Citrus Sinensis ID: 034039

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLSTG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccccccEEEEEccHHHHHHHHHHccccEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEcccccHHHcccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEccccEEEEEcccc
Coil and Loop (DISEMBL)
mqwlngsvrfshSVRFTRLLSDANSRTKLFIgglsydtnetVLKDAFGQHGEIIEVKVICDrvtgqsrgygfvKFASEAAAGEAIKEMDglvcrtskdtdmlstg
Flexible Loop (DISEMBL)
mqwlngsvrfshSVRFtrllsdansrTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGeaikemdglvcrtskdtdmlstg
Low Complexity Region (SEG)
MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLSTG
Disordered region (IsUnstruct)
*****GSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC************
Disordered Region (DISOPRED)
****************************LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD*****
Disordered Region (DISEMBL)
MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK********
Disordered Region (DISPRO)
***********HSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLSTG
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	105	2.2.26 [Sep-21-2011]
Q9SVM8	158	Glycine-rich RNA-binding	yes	no	0.771	0.512	0.511	1e-16
Q9LIS2	136	Glycine-rich RNA-binding	no	no	0.609	0.470	0.578	4e-15
Q9FNR1	309	Glycine-rich RNA-binding	no	no	0.628	0.213	0.515	4e-14
P39697	212	40S ribosomal protein S19	no	no	0.609	0.301	0.546	8e-13
Q43472	161	Glycine-rich RNA-binding	N/A	no	0.647	0.422	0.455	3e-12
Q96E39	390	RNA binding motif protein	yes	no	0.676	0.182	0.478	4e-12
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.676	0.422	0.450	4e-12
P10979	157	Glycine-rich RNA-binding,	N/A	no	0.676	0.452	0.450	4e-12
A5A6M3	391	RNA-binding motif protein	yes	no	0.676	0.181	0.464	8e-12
P38159	391	RNA-binding motif protein	yes	no	0.676	0.181	0.464	8e-12

>sp|Q9SVM8|RBG2_ARATH Glycine-rich RNA-binding protein 2, mitochondrial OS=Arabidopsis thaliana GN=RBG2 PE=1 SV=1

 Score = 85.5 bits (210), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/86 (51%), Positives = 58/86 (67%), Gaps = 5/86 (5%)

Query: 5  NGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT 64
          NG+V  +  +   RL+S     TKLFIGGLS+ T++  L+DAF   G++++ KVI DR T
Sbjct: 18 NGNVPVTSMLGSLRLMS-----TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRET 72

Query: 65 GQSRGYGFVKFASEAAAGEAIKEMDG 90
          G+SRG+GFV F  E AA  AI EMDG
Sbjct: 73 GRSRGFGFVNFNDEGAATAAISEMDG 98

Possibly has a role in RNA transcription or processing during stress.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIS2|RBG4_ARATH Glycine-rich RNA-binding protein 4, mitochondrial OS=Arabidopsis thaliana GN=RBG4 PE=2 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 48/64 (75%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +KLF+GGLS+ T+++ LK AF   GE+ E  VI DR TG+SRG+GFV F+ E +A  AIK
Sbjct: 35 SKLFVGGLSWGTDDSSLKQAFTSFGEVTEATVIADRETGRSRGFGFVSFSCEDSANNAIK 94

Query: 87 EMDG 90
          EMDG
Sbjct: 95 EMDG 98

Possibly has a role in RNA transcription or processing during stress. Binds sequence non-specifically to RNAs and DNAs.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 50/66 (75%)

Query: 25  SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
           S +KLFIGG++Y  +E  L++AF ++GE+++ +VI DR TG+SRG+GFV F S  AA  A
Sbjct: 38  SSSKLFIGGMAYSMDEDSLREAFTKYGEVVDTRVILDRETGRSRGFGFVTFTSSEAASSA 97

Query: 85  IKEMDG 90
           I+ +DG
Sbjct: 98  IQALDG 103

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

Arabidopsis thaliana (taxid: 3702)

>sp|P39697|RT19_ARATH 40S ribosomal protein S19, mitochondrial OS=Arabidopsis thaliana GN=RPS19 PE=1 SV=2

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 35/64 (54%), Positives = 45/64 (70%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TKL+IGGLS  T+E  LKDAF     + E +V+ ++VTG+SRGYGFV F SE +A  AI 
Sbjct: 31 TKLYIGGLSPGTDEHSLKDAFSSFNGVTEARVMTNKVTGRSRGYGFVNFISEDSANSAIS 90

Query: 87 EMDG 90
           M+G
Sbjct: 91 AMNG 94

The RNA-binding domain found in RPS19 may functionally replaces the missing mitochondrial RPS13.

Arabidopsis thaliana (taxid: 3702)

>sp|Q43472|GRP_HORVU Glycine-rich RNA-binding protein blt801 OS=Hordeum vulgare GN=blt801 PE=1 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 51/68 (75%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A+   + F+GGL + T++  L++AF ++G++I+ K+I DR TG+SRG+GFV FAS+ A  
Sbjct: 2  ADVEYRCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAMR 61

Query: 83 EAIKEMDG 90
          +AI+ M+G
Sbjct: 62 QAIEAMNG 69

Binds single-stranded DNA and homoribopolymers of guanine, uracil and adenine, but not cytosine. Also binds RNA, with a preference for RNA containing a high proportion of adenine within an open loop structure. Possibly has a role in RNA transcription or processing during stress.

Hordeum vulgare (taxid: 4513)

>sp|Q96E39|RMXL1_HUMAN RNA binding motif protein, X-linked-like-1 OS=Homo sapiens GN=RBMXL1 PE=1 SV=1

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/71 (47%), Positives = 50/71 (70%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          + +A+   KLFIGGL+ +TNE  L+  FG++G I+EV +I DR T +SRG+ FV F S A
Sbjct: 1  MVEADRPGKLFIGGLNTETNEKALETVFGKYGRIVEVLLIKDRETNKSRGFAFVTFESPA 60

Query: 80 AAGEAIKEMDG 90
           A +A ++M+G
Sbjct: 61 DAKDAARDMNG 71

RNA-binding protein which may be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

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

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/71 (45%), Positives = 50/71 (70%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          ++ A+   + F+GGL++ TN   L+ AF   G++I+ KVI DR TG+SRG+GFV F+SE 
Sbjct: 1  MAAADVEYRCFVGGLAWATNNETLEQAFANFGQVIDSKVITDRETGRSRGFGFVTFSSEQ 60

Query: 80 AAGEAIKEMDG 90
          +  +AI+ M+G
Sbjct: 61 SMLDAIENMNG 71

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

Sorghum bicolor (taxid: 4558)

>sp|P10979|GRPA_MAIZE Glycine-rich RNA-binding, abscisic acid-inducible protein OS=Zea mays GN=RAB15 PE=1 SV=1

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/71 (45%), Positives = 52/71 (73%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          ++ A+   + F+GGL++ T+   L++AF  +GEI++ KVI DR TG+SRG+GFV F+SE 
Sbjct: 1  MAAADVEYRCFVGGLAWATSNESLENAFASYGEILDSKVITDRETGRSRGFGFVTFSSEN 60

Query: 80 AAGEAIKEMDG 90
          +  +AI+ M+G
Sbjct: 61 SMLDAIENMNG 71

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

Zea mays (taxid: 4577)

>sp|A5A6M3|RBMX_PANTR RNA-binding motif protein, X chromosome OS=Pan troglodytes GN=RBMX PE=2 SV=1

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 33/71 (46%), Positives = 50/71 (70%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          + +A+   KLFIGGL+ +TNE  L+  FG++G I+EV ++ DR T +SRG+ FV F S A
Sbjct: 1  MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPA 60

Query: 80 AAGEAIKEMDG 90
           A +A ++M+G
Sbjct: 61 DAKDAARDMNG 71

RNA-binding protein that plays several role in the regulation of pre- and post-transcriptional processes. Implicated in tissue-specific regulation of gene transcription and alternative splicing of several pre-mRNAs. Binds to and stimulates transcription from the tumor suppressor TXNIP gene promoter; may thus be involved in tumor suppression. When associated with SAFB, binds to and stimulates transcription from the SREBF1 promoter. Associates with nascent mRNAs transcribed by RNA polymerase II. Component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Can either activate or suppress exon inclusion; acts additively with TRA2B to promote exon 7 inclusion of the survival motor neuron SMN2. Represses the splicing of MAPT/Tau exon 10. Binds preferentially to single-stranded 5'-CC[A/C]-rich RNA sequence motifs localized in a single-stranded conformation; probably binds RNA as a homodimer. Binds non-specifically to pre-mRNAs. Plays also a role in the cytoplasmic TNFR1 trafficking pathways; promotes both the IL-1-beta-mediated inducible proteolytic cleavage of TNFR1 ectodomains and the release of TNFR1 exosome-like vesicles to the extracellular compartment.

