GMKRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i--~g~~i~V~~a~~~~~   77 (81)
                      +|++||+|.++.++.++    ++|              ||||+|.++++|+.|++.|||..|  .++.|+|.+++++..
T Consensus        27 ~F~~~G~i~~~~i~~~~----~~g--------------~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          27 IFSKFGTVLKIITFTKN----NQF--------------QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             HHTTTSCEEEEEEEEET----TEE--------------EEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             HHccCCcEEEEEEEeeC----CCC--------------eEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            58999999999998775    367              999999999999999999999998  478999999977543

>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=99.55  E-value=2.7e-15  Score=85.66  Aligned_cols=56  Identities=16%  Similarity=0.122  Sum_probs=49.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.+|.|.      .++|              ||||+|.+.++|++|++.|||..+.|+.|.|+|+....
T Consensus        30 ~F~~fG~I~~v~l~------~~kg--------------~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          30 TFSRFGSLGRVLLP------EGGI--------------TAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHTTSCEEEEECC------SSSS--------------CEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             hhhccCCccEEEee------ccCc--------------eEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            58999999999874      2467              99999999999999999999999999999999996543

>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=99.54  E-value=1.5e-15  Score=92.67  Aligned_cols=63  Identities=19%  Similarity=0.365  Sum_probs=58.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|+.||.|..+.++.++.++.++|              ||||+|.++++|++|++ +++..+.|++|.|.+|.++.++
T Consensus       117 ~f~~~G~v~~~~i~~~~~~~~~~g--------------~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         117 YFEQYGKIEVIEIMTDRGSGKKRG--------------FAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHHHH
T ss_pred             hhccCCceeeeeeecccccCccce--------------eEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcccc
Confidence            488999999999999998899999              99999999999999997 7999999999999999887654

>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=99.53  E-value=1.4e-14  Score=82.00  Aligned_cols=58  Identities=22%  Similarity=0.311  Sum_probs=52.4

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      |++||+|..+.++.+    .++|              |+||+|.++++|.+|+..|||..++||+|.|+++.++.+
T Consensus        40 ~~~~G~V~~v~~~~~----~~~G--------------~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          40 CSKFGQIRKLLLFDR----HPDG--------------VASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             GGGTSCCSEEEEETT----CTTC--------------EEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             hcCcccEEEEeccCC----CCcc--------------EEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcCC
Confidence            789999999987755    3467              999999999999999999999999999999999988764

>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=99.52  E-value=5e-15  Score=81.13  Aligned_cols=54  Identities=22%  Similarity=0.468  Sum_probs=48.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEEC-CEEEEEEeeC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQLKR   73 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~-g~~i~V~~a~   73 (81)
                      +|++||+|.+++++.++     +|              ||||+|.+.++|..|++.|||..+. |+.|+|+||+
T Consensus        28 ~f~~~G~i~~v~~~~~~-----~g--------------~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          28 LFNQFPGFKEVRLVPNR-----HD--------------IAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             HHTTSTTEEEEEECTTT-----CS--------------CEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             hhccCccEEEeeeeccc-----ce--------------eEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            48999999999987653     67              9999999999999999999999985 6899999986

>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=99.52  E-value=2.3e-14  Score=77.28  Aligned_cols=55  Identities=20%  Similarity=0.179  Sum_probs=48.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||+|.+++++.++.  ..++              ||||+|.++++|++|+. +|+..|+|++|.|+.+
T Consensus        20 ~F~~~G~I~~v~~~~~~~--~~~~--------------~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          20 YFKHCGPIIHVDVADSLK--KNFR--------------FARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             HHGGGSCEEEEEEEECTT--SSSE--------------EEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             HHhcCCceEEEEEEeecc--ccce--------------EEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            489999999999999873  3346              99999999999999986 8999999999999865

>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=99.52  E-value=3.2e-14  Score=79.01  Aligned_cols=56  Identities=16%  Similarity=0.236  Sum_probs=49.8

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh--CCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l--ng~~i~g~~i~V~~a~~~~   76 (81)
                      ||++||+|.++.++.++      +              +|||+|++.++|..|++.+  ++..+.|++|+|+||++..
T Consensus        29 lF~~fG~I~~i~i~~~k------~--------------~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          29 LVEPFGVISNHLILNKI------N--------------EAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             TTGGGSCEEEEEECSSS------S--------------CEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             HHHhhCCeEEEEeeccc------e--------------EEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            79999999999988653      5              9999999999999999965  7889999999999997654

>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=99.51  E-value=9.1e-16  Score=84.90  Aligned_cols=54  Identities=19%  Similarity=0.223  Sum_probs=48.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+++++.+       |              ||||+|.+.++|++||..|||..+.|+.|.|.++.++
T Consensus        20 ~F~~~G~v~~~~i~~~-------g--------------~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1          20 HMREAGDVCYADVYRD-------G--------------TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             HHGGGSCEEEEEECTT-------S--------------EEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             HHhhhccccccccccc-------c--------------eeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5899999999998654       6              9999999999999999999999999999988877544

>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=99.51  E-value=2.1e-14  Score=81.57  Aligned_cols=63  Identities=16%  Similarity=0.172  Sum_probs=56.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|+.+|.|....++.++.++.++|              ||||+|.++++|++|++ +|+..|.||.|.|.++.+++..
T Consensus        35 ~F~~~g~v~~~v~~~~~~~~~~kG--------------~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          35 FFSGLEIVPNGMTLPVDFQGRSTG--------------EAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             HTTTCCEEEEEEECCBCSSSCBCS--------------EEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             HHHhcCCceEEEEEEeCCCCCcce--------------EEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            589999999877777777899999              99999999999999986 9999999999999999887644

>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=99.50  E-value=1.3e-14  Score=82.19  Aligned_cols=61  Identities=13%  Similarity=0.185  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|+.|| +..+.++.+. ++.++|              ||||+|.++++|++|++ ||+..|.||.|+|.++.++...
T Consensus        35 ~F~~~~-~~~v~~~~~~-~g~~~G--------------~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          35 FFSPLN-PMRVHIEIGP-DGRVTG--------------EADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             SSCSCC-CSEEEEEESS-SSCEEE--------------EEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             HHhccC-cceeeeEEec-CCcceE--------------EEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            588898 4578888876 678888              99999999999999986 8999999999999999776543

>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=99.50  E-value=1.2e-14  Score=80.25  Aligned_cols=57  Identities=14%  Similarity=0.343  Sum_probs=49.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE-CCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI-GMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i-~g~~i~V~~a~~~   75 (81)
                      +|++||.|.++.+..+    +++|              ||||+|.+.++|.+|+..|||..+ +|+.|+|+|++++
T Consensus        30 ~F~~~G~v~~~~~~~~----~~~~--------------~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          30 LFSSNGGVVKGFKFFQ----KDRK--------------MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             HHHTTSCCEEEEEECS----SSTT--------------CEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HhhccCCEEEEEEeee----cccc--------------eeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            4889999988876543    3467              999999999999999999999998 5899999999864

>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=99.49  E-value=3.8e-14  Score=76.40  Aligned_cols=55  Identities=22%  Similarity=0.289  Sum_probs=46.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++|| +..+.+      ++++|              ||||+|.+.++|++|++.|||..+.|++|+|+++.++.
T Consensus        18 ~F~~~g-~~~~~~------~~~~g--------------~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1          18 LLSDYE-LKYCFV------DKYKG--------------TAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             HTTTSC-EEEEEE------ETTTT--------------EEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             HHhccc-ccceee------cccce--------------eEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            588999 444332      34577              99999999999999999999999999999999996653

>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=99.49  E-value=6.8e-15  Score=81.45  Aligned_cols=57  Identities=19%  Similarity=0.352  Sum_probs=49.5

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++++.     .++|              ||||+|.++++|++|+.  ++..|+|++|.|++|.++...
T Consensus        25 ~F~~~G~v~~v~~~~-----~~~g--------------fafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          25 FFSQYGDVMDVFIPK-----PFRA--------------FAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             HSTTTSCCCEEECCS-----SCCS--------------CCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             HHHHcCCceEEEEee-----ccCc--------------eEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            589999999987543     4577              99999999999999986  889999999999999887654