Pan troglodytes (taxid: 9598)

>sp|P38159|RBMX_HUMAN RNA-binding motif protein, X chromosome OS=Homo sapiens GN=RBMX PE=1 SV=3

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 33/71 (46%), Positives = 50/71 (70%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          + +A+   KLFIGGL+ +TNE  L+  FG++G I+EV ++ DR T +SRG+ FV F S A
Sbjct: 1  MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPA 60

Query: 80 AAGEAIKEMDG 90
           A +A ++M+G
Sbjct: 61 DAKDAARDMNG 71

RNA-binding protein that plays several role in the regulation of pre- and post-transcriptional processes. Implicated in tissue-specific regulation of gene transcription and alternative splicing of several pre-mRNAs. Binds to and stimulates transcription from the tumor suppressor TXNIP gene promoter; may thus be involved in tumor suppression. When associated with SAFB, binds to and stimulates transcription from the SREBF1 promoter. Associates with nascent mRNAs transcribed by RNA polymerase II. Component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Can either activate or suppress exon inclusion; acts additively with TRA2B to promote exon 7 inclusion of the survival motor neuron SMN2. Represses the splicing of MAPT/Tau exon 10. Binds preferentially to single-stranded 5'-CC[A/C]-rich RNA sequence motifs localized in a single-stranded conformation; probably binds RNA as a homodimer. Binds non-specifically to pre-mRNAs. Plays also a role in the cytoplasmic TNFR1 trafficking pathways; promotes both the IL-1-beta-mediated inducible proteolytic cleavage of TNFR1 ectodomains and the release of TNFR1 exosome-like vesicles to the extracellular compartment.

Homo sapiens (taxid: 9606)

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	105
351722320	146	uncharacterized protein LOC100306540 [Gl	0.838	0.602	0.633	7e-24
356526775	146	PREDICTED: glycine-rich RNA-binding prot	0.838	0.602	0.622	5e-23
194466189	112	unknown [Arachis hypogaea]	0.752	0.705	0.620	4e-21
359478318	108	PREDICTED: glycine-rich RNA-binding prot	0.857	0.833	0.619	2e-20
57899926	203	hypothetical protein [Oryza sativa Japon	0.619	0.320	0.738	3e-20
297598418	116	Os01g0974600 [Oryza sativa Japonica Grou	0.619	0.560	0.738	7e-20
218189840	116	hypothetical protein OsI_05421 [Oryza sa	0.619	0.560	0.738	9e-20
357472741	112	Glycine-rich RNA-binding protein [Medica	0.657	0.616	0.666	1e-19
357127016	109	PREDICTED: glycine-rich RNA-binding prot	0.619	0.596	0.661	4e-18
294461052	150	unknown [Picea sitchensis]	0.6	0.42	0.650	4e-17

>gi|351722320|ref|NP_001236472.1| uncharacterized protein LOC100306540 [Glycine max] gi|255628821|gb|ACU14755.1| unknown [Glycine max]

 Score =  114 bits (285), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 57/90 (63%), Positives = 66/90 (73%), Gaps = 2/90 (2%)

Query: 3   WLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR 62
            +NGS    H  RF  L    +S TKLF+ GLSYDTNE +L+DAFGQHGEIIEVKVICD 
Sbjct: 36  LVNGSALRFHLPRF--LCVRHHSSTKLFVTGLSYDTNEPILRDAFGQHGEIIEVKVICDH 93

Query: 63  VTGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
           VTG+SRGYGFV+F SE  A  A KEM+G +
Sbjct: 94  VTGKSRGYGFVRFVSETTAAAARKEMNGQI 123

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526775|ref|XP_003531992.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Glycine max]

 Score =  111 bits (278), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 56/90 (62%), Positives = 64/90 (71%), Gaps = 2/90 (2%)

Query: 3   WLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR 62
            +NGS    H  RF  L    +S  KLF+ GLSYDTNE VL+DAFGQHGEIIEVKVICD 
Sbjct: 36  LVNGSALHFHLPRF--LYVRHHSSIKLFVTGLSYDTNEPVLRDAFGQHGEIIEVKVICDH 93

Query: 63  VTGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
           VTG+SRGYGFV+F SE  A    KEM+G +
Sbjct: 94  VTGKSRGYGFVRFLSETIAAATHKEMNGQI 123

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|194466189|gb|ACF74325.1| unknown [Arachis hypogaea]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 60/79 (75%)

Query: 10 FSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRG 69
          F +S  F+ LL   +S T L + GLSYDTNETVL+DAF QHGE+IEVKVICD VTG+S+G
Sbjct: 15 FKNSCPFSPLLFPRHSSTNLLVTGLSYDTNETVLRDAFEQHGELIEVKVICDHVTGKSKG 74

Query: 70 YGFVKFASEAAAGEAIKEM 88
          YGFV+F +E +A    KEM
Sbjct: 75 YGFVRFTTETSAATGRKEM 93

Source: Arachis hypogaea

Species: Arachis hypogaea

Genus: Arachis

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478318|ref|XP_003632106.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Vitis vinifera] gi|296084274|emb|CBI24662.3| unnamed protein product [Vitis vinifera]

 Score =  103 bits (257), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 57/92 (61%), Positives = 66/92 (71%), Gaps = 2/92 (2%)

Query: 1  MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIG--GLSYDTNETVLKDAFGQHGEIIEVKV 58
          MQ LN     S +    R L    S  KLFIG  GLSYDTNET+LKDAFGQ+GEIIEVKV
Sbjct: 1  MQSLNRFRCLSPASPCFRWLVSRGSCRKLFIGDAGLSYDTNETILKDAFGQYGEIIEVKV 60

Query: 59 ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          ICD V+G+S+GYGFV+F S+  A  A+KEMDG
Sbjct: 61 ICDHVSGKSKGYGFVQFTSDDDAHIALKEMDG 92

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|57899926|dbj|BAD87838.1| hypothetical protein [Oryza sativa Japonica Group]

 Score =  102 bits (255), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/65 (73%), Positives = 53/65 (81%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGLSYDTNET LKDAF QHG II+VKVIC  VTG+S+GYGFVKFASE  A  A+ +
Sbjct: 125 KLFIGGLSYDTNETALKDAFSQHGHIIQVKVICHPVTGKSKGYGFVKFASEDEAAAALHK 184

Query: 88  MDGLV 92
           M G V
Sbjct: 185 MGGEV 189

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297598418|ref|NP_001045556.2| Os01g0974600 [Oryza sativa Japonica Group] gi|215768629|dbj|BAH00858.1| unnamed protein product [Oryza sativa Japonica Group] gi|222619969|gb|EEE56101.1| hypothetical protein OsJ_04953 [Oryza sativa Japonica Group] gi|255674125|dbj|BAF07470.2| Os01g0974600 [Oryza sativa Japonica Group]

 Score =  101 bits (251), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 48/65 (73%), Positives = 53/65 (81%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGLSYDTNET LKDAF QHG II+VKVIC  VTG+S+GYGFVKFASE  A  A+ +
Sbjct: 38  KLFIGGLSYDTNETALKDAFSQHGHIIQVKVICHPVTGKSKGYGFVKFASEDEAAAALHK 97

Query: 88  MDGLV 92
           M G V
Sbjct: 98  MGGEV 102

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218189840|gb|EEC72267.1| hypothetical protein OsI_05421 [Oryza sativa Indica Group]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/65 (73%), Positives = 53/65 (81%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGLSYDTNET LKDAF QHG II+VKVIC  VTG+S+GYGFVKFASE  A  A+ +
Sbjct: 38  KLFIGGLSYDTNETALKDAFSQHGHIIQVKVICHPVTGKSKGYGFVKFASEDEAAAALHK 97

Query: 88  MDGLV 92
           M G V
Sbjct: 98  MGGEV 102

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472741|ref|XP_003606655.1| Glycine-rich RNA-binding protein [Medicago truncatula] gi|355507710|gb|AES88852.1| Glycine-rich RNA-binding protein [Medicago truncatula]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/69 (66%), Positives = 56/69 (81%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +S TKLFI GLSY+TNETVL+D F QHG+IIEVKVIC+  TG+S+GYGFV+F SE AA  
Sbjct: 30 HSSTKLFIAGLSYNTNETVLRDTFEQHGQIIEVKVICNHRTGESKGYGFVRFNSETAAAT 89

Query: 84 AIKEMDGLV 92
          A KE+ G +
Sbjct: 90 ARKELHGQI 98

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357127016|ref|XP_003565182.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Brachypodium distachyon]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 43/65 (66%), Positives = 54/65 (83%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +S +KLF+GGLSYDTNE  LKDAF QHG + EVKVIC  VTG+S+GYGFVKF+SE+ A  
Sbjct: 27 SSCSKLFVGGLSYDTNEIALKDAFSQHGTVTEVKVICHPVTGRSKGYGFVKFSSESEAAA 86

Query: 84 AIKEM 88
          A+++M
Sbjct: 87 ALEKM 91

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294461052|gb|ADE76094.1| unknown [Picea sitchensis]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 41/63 (65%), Positives = 53/63 (84%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+GGLS+DTNE VL+DAF  +GEI+EV+VI +R +G S+G+GFV+FASE  A  A+KE
Sbjct: 36 KLFVGGLSFDTNEKVLRDAFSLYGEILEVRVIINRASGLSKGFGFVQFASETDAVNALKE 95

Query: 88 MDG 90
          MDG
Sbjct: 96 MDG 98

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	105
TAIR|locus:2119495	158	GR-RBP2 "AT4G13850" [Arabidops	0.771	0.512	0.511	1.1e-16
TAIR|locus:2076096	136	GRP4 "glycine-rich RNA-binding	0.609	0.470	0.578	3.3e-15
TAIR|locus:2159401	309	GR-RBP3 "glycine-rich RNA-bind	0.809	0.275	0.448	1.1e-14
TAIR|locus:2077427	143	AT3G08000 [Arabidopsis thalian	0.666	0.489	0.514	2.1e-13
TAIR|locus:2019622	289	GR-RBP5 "AT1G74230" [Arabidops	0.752	0.273	0.414	4.3e-13
TAIR|locus:2171539	212	RPS19 "ribosomal protein S19"	0.609	0.301	0.546	4.4e-13
TAIR|locus:2088756	374	AT3G20930 [Arabidopsis thalian	0.619	0.173	0.492	1.1e-12
UNIPROTKB|Q43472	161	blt801 "Glycine-rich RNA-bindi	0.647	0.422	0.455	1.2e-12
UNIPROTKB|H3BR27	78	RBMX "RNA-binding motif protei	0.657	0.884	0.478	2.4e-12
UNIPROTKB|K7GKR9	196	RBMX "Uncharacterized protein"	0.657	0.352	0.478	2.4e-12

TAIR|locus:2119495 GR-RBP2 "AT4G13850" [Arabidopsis thaliana (taxid:3702)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 44/86 (51%), Positives = 58/86 (67%)

Query:     5 NGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT 64
             NG+V  +  +   RL+S     TKLFIGGLS+ T++  L+DAF   G++++ KVI DR T
Sbjct:    18 NGNVPVTSMLGSLRLMS-----TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRET 72

Query:    65 GQSRGYGFVKFASEAAAGEAIKEMDG 90
             G+SRG+GFV F  E AA  AI EMDG
Sbjct:    73 GRSRGFGFVNFNDEGAATAAISEMDG 98

GO:0003723 "RNA binding" evidence=ISS;IDA

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009409 "response to cold" evidence=IGI;IEP;IMP

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IEP

GO:0005524 "ATP binding" evidence=IDA

GO:0001072 "RNA binding transcription antitermination factor activity" evidence=IDA

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009631 "cold acclimation" evidence=IMP

GO:0009651 "response to salt stress" evidence=IMP

GO:0009845 "seed germination" evidence=IMP

GO:0031564 "transcription antitermination" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

TAIR|locus:2076096 GRP4 "glycine-rich RNA-binding protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 37/64 (57%), Positives = 48/64 (75%)

Query:    27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             +KLF+GGLS+ T+++ LK AF   GE+ E  VI DR TG+SRG+GFV F+ E +A  AIK
Sbjct:    35 SKLFVGGLSWGTDDSSLKQAFTSFGEVTEATVIADRETGRSRGFGFVSFSCEDSANNAIK 94

Query:    87 EMDG 90
             EMDG
Sbjct:    95 EMDG 98

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS;IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2159401 GR-RBP3 "glycine-rich RNA-binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 39/87 (44%), Positives = 57/87 (65%)

Query:     4 LNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV 63
             LN  V  S    F  +   ++S  KLFIGG++Y  +E  L++AF ++GE+++ +VI DR 
Sbjct:    19 LNAQVSLSSPSLFQAIRCMSSS--KLFIGGMAYSMDEDSLREAFTKYGEVVDTRVILDRE 76

Query:    64 TGQSRGYGFVKFASEAAAGEAIKEMDG 90
             TG+SRG+GFV F S  AA  AI+ +DG
Sbjct:    77 TGRSRGFGFVTFTSSEAASSAIQALDG 103

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0034968 "histone lysine methylation" evidence=RCA

TAIR|locus:2077427 AT3G08000 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 2.1e-13, P = 2.1e-13
 Identities = 36/70 (51%), Positives = 47/70 (67%)

Query:    21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             S A+  +KLFIGGLS+  +E  LKDAF   GE+ EV++  D+ +G+SRG+GFV FA E  
Sbjct:    35 SSASPSSKLFIGGLSWSVDEQSLKDAFSSFGEVAEVRIAYDKGSGRSRGFGFVDFAEEGD 94

Query:    81 AGEAIKEMDG 90
             A  A   MDG
Sbjct:    95 ALSAKDAMDG 104

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2019622 GR-RBP5 "AT1G74230" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 4.3e-13, P = 4.3e-13
 Identities = 34/82 (41%), Positives = 54/82 (65%)

Query:    11 SHSVRFTRLLSDAN--SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR 68
             SH    + +L      S +K+F+GG+SY T+E  L++AF ++GE+++ K+I DR TG+SR
Sbjct:    16 SHVTASSSMLQSIRCMSSSKIFVGGISYSTDEFGLREAFSKYGEVVDAKIIVDRETGRSR 75

Query:    69 GYGFVKFASEAAAGEAIKEMDG 90
             G+ FV F S   A  A+ ++DG
Sbjct:    76 GFAFVTFTSTEEASNAM-QLDG 96

GO:0003723 "RNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

TAIR|locus:2171539 RPS19 "ribosomal protein S19" [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 35/64 (54%), Positives = 45/64 (70%)

Query:    27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             TKL+IGGLS  T+E  LKDAF     + E +V+ ++VTG+SRGYGFV F SE +A  AI 
Sbjct:    31 TKLYIGGLSPGTDEHSLKDAFSSFNGVTEARVMTNKVTGRSRGYGFVNFISEDSANSAIS 90

Query:    87 EMDG 90
              M+G
Sbjct:    91 AMNG 94

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;NAS

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

GO:0005763 "mitochondrial small ribosomal subunit" evidence=IDA

TAIR|locus:2088756 AT3G20930 [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 32/65 (49%), Positives = 50/65 (76%)

Query:    28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
             KLFI GLS+ T+E  L+ AF   GE++EVK+I D+++ +S+GY F+++ +E AAG A+KE
Sbjct:   283 KLFITGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFLEYTTEEAAGTALKE 342

Query:    88 MDGLV 92
             M+G +
Sbjct:   343 MNGKI 347

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

UNIPROTKB|Q43472 blt801 "Glycine-rich RNA-binding protein blt801" [Hordeum vulgare (taxid:4513)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 31/68 (45%), Positives = 51/68 (75%)

Query:    23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
             A+   + F+GGL + T++  L++AF ++G++I+ K+I DR TG+SRG+GFV FAS+ A  
Sbjct:     2 ADVEYRCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAMR 61

Query:    83 EAIKEMDG 90
             +AI+ M+G
Sbjct:    62 QAIEAMNG 69

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

UNIPROTKB|H3BR27 RBMX "RNA-binding motif protein, X chromosome, N-terminally processed" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 33/69 (47%), Positives = 49/69 (71%)

Query:    22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
             +A+   KLFIGGL+ +TNE  L+  FG++G I+EV ++ DR T +SRG+ FV F S A A
Sbjct:     3 EADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADA 62

Query:    82 GEAIKEMDG 90
              +A ++M+G
Sbjct:    63 KDAARDMNG 71

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|K7GKR9 RBMX "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 33/69 (47%), Positives = 49/69 (71%)

Query:    22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
             +A+   KLFIGGL+ +TNE  L+  FG++G I+EV ++ DR T +SRG+ FV F S A A
Sbjct:     3 EADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADA 62

Query:    82 GEAIKEMDG 90
              +A ++M+G
Sbjct:    63 KDAARDMNG 71

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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: OsI_05421 RNA recognition motif containing protein, putative, expressed (116 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	105
smart00360	73	smart00360, RRM, RNA recognition motif	2e-23
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-23
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-21
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-20
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-20
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-19
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-19
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-18
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-17
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-17
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-16
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-16
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-16
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-15
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-15
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	5e-15
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-15
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-14
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-14
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-14
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-14
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	5e-14
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	6e-14
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	7e-14
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-13
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-13
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-13
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-13
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-13
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-13
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-13
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-12
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-12
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-12
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-12
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-12
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-12
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-12
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-12
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-12
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-12
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-12
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-12
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-12
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-11
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-11
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-11
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-11
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-11
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-11
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-11
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	5e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-11
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-11
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	6e-11
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	7e-11
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	7e-11
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	7e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-11
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-10
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-10
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-10
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	1e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-10
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-10
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-10
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-10
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-10
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	3e-10
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	3e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-10
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-10
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	5e-10
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-10
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-10
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	1e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-09
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-09
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-09
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-09
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-09
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-09
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	5e-09
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-09
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	6e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	6e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-09
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-09
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-09
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	8e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-09
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	1e-08
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-08
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-08
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-08
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-08
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-08
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-08
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	4e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-08
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-08
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-08
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	2e-07
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-07
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-07
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-07
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	3e-07
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	3e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-07
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	8e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-07
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	9e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	3e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-06
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	4e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	5e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-06
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	8e-06
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	8e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	9e-06
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	9e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	9e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	1e-05
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	1e-05
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	1e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	1e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	1e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	2e-05
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	2e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	3e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	3e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	4e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	4e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	4e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	4e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	5e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	6e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	8e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	8e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	9e-05
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	1e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	1e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-04
cd12511	73	cd12511, RRM2_RBM12_like, RNA recognition motif 2	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-04
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	3e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	3e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	4e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	4e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	6e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	8e-04
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	8e-04
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.001
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.001
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.001
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.001
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.002
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.002
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.002
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.002
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.002
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	0.003
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.003
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.003
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.003
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.003
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.003
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.004
cd12481	80	cd12481, RRM2_U2B, RNA recognition motif 2 found i	0.004
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	0.004
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.004
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.004