>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=99.49  E-value=7e-15  Score=83.05  Aligned_cols=57  Identities=12%  Similarity=0.122  Sum_probs=50.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.+++|..       +|              ||||+|.++++|++||+.|||..+.|+.|+|.+++++.++
T Consensus        35 ~F~~~G~v~~~~i~~-------~g--------------~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~~   91 (98)
T d1wg4a_          35 HMREAGDVCYADVQK-------DG--------------MGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPER   91 (98)
T ss_dssp             HHTTSSCEEEEEEET-------TT--------------EEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECCC
T ss_pred             HHHhhcccccccccc-------cc--------------eEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCCC
Confidence            589999999998763       46              9999999999999999999999999999999998765543

>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=99.49  E-value=1.6e-14  Score=82.28  Aligned_cols=59  Identities=17%  Similarity=0.156  Sum_probs=52.1

Q ss_pred             ccCCceeeEEEEEecCCCCC--cccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQ--SKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~--~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |++||+|.++.|++++.+..  ..|              ++||+|.++++|.+|+..|||..++||.|.|.+..+
T Consensus        35 ~~k~G~v~~v~I~~~~~~~~~~~~g--------------~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          35 CSKYGLVKSIEIPRPVDGVEVPGCG--------------KIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HTTTSCEEEEECCCCTTSSSCTTCC--------------EEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             hcccCceEEEEEeecCCCCccCCce--------------EEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            78999999999988765433  345              999999999999999999999999999999999864

>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=99.47  E-value=2e-14  Score=79.56  Aligned_cols=39  Identities=31%  Similarity=0.354  Sum_probs=36.6

Q ss_pred             EEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCCC
Q psy16913         39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA   77 (81)
Q Consensus        39 ~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~~   77 (81)
                      ||||+|.++++|++|++.|||..++|++|+|+++.++..
T Consensus        42 ~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_          42 TAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             EEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             ceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            999999999999999999999999999999999976543

>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=99.46  E-value=2.2e-14  Score=81.21  Aligned_cols=59  Identities=10%  Similarity=0.045  Sum_probs=51.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|+.||.|..+.++.+..+|.++|              ||||+|.++++|++|++ +||..|.|+.|.|.++.+
T Consensus        28 ~F~~~g~i~~~~~~~~~~~g~~~G--------------~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1          28 FLEGIPVDENAVHVLVDNNGQGLG--------------QALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             HTTTSCCCSTTEEECCCTTSSCSS--------------CEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             hhcccceEEEEEEEEeCCCCCcCc--------------cEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            489999998765566666899999              99999999999999996 999999999999998754

>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=99.46  E-value=2.5e-13  Score=74.84  Aligned_cols=56  Identities=20%  Similarity=0.272  Sum_probs=49.6

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh--CCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l--ng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||.|.+++++.+      ++              ||||+|.+.++|+.|++.+  ++..+.|++|+|++++.+.
T Consensus        28 ~f~~~G~i~~v~~~~~------~~--------------~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          28 LGLPFGKVTNILMLKG------KN--------------QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTTSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             HHhccccccccccccc------ce--------------EEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            6999999999998754      46              9999999999999999865  6789999999999998765

>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=99.45  E-value=5.1e-14  Score=79.50  Aligned_cols=56  Identities=14%  Similarity=0.247  Sum_probs=50.0

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHH--hhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQ--AMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~--~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.++.+      +|              ||||+|.+.++|.+|++  .+++..++|+.|+|++|+.+.
T Consensus        39 ~F~~fG~V~~v~~~~~------k~--------------~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          39 LAEPYGKIKNYILMRM------KS--------------QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             TTTTTSCCSEEEEETT------TT--------------EEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             hhccccceeEEEEeec------CC--------------cEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            6999999999998755      46              99999999999999997  578889999999999997654

>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=99.45  E-value=4.9e-14  Score=79.15  Aligned_cols=57  Identities=23%  Similarity=0.507  Sum_probs=50.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECC--EEEEEEeeCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQLKRPKDA   77 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g--~~i~V~~a~~~~~   77 (81)
                      +|++||+|..+++.++      ++              ||||+|.+.++|..|++.|||..|.|  ++|+|+||++.+.
T Consensus        37 ~f~~~G~i~~~~~~~~------~~--------------~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~~   95 (97)
T d1whya_          37 EFDRFGSIRTIDHVKG------DS--------------FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             HHHTTSCEEEEEECSS------SC--------------CEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             HHHhhcccceEeeecc------cc--------------EEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCCC
Confidence            5899999999998754      46              99999999999999999999999986  5899999987653

>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=99.43  E-value=1.4e-13  Score=78.04  Aligned_cols=59  Identities=19%  Similarity=0.167  Sum_probs=50.3

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhh--CCcEECCEEEEEEeeCCCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQIGMKRLKVQLKRPKDAA   78 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~l--ng~~i~g~~i~V~~a~~~~~~   78 (81)
                      +|++||+|.++.+.++      ++              +|||+|.+.++|+.|++.|  ++..+.|++|+|+|+..+...
T Consensus        35 ~F~~fG~I~~~~~~~~------k~--------------~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~~   94 (104)
T d1wexa_          35 ALEKFGTICYVMMMPF------KR--------------QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             HHTTTSCEEEEEEETT------TT--------------EEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             hhhhcccceEEEEEec------ce--------------eEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCccC
Confidence            5899999999988754      56              9999999999999999987  566788999999999776544


Q ss_pred             C
Q psy16913         79 R   79 (81)
Q Consensus        79 ~   79 (81)
                      +
T Consensus        95 ~   95 (104)
T d1wexa_          95 R   95 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.33  E-value=6.1e-14  Score=80.63  Aligned_cols=60  Identities=22%  Similarity=0.219  Sum_probs=52.7

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|+.||.+..+.++.+..+|.++|              ||||+|.+.++|++|++ |||..|+||.|.|..+.++
T Consensus        38 ~F~~~g~~~~~~~~~~~~~g~~~G--------------~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~~   97 (112)
T d1wela1          38 FFKKLDIVEDSIYIAYGPNGKATG--------------EGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK   97 (112)
T ss_dssp             HSCSSCBCTTTCEEEECTTSSEEE--------------EEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHH
T ss_pred             HHhhccccccceeeecCcccceee--------------EEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcChH
Confidence            488999998766666667889889              99999999999999996 9999999999999988654

>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=99.29  E-value=3.2e-12  Score=69.81  Aligned_cols=53  Identities=17%  Similarity=0.276  Sum_probs=45.0

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEE-EEEEeeCCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKR-LKVQLKRPK   75 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~-i~V~~a~~~   75 (81)
                      |++||+|.++++..      ++|              ||||+|.++++|++|++ +||..+.|+. |.|..+..+
T Consensus        24 F~~~G~I~~~~~~~------~~~--------------~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          24 FAQYGNILKHVMSN------TGN--------------WMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             HHTTSCEEEEEECS------SSS--------------EEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             HHhhhhhheEEecC------CCC--------------EEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            88999999998643      357              99999999999999996 9999999974 568877654

>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=99.16  E-value=8.3e-14  Score=77.06  Aligned_cols=57  Identities=19%  Similarity=0.257  Sum_probs=45.0

Q ss_pred             CccCCceeeEEEEE-----ecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEee
Q psy16913          1 MFLPFGNVISSKVF-----IDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK   72 (81)
Q Consensus         1 lF~~~G~i~~v~i~-----~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a   72 (81)
                      +|++||.|..+.+.     .+..++.++|              ||||+|.++++|+.|++ |||..+.|+.|+|+.+
T Consensus        21 ~F~~~g~~~~~~~~~~~~~~~~~~~~~kg--------------~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~   82 (90)
T d1u2fa_          21 FFNAQMRLGGLTQAPGNPVLAVQINQDKN--------------FAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRP   82 (90)
T ss_dssp             HHHHHHTTTTSCCSSSCSEEECCEETTTT--------------EEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCT
T ss_pred             HHHhhCcEEEEEEeccceeeecccCCCce--------------EEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCC
Confidence            36777777655442     3445566777              99999999999999985 9999999999999754