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

 Score = 85.0 bits (211), Expect = 2e-23
 Identities = 24/65 (36%), Positives = 43/65 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           LF+G L  DT E  L++ F + G++  V+++ D+ TG+S+G+ FV+F SE  A +A++ 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 88 MDGLV 92
          ++G  
Sbjct: 61 LNGKE 65

Length = 73

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

 Score = 85.0 bits (211), Expect = 2e-23
 Identities = 29/63 (46%), Positives = 42/63 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           L++G L Y+  E  LKD FGQ GE+   +VI DR TG+SRG+GFV+  +   A  AI++
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 88 MDG 90
          ++G
Sbjct: 61 LNG 63

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

 Score = 82.0 bits (202), Expect = 2e-21
 Identities = 38/64 (59%), Positives = 48/64 (75%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TKLFIGGLS+ T++  L+DAF   G++++ KVI DR TG+SRG+GFV F  E AA  AI 
Sbjct: 35 TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94

Query: 87 EMDG 90
          EMDG
Sbjct: 95 EMDG 98

Length = 144

>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 = 79.2 bits (196), Expect = 5e-21
 Identities = 28/64 (43%), Positives = 40/64 (62%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           KLF+ GLS  T E  L+  F + G + EV ++ D  TG+SRG+GFV F S   A  AI+
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 87 EMDG 90
          +++G
Sbjct: 62 DLNG 65

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

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

 Score = 77.6 bits (192), Expect = 1e-20
 Identities = 25/62 (40%), Positives = 40/62 (64%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G L  DT E  LKD F + G I  ++++ D  TG+S+G+ FV+F  E  A +A++ +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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

 Score = 76.9 bits (190), Expect = 3e-20
 Identities = 25/59 (42%), Positives = 42/59 (71%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          LFIGGLS+DT E  L++ F ++GE+++  ++ D +TG+SRG+GFV FA  ++  + +  
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 74.2 bits (183), Expect = 4e-19
 Identities = 34/68 (50%), Positives = 43/68 (63%), Gaps = 4/68 (5%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TK+F+GGL Y T +  L+  F Q GEI E  VI DR TG+SRGYGFV F  + +A  A K
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 87 E----MDG 90
          +    +DG
Sbjct: 61 DPNPIIDG 68

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

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

 Score = 73.5 bits (181), Expect = 6e-19
 Identities = 24/62 (38%), Positives = 41/62 (66%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G L  DT E  L++ F + GEI  V+++ D+  G+S+G+ FV+F S   A +A++ +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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|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 = 73.3 bits (180), Expect = 9e-19
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLFIGGLS+DTNE  L+  F ++G+I EV V+ DR T +SRG+GFV F +   A +A+  
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 88 MDG 90
          M+G
Sbjct: 62 MNG 64

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

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

 Score = 72.3 bits (178), Expect = 3e-18
 Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
            ++F+GG+  DT E  L+D F + G + +VK+I DR  G S+GYGFV F ++  A E I
Sbjct: 2  PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDA-EKI 59

Query: 86 KEMDGLVCRTSK 97
            M  L  R  K
Sbjct: 60 LAMGNLNFRGKK 71

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

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

 Score = 69.7 bits (171), Expect = 2e-17
 Identities = 28/63 (44%), Positives = 41/63 (65%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           LF+G LS+  ++  LK  F + G ++  +VI DR TG+SRG+G+V F S   A +AI+ 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 88 MDG 90
          MDG
Sbjct: 61 MDG 63

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

 Score = 74.2 bits (181), Expect = 4e-17
 Identities = 28/66 (42%), Positives = 44/66 (66%)

Query: 25  SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
               LF+G L YD  E  L++ F + G +  V+++ DR TG+SRG+ FV+F SE +A +A
Sbjct: 114 ENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Query: 85  IKEMDG 90
           I+E++G
Sbjct: 174 IEELNG 179

Length = 306

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

 Score = 67.7 bits (166), Expect = 2e-16
 Identities = 24/62 (38%), Positives = 38/62 (61%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L+YDT E+ L+  F ++G I  ++++ D+ TG+ RGY F++F  E     A K  
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 89 DG 90
          DG
Sbjct: 64 DG 65

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

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

 Score = 66.9 bits (164), Expect = 3e-16
 Identities = 25/62 (40%), Positives = 42/62 (67%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L    +E  +  AF + GE+  VK+I ++ TG+S GYGFV+FA+  AA +A++ +
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 89 DG 90
          +G
Sbjct: 62 NG 63

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

>gnl|CDD|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 = 66.1 bits (162), Expect = 6e-16
 Identities = 21/61 (34%), Positives = 36/61 (59%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD 89
          F+G + YD  E  L + F + G ++  +++ DR TG+ +GYGF +F     A  AI+ ++
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 90 G 90
          G
Sbjct: 62 G 62

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|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 = 65.3 bits (160), Expect = 1e-15
 Identities = 27/63 (42%), Positives = 39/63 (61%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G L     E  ++  F ++G I EV +I D+ TGQS+G  FVKF+S   A +AI+ 
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 88 MDG 90
          + G
Sbjct: 61 LHG 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 65.1 bits (159), Expect = 2e-15
 Identities = 30/59 (50%), Positives = 39/59 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          KLFIGGLSY+T +  LK+ F Q GEI +  V+ D  T +SRG+GFV FAS +    A+ 
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

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

 Score = 63.9 bits (156), Expect = 3e-15
 Identities = 26/62 (41%), Positives = 39/62 (62%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G LS + +   L+ AF   GEI + +V+ D  TG+S+GYGFV F  +  A  AI+ M
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 89 DG 90
          +G
Sbjct: 62 NG 63

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

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

 Score = 64.1 bits (156), Expect = 5e-15
 Identities = 23/49 (46%), Positives = 37/49 (75%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
          KLF+GGLS++T +  L+  F Q+GE+++  ++ D+ T +SRG+GFVKF 
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFK 49

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

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

 Score = 63.9 bits (156), Expect = 5e-15
 Identities = 26/69 (37%), Positives = 36/69 (52%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L +  L  D  +  L+  F   G I   K++ DR+TGQS GYGFV +  E  A +AI 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 87 EMDGLVCRT 95
           ++G   R 
Sbjct: 61 TLNGFEIRN 69

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

 Score = 63.2 bits (154), Expect = 1e-14
 Identities = 24/54 (44%), Positives = 37/54 (68%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          K+F+GGL  D  E   K+ F Q G++++ +++ D  TG+SRG+GFV F SE+A 
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAV 54

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

 Score = 63.0 bits (154), Expect = 1e-14
 Identities = 24/63 (38%), Positives = 40/63 (63%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+G L  +  + VL  AF ++    + KV+ D+ TG+S+GYGFV F+      +A+KE
Sbjct: 8  RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 88 MDG 90
          M+G
Sbjct: 68 MNG 70

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

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

 Score = 61.6 bits (150), Expect = 3e-14
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           L + GL + T E  LKD F   GE++ V+V  D  TGQS+G+GFV+FA      + + +
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 88 ---MDGLVC 93
             +DG  C
Sbjct: 61 RHMIDGRWC 69

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

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

 Score = 61.9 bits (151), Expect = 4e-14
 Identities = 25/64 (39%), Positives = 40/64 (62%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G LS  T E  L++ F ++G+I  ++++ D VTG S+GY FV++  E  A  A ++ 
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 89 DGLV 92
            LV
Sbjct: 66 HKLV 69

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

>gnl|CDD|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 = 61.1 bits (149), Expect = 5e-14
 Identities = 24/63 (38%), Positives = 34/63 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LFI  L  +  +  L   F   G +I  KV  D+ TGQS+ +GFV + +  +A  AIK M
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 89 DGL 91
          +G 
Sbjct: 61 NGF 63

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

 Score = 61.2 bits (149), Expect = 6e-14
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGE-IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          L++G L    +E  +K AF   GE ++ VK+I +++TG   GY FV+FA EA A   + +
Sbjct: 2  LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 88 MDGL 91
          ++G 
Sbjct: 62 LNGK 65

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

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

 Score = 61.1 bits (148), Expect = 7e-14
 Identities = 26/67 (38%), Positives = 44/67 (65%), Gaps = 3/67 (4%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE- 87
          +FIGGL+++T +  L++ FGQ GE+ +  V+ D  TG+SRG+GF+ F    +  E +K+ 
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 88 --MDGLV 92
            +DG +
Sbjct: 61 HILDGKI 67

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 60.4 bits (147), Expect = 1e-13
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 1/66 (1%)

Query: 29 LFIGGLSYDTNETVLKDAF-GQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +F+G L+ D  + +L++ F  ++  +   KV+ D VTG+S+GYGFV+F  E     A+ E
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 88 MDGLVC 93
          M+G+ C
Sbjct: 64 MNGVYC 69

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

 Score = 59.5 bits (145), Expect = 3e-13
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L  D  E +L + F   G ++ ++V  D +T +S GY +V F + A A  A+  +
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

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

 Score = 59.3 bits (144), Expect = 3e-13
 Identities = 25/62 (40%), Positives = 44/62 (70%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G LS+D +E  + +AFG++GEI  V++  D  +G+ +G+G+V+F+S+ AA  A+  +
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 89 DG 90
           G
Sbjct: 61 GG 62