>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=99.16  E-value=1e-11  Score=70.08  Aligned_cols=42  Identities=17%  Similarity=0.256  Sum_probs=37.9

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEE
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI   62 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i   62 (81)
                      +|++||+|.++.++.+      ++              ||||+|.+.++|..|+..|||+.+
T Consensus        40 ~F~~~G~i~~i~~~~~------k~--------------~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          40 VLEKCGLVDALLMPPN------KP--------------YSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             HHHHHSCEEEEECCTT------CS--------------CEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             HHHhhCcccEEeeccC------cc--------------EEEEEECCHHHHHHHHHHhCCCCC
Confidence            5899999999987754      46              999999999999999999999987

>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=99.15  E-value=8.7e-12  Score=71.56  Aligned_cols=55  Identities=13%  Similarity=0.144  Sum_probs=47.2

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCH-HHHHHHHHhhCCcEECCEEEEEEeeCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNP-ASAHTAIQAMNGFQIGMKRLKVQLKRPK   75 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~-~~A~~Ai~~lng~~i~g~~i~V~~a~~~   75 (81)
                      +|++||+|.+|.|+.+      +|              ||||.|.++ ++|..|+..||+..+.++.+.|.++..+
T Consensus        31 ~F~~fG~V~~v~i~~~------kg--------------~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          31 LFSNHGEIKWIDFVRG------AK--------------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             HTCSSCCEEEEECCTT------CS--------------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             HHHhcCChheEEEecC------Cc--------------eEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            5999999999999854      57              999999996 6789999999999999888888777543

>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=99.09  E-value=1.8e-10  Score=69.61  Aligned_cols=61  Identities=18%  Similarity=0.367  Sum_probs=54.1

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCCCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD   76 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~~~   76 (81)
                      +|++||+|.++.+++++.++.++|              ||||+|.++++|..|+. +++..+.++.+.+....++.
T Consensus        26 ~F~~~G~v~~~~~~~~~~~~~~~g--------------~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~~   86 (183)
T d1u1qa_          26 HFEQWGTLTDCVVMRDPNTKRSRG--------------FGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSRE   86 (183)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEE--------------EEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCTT
T ss_pred             HHHHcCCEEEEEeeecccCCCccC--------------ceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhcc
Confidence            489999999999999999999999              99999999999999998 56788899988888775544

>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=97.99  E-value=1e-05  Score=42.39  Aligned_cols=57  Identities=25%  Similarity=0.324  Sum_probs=47.4

Q ss_pred             CccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         1 lF~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      +|.++|+|.++.+.... .+..                .|-|...+..+|..|+..|+..+|.+++|.|.++..
T Consensus        16 ~f~~h~~V~sv~l~~~~-dg~~----------------~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          16 AFARHGKVKSVELSPHT-DYQL----------------KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHSCEEEEEECSCC-STTC----------------CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHhheeEEEEEEEecc-CCcE----------------EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            37788999998875443 2332                678999999999999999999999999999999753

>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=97.75  E-value=1.7e-05  Score=43.44  Aligned_cols=50  Identities=14%  Similarity=0.329  Sum_probs=42.9

Q ss_pred             ccCCceeeEEEEEecCCCCCcccccccccccccCcceEEEEEEcCHHHHHHHHHhhCCcEECCEEEEEEeeCC
Q psy16913          2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP   74 (81)
Q Consensus         2 F~~~G~i~~v~i~~~~~~~~~kg~~~~~~~~~~~~~~~~fV~f~~~~~A~~Ai~~lng~~i~g~~i~V~~a~~   74 (81)
                      |+.||+|.-++.+.|                      -..|+|.+-+.|-+|++ ++|.++.|+.|.|....|
T Consensus        45 l~~~GeViLvRFv~d----------------------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          45 LGSYGTIVLVRINQG----------------------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHSCCSEEEEETT----------------------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HhhCCeEEEEEEeCC----------------------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCCC
Confidence            677899888888866                      46899999999999988 999999999999886543