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

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

 Score = 59.3 bits (144), Expect = 3e-13
 Identities = 21/59 (35%), Positives = 39/59 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          K+F+GGLS +T E  +++ FG+ G I+E+++  D+ T + RG+ F+ F SE    + ++
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59

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

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

 Score = 58.8 bits (143), Expect = 4e-13
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++GGL+ + +E VL  AF   G+I ++++  D  T + RG+ FV+F     A  AI  M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 89 DG 90
          + 
Sbjct: 61 NE 62

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

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

 Score = 58.9 bits (143), Expect = 4e-13
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++ GL     +  L+  F  +G II  +++CD VTG SRG GF++F     A  AIK +
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 89 DG 90
          +G
Sbjct: 63 NG 64

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

 Score = 58.6 bits (142), Expect = 6e-13
 Identities = 25/66 (37%), Positives = 37/66 (56%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          +T L +  L  +  +  ++  F   GEI   K+I D+VTGQS GYGFV +     A +AI
Sbjct: 1  KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 86 KEMDGL 91
            ++GL
Sbjct: 61 NTLNGL 66

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

 Score = 58.4 bits (142), Expect = 7e-13
 Identities = 22/63 (34%), Positives = 35/63 (55%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L YDT +  L++ F + G I    V+ D+ + + RG+G+V FA E  A  A++E 
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 89 DGL 91
             
Sbjct: 62 KKT 64

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

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

 Score = 57.9 bits (140), Expect = 1e-12
 Identities = 25/62 (40%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G LS +  +  L  AF       + +V+ D  +G+SRGYGFV F S+  A  AI EM
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 89 DG 90
          +G
Sbjct: 62 NG 63

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

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

 Score = 57.8 bits (140), Expect = 1e-12
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +LF+  L Y   E  L+  F + GE+ EV V  D+ +G+S+G+ +V F     A +A KE
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 88 MDG 90
          +DG
Sbjct: 64 LDG 66

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

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

 Score = 57.4 bits (139), Expect = 1e-12
 Identities = 24/52 (46%), Positives = 34/52 (65%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +FIGGLS+ T    L++ F + GEI E  V+ D  T +SRG+GFV F+  A+
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPAS 52

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 57.6 bits (140), Expect = 1e-12
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L +G L+ + N+  LK+ F  +G + +V +  DR     RGY +V+F S   A +AIK M
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 89 DG 90
          DG
Sbjct: 61 DG 62

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

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

 Score = 57.7 bits (140), Expect = 2e-12
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          LFIG L  + +E +L D F   G I++  K++ D  TG S+G+ F+ + S  A+  AI+ 
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 88 MDG 90
          M+G
Sbjct: 64 MNG 66

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

 Score = 61.4 bits (149), Expect = 2e-12
 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 5/103 (4%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSR----TKLFIGGLSYDTNETVLKDAFGQHGEIIEV 56
           ++ +N        +R      D + R      +F+  L    +   L D F + G I+  
Sbjct: 59  LETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSC 118

Query: 57  KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT 99
           KV  D   G+SRGYGFV F  E +A  AI++++G++    +  
Sbjct: 119 KVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160

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

 Score = 57.3 bits (139), Expect = 2e-12
 Identities = 25/64 (39%), Positives = 38/64 (59%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T ++I GL  +T +  L+      G+II  K I D+ T + +GYGFV F S  AA +AI+
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 87 EMDG 90
           ++G
Sbjct: 61 GLNG 64

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

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

 Score = 56.9 bits (138), Expect = 2e-12
 Identities = 26/59 (44%), Positives = 40/59 (67%)

Query: 33 GLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL 91
          GLS  T E  L++ F ++G I +V+V+ D+ TG+SRG+GFV F S   A EA + ++G+
Sbjct: 6  GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGM 64

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

 Score = 56.9 bits (138), Expect = 2e-12
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          KLF+GGL  D  E  L++ F Q+G +  V+++ D+ TG+ RG+ FV F
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

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

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

 Score = 56.4 bits (137), Expect = 3e-12
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++  L     E  L++ F  +G++  V+++ +    + RG+ FV+FAS   A  A+K++
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 89 DGLV 92
          +GLV
Sbjct: 59 NGLV 62

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

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

 Score = 56.9 bits (138), Expect = 3e-12
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +L +  L +   E  LK  F   G + EV +      G+ +G+ FV+F S+A A +AIK 
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59

Query: 88 MDGL 91
          ++G 
Sbjct: 60 VNGK 63

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

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

 Score = 56.8 bits (137), Expect = 3e-12
 Identities = 24/52 (46%), Positives = 37/52 (71%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +F+GGLS+DT +  LK+ F + GE+++  +  D VTG+SRG+GFV F   A+
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAAS 52

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|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 = 56.5 bits (137), Expect = 3e-12
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +LF+  L + T E  L++ F   GEI EV +  D+ T +S+G+ FV F     A +A  E
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 88 MDG 90
          +DG
Sbjct: 61 LDG 63

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

 Score = 57.0 bits (138), Expect = 3e-12
 Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 3/67 (4%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          NSR  LFI        E  L++AF   GEI ++ V+ D+ T +S+G  +VKFA  ++A  
Sbjct: 3  NSR--LFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59

Query: 84 AIKEMDG 90
          A++EM+G
Sbjct: 60 AMEEMNG 66

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

 Score = 56.8 bits (138), Expect = 3e-12
 Identities = 24/64 (37%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T +++  L  D ++  LK+ FG++G+I   KV+ D   G+S+G+GFV F +  AA +A++
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 87 EMDG 90
          E++G
Sbjct: 61 ELNG 64

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

 Score = 60.0 bits (145), Expect = 5e-12
 Identities = 26/77 (33%), Positives = 41/77 (53%)

Query: 14  VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           V + R  SD+     L++ GL     +  L+  F   G+II  +++ D VTG S+G GF+
Sbjct: 77  VSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFI 136

Query: 74  KFASEAAAGEAIKEMDG 90
           +F     A  AIK ++G
Sbjct: 137 RFDKRDEADRAIKTLNG 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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 56.0 bits (135), Expect = 5e-12
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 29 LFIGGLSYDTNETVLKDAF-GQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +F+G LS + NE+ L   F  +       K++ D VTG SRGYGFV+F+ E     A+ E
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 88 MDGLVC 93
          M G+ C
Sbjct: 64 MQGVYC 69

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

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

 Score = 56.1 bits (136), Expect = 5e-12
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           L++  L    ++  L++ F   G I   KV+ D   G+S+G+GFV F+S   A +A+ E
Sbjct: 3  NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTE 61

Query: 88 MDG 90
          M+G
Sbjct: 62 MNG 64

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

 Score = 55.9 bits (135), Expect = 6e-12
 Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 1/64 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+ GL +   +  L+  F +HG +  V+++ +R +G+ +G  +V++ +E++A +A+ +
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLK 62

Query: 88 MDGL 91
          MDG 
Sbjct: 63 MDGT 66

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 56.0 bits (135), Expect = 6e-12
 Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+GG+ + TNE  L+  F Q+G + EVK++ DR  G S+GYGFV F ++  A + ++E
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62

Query: 88 MDGLVCRTSK 97
           + L  R  K
Sbjct: 63 ANRLCFRDKK 72

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

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

 Score = 55.4 bits (134), Expect = 9e-12
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L +  L+Y T    L+  F ++GE+ +V +  DR T +SRG+ FV+F  +  A +A+  M
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 89 DG 90
          DG
Sbjct: 61 DG 62

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 55.5 bits (133), Expect = 1e-11
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 4/66 (6%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA----GE 83
          K+FIGGLS+ T+   L+D F + GEI E  V+ D  T +SRG+GFV FA  A+      +
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 84 AIKEMD 89
             E+D
Sbjct: 61 PHHELD 66

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 54.9 bits (133), Expect = 1e-11
 Identities = 25/62 (40%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G L     E +L + F Q G ++ V +  DRVT   +GYGFV+F SE  A  AIK M
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 89 DG 90
          + 
Sbjct: 61 NM 62

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

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

 Score = 54.9 bits (133), Expect = 1e-11
 Identities = 23/57 (40%), Positives = 34/57 (59%)

Query: 34 LSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          LS D +E  L++ F   G I  V +  D+ TGQSRG+ FV F +   A  AI++++G
Sbjct: 7  LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

 Score = 54.8 bits (131), Expect = 3e-11
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          + DAN    L++ GL     +  L+  F Q+G II  +++ D+VTG SRG GF++F    
Sbjct: 3  IRDAN----LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 58

Query: 80 AAGEAIKEMDG 90
           A EAIK ++G
Sbjct: 59 EAEEAIKGLNG 69

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 54.2 bits (130), Expect = 3e-11
 Identities = 24/61 (39%), Positives = 40/61 (65%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +FIGGLS+DT +  LKD F + GE+++  +  D +TG+SRG+GFV F    +  + + + 
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 89 D 89
          +
Sbjct: 61 E 61

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

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

 Score = 54.1 bits (131), Expect = 3e-11
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 33 GLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAG---EAIKE 87
          GL   T E  +  A        I +V++I D++TG SRG+ FV+F S   A    +A+  
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 88 MDGLV 92
          +D  V
Sbjct: 69 LDPFV 73

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

>gnl|CDD|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 = 53.8 bits (130), Expect = 4e-11
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T +F+GGL     E  L+  FG  GEI+ VK+         +G GFV+F   AAA  AI+
Sbjct: 2  TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQ 55

Query: 87 EMDGLVCRTS 96
          ++ G +   S
Sbjct: 56 QLQGTIIGGS 65

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

 Score = 54.0 bits (129), Expect = 4e-11
 Identities = 28/72 (38%), Positives = 42/72 (58%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +S+T L +  L  +  +  LK  FG  GEI   K++ D++TGQS GYGFV +     A +
Sbjct: 2  DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 84 AIKEMDGLVCRT 95
          AI  ++GL  +T
Sbjct: 62 AINTLNGLRLQT 73

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

 Score = 53.6 bits (129), Expect = 5e-11
 Identities = 20/62 (32%), Positives = 39/62 (62%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G + Y+  E  LKD F + G ++  +++ DR TG+ +GYGF ++  +  A  A++ +
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 89 DG 90
          +G
Sbjct: 61 NG 62

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

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

 Score = 53.8 bits (129), Expect = 5e-11
 Identities = 25/58 (43%), Positives = 36/58 (62%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          KLF+GGL  D  E  L + F Q G + + +VI D+ TG+ RG+GFV F +  +A +A 
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

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

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

 Score = 53.4 bits (129), Expect = 5e-11
 Identities = 23/63 (36%), Positives = 40/63 (63%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L ++  E  L+  F   GEI  V++  D  TG+S+GYGF++FA    A +A++++
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 89 DGL 91
          +G 
Sbjct: 61 NGF 63

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

 Score = 53.4 bits (128), Expect = 6e-11
 Identities = 24/64 (37%), Positives = 38/64 (59%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++ GL     +  L+  F Q+G II  +++ D++TG SRG GF++F     A EAIK
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 87 EMDG 90
           ++G
Sbjct: 61 GLNG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 53.5 bits (128), Expect = 6e-11
 Identities = 23/60 (38%), Positives = 41/60 (68%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GGLS+DT++  LKD F + GE+ +  +  D  TG+SRG+GF+ F   ++  + +++
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 53.5 bits (128), Expect = 7e-11
 Identities = 26/60 (43%), Positives = 40/60 (66%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A   + + +
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

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

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

 Score = 53.3 bits (128), Expect = 7e-11
 Identities = 24/61 (39%), Positives = 41/61 (67%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+GGL+  T+++ L+  F ++G++ E  V+ D  T +SRG+GF+ F+S   A EA++ 
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 88 M 88
           
Sbjct: 64 Q 64

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

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

 Score = 53.5 bits (128), Expect = 7e-11
 Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 4/69 (5%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          DAN    L++ GL    ++  ++  F Q+G II  +++ D+VTG SRG GF++F     A
Sbjct: 1  DAN----LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEA 56

Query: 82 GEAIKEMDG 90
           EAIK ++G
Sbjct: 57 EEAIKGLNG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 53.4 bits (129), Expect = 8e-11
 Identities = 23/62 (37%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          RT +FI  L +D  E  LK+ F Q GE+   +++ D++TG S+G  FVKF ++ +A + +
Sbjct: 1  RT-VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

Query: 86 KE 87
          + 
Sbjct: 60 EA 61

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

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

 Score = 53.2 bits (127), Expect = 1e-10
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          DAN    L++ GL     +  L+  F Q+G II  +++ D+VTG SRG GF++F     A
Sbjct: 2  DAN----LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 57

Query: 82 GEAIKEMDG 90
           EAIK ++G
Sbjct: 58 EEAIKGLNG 66

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 52.6 bits (127), Expect = 1e-10
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T +++G L +   E  L+  F   G I EV+V  D      +GY FV+F +  AA  AI 
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 87 EMDG 90
           ++G
Sbjct: 55 AVNG 58

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

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

 Score = 52.7 bits (127), Expect = 1e-10
 Identities = 22/53 (41%), Positives = 30/53 (56%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          KLF+G L +      LK+ F Q G++    V  D+ TG S+GYGFV F+S   
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDG 53

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 52.7 bits (127), Expect = 1e-10
 Identities = 21/64 (32%), Positives = 36/64 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L+  T +  L+  F + G+I   +VI D+ TG S  Y F++F ++    EA  +M
Sbjct: 6  LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 89 DGLV 92
          D ++
Sbjct: 66 DNVL 69

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

 Score = 52.7 bits (126), Expect = 1e-10
 Identities = 24/59 (40%), Positives = 40/59 (67%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          K+FIGGLS+DT++  L +   + GE+++  +  D VTG+SRG+GFV F   A+  + ++
Sbjct: 1  KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE 59

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

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

 Score = 52.7 bits (126), Expect = 1e-10
 Identities = 25/71 (35%), Positives = 41/71 (57%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T++F+G +  D  E  L   F + G I +++++ D ++GQ+RGY F+ F  + AA EA+K
Sbjct: 2  TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

Query: 87 EMDGLVCRTSK 97
            D    R  K
Sbjct: 62 LCDNYEIRPGK 72

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

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

 Score = 52.2 bits (126), Expect = 1e-10
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          F+G L +D  E  L+  F   G++  V+++ DR TG  +G+G+V F ++ +   A+K
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK 59

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

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

 Score = 55.6 bits (134), Expect = 2e-10
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           L++  L     +  L++ F + GEI   KV+ D   G SRG+GFV F++   A  A+ EM
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 89  DG 90
            G
Sbjct: 347 HG 348

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

 Score = 55.6 bits (134), Expect = 2e-10
 Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 1/91 (1%)

Query: 15  RFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVK 74
           +  R  +     T L++  L    NE  L++ F + GEI    V     +G+SRG+ FV 
Sbjct: 167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV-MKDGSGRSRGFAFVN 225

Query: 75  FASEAAAGEAIKEMDGLVCRTSKDTDMLSTG 105
           F     A +A++EM+G     +K+   L  G
Sbjct: 226 FEKHEDAAKAVEEMNGKKIGLAKEGKKLYVG 256

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

 Score = 52.4 bits (126), Expect = 2e-10
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          K+F+GGL  +  ET L+  F Q G + EV V+ D    + RG+GF+ F SE +
Sbjct: 4  KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDS 56

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

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

 Score = 52.1 bits (125), Expect = 2e-10
 Identities = 22/54 (40%), Positives = 34/54 (62%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          K+F+GGLS +T E  +K  F Q G++ +  ++ D+ T + RG+GFV F SE   
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54

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

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 52.0 bits (125), Expect = 2e-10
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          LF+G L YDT    L   F   G    V+++ D+ TG+S+G  FV+F +  A  +A+K
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

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

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

 Score = 51.8 bits (125), Expect = 2e-10
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +FI  L    +   L D F   G I+  KV  D   G S+GYGFV F +E AA  AI+++
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 89 DG 90
          +G
Sbjct: 64 NG 65

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

 Score = 51.8 bits (124), Expect = 3e-10
 Identities = 23/60 (38%), Positives = 32/60 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L++   +  L D F     I    V+ D  TG+SRGYGFV FA    A EA+ ++
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

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

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

 Score = 51.8 bits (125), Expect = 3e-10
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ-----SRGYGFVKFASEAAA 81
          T LF+  L++ T E  LK  F + G +  V +   +         S GYGFV+F S+ AA
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 82 GEAIKEMDGLV 92
           +A+K + G V
Sbjct: 61 QKALKRLQGTV 71

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

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

 Score = 51.9 bits (124), Expect = 3e-10
 Identities = 23/62 (37%), Positives = 35/62 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L+I GL     +  ++D F + G II  +V+ D+ TG SRG  F++F   + A EAI   
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 89 DG 90
          +G
Sbjct: 63 NG 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 52.0 bits (124), Expect = 3e-10
 Identities = 27/72 (37%), Positives = 41/72 (56%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +S+T L +  L  +  +   K  FG  GEI   K++ D++TGQS GYGFV +     A +
Sbjct: 1  DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 84 AIKEMDGLVCRT 95
          AI  ++GL  +T
Sbjct: 61 AINTLNGLKLQT 72

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

 Score = 51.5 bits (123), Expect = 3e-10
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 2  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

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

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

 Score = 51.6 bits (124), Expect = 3e-10
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L  D +E++L   F   G +  VKVI D  T + +GYGFV   +   A  AI  +
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 89 DG 90
          +G
Sbjct: 64 NG 65

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

 Score = 51.5 bits (124), Expect = 4e-10
 Identities = 17/48 (35%), Positives = 33/48 (68%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
          ++IGGL Y+  E  +   F Q+GEI+++ ++ D+ TG+S+G+ F+ + 
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYE 59

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

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

 Score = 51.5 bits (123), Expect = 4e-10
 Identities = 21/59 (35%), Positives = 35/59 (59%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          KLF+G +     E  ++  F +HG ++EV +I D+ TG  +G  FVK+++   A  AI+
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIR 59

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

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

 Score = 54.2 bits (130), Expect = 5e-10
 Identities = 24/68 (35%), Positives = 37/68 (54%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           S+T L +  L     +  ++  F   GEI   K++ D+VTGQS GYGFV +     A +
Sbjct: 1  ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 84 AIKEMDGL 91
          A+  ++GL
Sbjct: 61 AVNSLNGL 68

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

 Score = 51.0 bits (122), Expect = 5e-10
 Identities = 29/61 (47%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G LS   NE  ++  F   G I E  V+ D+  GQSRG  FV FAS   A  AIK 
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61

Query: 88 M 88
          M
Sbjct: 62 M 62

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

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

 Score = 51.3 bits (122), Expect = 5e-10
 Identities = 26/71 (36%), Positives = 40/71 (56%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+T L +  L  +  +   +  FG  GEI   K++ D++TGQS GYGFV +     A +A
Sbjct: 1  SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 85 IKEMDGLVCRT 95
          I  ++GL  +T
Sbjct: 61 INTLNGLRLQT 71

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

 Score = 54.1 bits (130), Expect = 6e-10
 Identities = 23/64 (35%), Positives = 40/64 (62%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KL++G L ++  E  L+  F   G+I +V++  D  TG+S+G+GF++F     A EA++ 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 88  MDGL 91
           M+G 
Sbjct: 248 MNGF 251

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

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

 Score = 51.0 bits (122), Expect = 6e-10
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L++  L     E  L+  F  +G I++  ++ D+ TG  RG  FV++     A  AI 
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 87 EMDGLV 92
           ++G +
Sbjct: 61 SLNGTI 66

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 53.8 bits (129), Expect = 8e-10
 Identities = 27/62 (43%), Positives = 36/62 (58%)

Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +F+  LS DT+ETVL   FG  G +  VK+I D  T Q +GYGFV   +   A  AI  +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 89  DG 90
           +G
Sbjct: 332 NG 333

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

 Score = 50.2 bits (119), Expect = 1e-09
 Identities = 26/67 (38%), Positives = 39/67 (58%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D  S+T L+I GL  +T +  L      +G+I+  K I D+ T + +GYGFV F S AAA
Sbjct: 3  DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62

Query: 82 GEAIKEM 88
           +A+  +
Sbjct: 63 QKAVSAL 69

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

>gnl|CDD|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 = 49.9 bits (119), Expect = 2e-09
 Identities = 25/63 (39%), Positives = 34/63 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LFI  L  +  +  L   F   G +I  KV  DR T QS+ +GFV F + A+A  AI+ M
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 89 DGL 91
          +G 
Sbjct: 67 NGF 69

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

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

 Score = 49.8 bits (119), Expect = 2e-09
 Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 1/50 (2%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          +F+GG+    +ET ++  F ++G + EVK+I DR TG S+GYGFV F  +
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDD 56

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

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

 Score = 49.8 bits (118), Expect = 2e-09
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+T L+I GL   T +  L      +G+I+  K I D+ T Q +GYGFV F S AAA +A
Sbjct: 3  SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62

Query: 85 IKEM 88
          +  +
Sbjct: 63 VASL 66

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 49.7 bits (118), Expect = 2e-09
 Identities = 23/58 (39%), Positives = 37/58 (63%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          KLFIGGLS++T E  L++ + Q G++ +  V+ D  + +SRG+GFV F+       A+
Sbjct: 4  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 49.3 bits (118), Expect = 3e-09
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +LFI  L+Y   E  L+  F ++G + EV +  D++T + +G+ FV +     A +A  E
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 88 MDGLV 92
          +DG V
Sbjct: 64 LDGTV 68

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

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 48.9 bits (117), Expect = 3e-09
 Identities = 24/66 (36%), Positives = 42/66 (63%), Gaps = 4/66 (6%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          +RT LFIG L   T  + L++AF + GEII++ +   +  G +  Y F+++A  A+  +A
Sbjct: 2  TRT-LFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKA 57

Query: 85 IKEMDG 90
          +++MDG
Sbjct: 58 MRKMDG 63

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 48.8 bits (117), Expect = 4e-09
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +++ +  L     E  L++ F   GE+ +VKV+  R  G+SR +GFV F SE  A +A+K
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59

Query: 87 EMDGLVCRTSK 97
            +     TSK
Sbjct: 60 YFNKTFIDTSK 70

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

 Score = 48.9 bits (116), Expect = 4e-09
 Identities = 25/62 (40%), Positives = 38/62 (61%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G LS +     +K AF   G I + +V+ D  TG+S+GYGFV F ++  A  AI++M
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 89 DG 90
           G
Sbjct: 64 GG 65

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

 Score = 48.5 bits (116), Expect = 4e-09
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++ GLS  T    LK  F ++G+++  K++ +  +  +R +GFV  AS   A + I+ +
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 89 D 89
           
Sbjct: 62 H 62

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

 Score = 48.9 bits (117), Expect = 4e-09
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G LS D  +  L + F +HG+I+EV +I  +    +  + F+KF  E AA  A++  
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 89 DG 90
          + 
Sbjct: 64 NH 65

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

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

 Score = 48.4 bits (116), Expect = 4e-09
 Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 2/61 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L Y   E  L+  F + GEI +V+++ +   G+S+GY +V+F +E +  EA+K +
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALK-L 59

Query: 89 D 89
          D
Sbjct: 60 D 60

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 51.3 bits (123), Expect = 5e-09
 Identities = 24/60 (40%), Positives = 34/60 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L  D  E  L D F   G ++ V+V  D VT +S GYG+V F + A A  A++ M
Sbjct: 3  LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

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

 Score = 48.4 bits (116), Expect = 5e-09
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L +G L  +  +   ++     G +    ++    TG+S+GYGFV++AS+A+A +A  ++
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 89 DG 90
          DG
Sbjct: 62 DG 63

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

 Score = 48.5 bits (115), Expect = 5e-09
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          K+F+GGLS DT E  +K+ FG  GEI  +++  D  T + RG+ FV +  E
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDE 51

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

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

 Score = 48.5 bits (115), Expect = 6e-09
 Identities = 23/48 (47%), Positives = 35/48 (72%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          KLF+GG+  DT E  L+D F ++G+I  +++I DR +G+ RG+GFV F
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

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

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

 Score = 48.3 bits (115), Expect = 6e-09
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          ++IG L +   E  LK  F Q G +  V+V   + TG S+ YGF++F +   A  A K M
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 89 DG 90
          + 
Sbjct: 62 NN 63

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

 Score = 48.0 bits (115), Expect = 6e-09
 Identities = 17/65 (26%), Positives = 35/65 (53%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           ++++  +  D +E  +K  F   G+I    +  D  TG+ +GYGF+++ +  +A +AI 
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 87 EMDGL 91
           M+  
Sbjct: 61 SMNLF 65

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

 Score = 51.0 bits (122), Expect = 7e-09
 Identities = 18/70 (25%), Positives = 34/70 (48%)

Query: 24  NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           +S+ +++IG L     E  +K+     G++    +I D  TG S+GY F ++   +    
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 84  AIKEMDGLVC 93
           AI  ++G   
Sbjct: 353 AIAALNGKDT 362

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

 Score = 47.6 bits (114), Expect = 8e-09
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 8/62 (12%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++  L   T E  L++ F ++GE+  VK I D        Y FV F     A +A++EM
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 89 DG 90
          +G
Sbjct: 56 NG 57

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

 Score = 47.7 bits (114), Expect = 8e-09
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 6/65 (9%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R +LF+G L  D  E   K+ F ++GE+ EV +       + +G+GF++  +   A +A 
Sbjct: 1  RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAK 54

Query: 86 KEMDG 90
           E+DG
Sbjct: 55 AELDG 59

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

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

 Score = 48.0 bits (114), Expect = 8e-09
 Identities = 27/61 (44%), Positives = 38/61 (62%), Gaps = 3/61 (4%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ GLS DT E  LK++F      I  +++ DR TG S+G+GFV F+SE  A  A + M
Sbjct: 3  LFVKGLSEDTTEETLKESFDGS---IAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 89 D 89
          +
Sbjct: 60 E 60

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

 Score = 47.8 bits (114), Expect = 9e-09
 Identities = 21/58 (36%), Positives = 34/58 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          LF+G LS++T E  L+  FG+ G I  V+++    +G+ +G+ FV F     A  A+K
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK 58

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

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

 Score = 47.7 bits (113), Expect = 1e-08
 Identities = 25/71 (35%), Positives = 41/71 (57%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T++F+G +  D  E  L   F + G I +++++ D +TG +RGY FV F ++ AA EA+K
Sbjct: 2  TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

Query: 87 EMDGLVCRTSK 97
            +    R  K
Sbjct: 62 LYNNHEIRPGK 72

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

>gnl|CDD|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 = 47.7 bits (114), Expect = 1e-08
 Identities = 20/66 (30%), Positives = 40/66 (60%), Gaps = 2/66 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          L++G L++ T +  L+ A  + G  ++  +K    +  G+S+G+ +V+FASEAAA    +
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 87 EMDGLV 92
          +++G  
Sbjct: 61 KLEGRE 66

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

 Score = 47.3 bits (113), Expect = 1e-08
 Identities = 21/59 (35%), Positives = 41/59 (69%), Gaps = 1/59 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          LF+G LS+   +  L++ F + GE+++V++  D   G+S+G+G V+FA+E  A +A+++
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59

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

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

 Score = 47.4 bits (112), Expect = 1e-08
 Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 4/69 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFAS----EAAAGE 83
          KLFIGGLS++T +  L+  F Q G + +  V+ D  T +SRG+GFV ++S    +AA   
Sbjct: 4  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 84 AIKEMDGLV 92
             ++DG V
Sbjct: 64 RPHKVDGRV 72

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

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

 Score = 47.1 bits (112), Expect = 2e-08
 Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G L+    E  +++ F  +G + ++ ++ D +  QSRG  FVK++S+  A  AIK 
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKA 59

Query: 88 MDGL 91
          ++G+
Sbjct: 60 LNGV 63

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 47.4 bits (112), Expect = 2e-08
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGLS++T +  L++ F + G + +  V+ D  T +SRG+GFV ++        ++E
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYS-------CVEE 56

Query: 88  MDGLVCRTSKDTD 100
           +D  +       D
Sbjct: 57  VDAAMSARPHKVD 69

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|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 = 46.8 bits (112), Expect = 2e-08
 Identities = 19/66 (28%), Positives = 35/66 (53%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+FIGGL    +E  +K+     G++    ++ D  TG S+GY F ++   +   +AI  
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 88 MDGLVC 93
          ++G+  
Sbjct: 62 LNGMQL 67

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

 Score = 46.5 bits (111), Expect = 2e-08
 Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G L   T    L+  F ++G + E    CD V    + YGFV    E  A +AIK 
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTE----CDVV----KNYGFVHMEEEEDAEDAIKA 52

Query: 88 MDG 90
          ++G
Sbjct: 53 LNG 55

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

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

 Score = 46.9 bits (112), Expect = 2e-08
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV---TGQSRGYGFVKFASEAAAGE 83
          T L++G L+    E VL   FG+ G +  VK++  R      ++R  GFV F + A A  
Sbjct: 2  TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 84 AIKEMDG 90
          A+ E+DG
Sbjct: 62 ALDELDG 68

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

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 18/61 (29%), Positives = 31/61 (50%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +LF+G L +D  E  LK+ F + G ++EV++      G+   +GFV F    A  + +  
Sbjct: 5  QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 88 M 88
           
Sbjct: 65 K 65

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

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

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+ G+  +  E  + D F + GEI  + +  DR TG  +GY  +++ ++  A  AI+ +
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 89 DG 90
          +G
Sbjct: 69 NG 70

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
           KLF+G +  +  E  L+  F Q G+I E+ V+ D+ TG  +G  F+ + +  +A +A
Sbjct: 6  IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 46.6 bits (111), Expect = 2e-08
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
           T+LF+  +     E  L++ F + G+I  V ++ D+ TG+S+G+G+VKF   + A  A+
Sbjct: 1  LTRLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

Query: 86 KEMD 89
          +  D
Sbjct: 60 ENCD 63

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

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

 Score = 46.4 bits (111), Expect = 2e-08
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          ++IG L +   E  L+  F Q G +  +++   + TG+S+GY FV+F S   A    + M
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 89 DG 90
          + 
Sbjct: 62 NN 63

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

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQH-GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          LF+G L+ D ++  L + F +        KV+ D+  G SRGYGFV+F+ E+    A+ E
Sbjct: 4  LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRALTE 62

Query: 88 MDG 90
          M G
Sbjct: 63 MQG 65

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

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

 Score = 47.2 bits (112), Expect = 3e-08
 Identities = 18/60 (30%), Positives = 28/60 (46%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            LF+  L YD  E  L   F + G +     + D+ TG+++G GFV F  +      +K
Sbjct: 2  FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

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

 Score = 46.6 bits (110), Expect = 3e-08
 Identities = 25/62 (40%), Positives = 37/62 (59%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G LS +     +K AF   G+I + +V+ D  TG+S+GYGFV F ++  A  AI  M
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 89 DG 90
           G
Sbjct: 64 GG 65

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

 Score = 46.5 bits (110), Expect = 3e-08
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          K+F+GG+  DT E  L+D F ++G+I  ++V+ DR +G+ RG+ FV F
Sbjct: 2  KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

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

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

 Score = 46.2 bits (109), Expect = 4e-08
 Identities = 20/61 (32%), Positives = 36/61 (59%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GGLS DT E  +++ FG  GE+  +++  D  T + RG+ F+ F  E    + +++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 88 M 88
           
Sbjct: 61 K 61

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

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

 Score = 46.2 bits (109), Expect = 4e-08
 Identities = 24/66 (36%), Positives = 35/66 (53%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          RT L +  L  +  +  L+  F   GE+   K+I D+V G S GYGFV + +   A  AI
Sbjct: 1  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 86 KEMDGL 91
            ++GL
Sbjct: 61 NTLNGL 66

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

 Score = 46.1 bits (110), Expect = 4e-08
 Identities = 16/56 (28%), Positives = 33/56 (58%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          F+G + Y T    L++ F   G I  + ++CD+ TGQ +G+ +++F  +++   A+
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 45.7 bits (109), Expect = 5e-08
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L++GGL     E  L+D F Q GEI  + V+        +   FV F +  AA +A +
Sbjct: 2  TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAE 55

Query: 87 E 87
           
Sbjct: 56 R 56

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

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

 Score = 45.3 bits (108), Expect = 6e-08
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L +      LKD F + G ++   V  D   G+S+G+G V F S   A  AI+  
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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

 Score = 45.1 bits (107), Expect = 1e-07
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +IG L++D  E  +++ F    EI  V++  D+ TG+ +G+G V FA E +   A+K
Sbjct: 3  YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK 58

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

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

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            ++F+G +  D  E  L   F + G I E++++ D  +GQ+RGY FV F  +  A EA+K
Sbjct: 59  CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVK 117

Query: 87  EMDGLVCRTSK 97
            ++    R  +
Sbjct: 118 LLNNYEIRPGR 128

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 44.4 bits (104), Expect = 2e-07
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          +T L+I GL   T +  L      +G+I+  K I D+ T + +GYGFV F S +AA +A+
Sbjct: 1  KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 86 KEM 88
            +
Sbjct: 61 TAL 63

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

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

 Score = 44.2 bits (104), Expect = 2e-07
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          K+F+GGLS +T    +K  F Q G++ +  ++ D+ T + RG+GFV F SE
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

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

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

 Score = 44.1 bits (104), Expect = 2e-07
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G L  +  E  ++  F Q+G+++E    CD +    + YGFV    + AA EAI+ 
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLE----CDII----KNYGFVHMDDKTAADEAIRN 53

Query: 88 M 88
          +
Sbjct: 54 L 54

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

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

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 27/74 (36%), Positives = 37/74 (50%)

Query: 24  NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           NS T L +  L  D  +  L   F   G I   +++ D  TG S GY FV F SEA +  
Sbjct: 105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQR 164

Query: 84  AIKEMDGLVCRTSK 97
           AIK ++G+  R  +
Sbjct: 165 AIKNLNGITVRNKR 178

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

 Score = 44.2 bits (105), Expect = 2e-07
 Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR---GYGFVKFASEAAAGEA 84
          ++++  L +  +E  L+  F + GE+  +++   +   Q R   G+ FV F   ++A  A
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 85 IKEMDG 90
          + +++G
Sbjct: 62 L-QLNG 66

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

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

 Score = 44.3 bits (105), Expect = 2e-07
 Identities = 18/65 (27%), Positives = 40/65 (61%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++++G +S++  E  ++ AF   G I  + +  D VT + +G+ FV++    AA  A+++
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 88 MDGLV 92
          M+G++
Sbjct: 62 MNGVM 66

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

 Score = 44.2 bits (105), Expect = 2e-07
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          RT LF+G L     E +L + F Q G +  VK I     G+ + + FV F  E +   AI
Sbjct: 2  RT-LFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAI 59

Query: 86 KEMDGL 91
          + ++G+
Sbjct: 60 QLLNGI 65

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

 Score = 43.9 bits (104), Expect = 2e-07
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L+IG LS D NE+ L+  F +H      K+    V  +  GY FV    ++ A +AI+++
Sbjct: 1  LYIGNLSSDVNESDLRQLFEEH------KIPVSSVLVKKGGYAFVDCPDQSWADKAIEKL 54

Query: 89 DGLVC 93
          +G + 
Sbjct: 55 NGKIL 59

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

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

 Score = 44.3 bits (104), Expect = 2e-07
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  LS D++E+VL   FG  G +  VKVI D  T + +G+GFV   +   A  AI  +
Sbjct: 6  IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 89 DG 90
          +G
Sbjct: 66 NG 67

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

 Score = 44.3 bits (104), Expect = 2e-07
 Identities = 23/62 (37%), Positives = 35/62 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  LS + +E+VL   FG  G +  VKVI D  T + +G+GFV   +   A  AI  +
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 89 DG 90
          +G
Sbjct: 64 NG 65

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

 Score = 43.7 bits (104), Expect = 3e-07
 Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T+L +  L YD  E  L++ FG+ GE+ +VK+  DR +G+S G   V F     A  AIK
Sbjct: 1  TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 87 EMDG 90
          + +G
Sbjct: 60 QFNG 63

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

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

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG--QSRGYGFVKFASEAAAGEA- 84
          K+F+G +    +E  L++ F Q+G + ++ V+ DR     QS+G  FV F +  AA EA 
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 85 -----IKEMDGL 91
               +K + G+
Sbjct: 63 NALHNMKTLPGM 74

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

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 43.8 bits (103), Expect = 3e-07
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R +LF+G L  D  E   K  F ++GE  EV +       + +G+GF+K  S A A  A 
Sbjct: 1  RCRLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAK 54

Query: 86 KEMDGLVCR 94
           E+D    R
Sbjct: 55 AELDDTPMR 63

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 45.8 bits (108), Expect = 5e-07
 Identities = 27/91 (29%), Positives = 48/91 (52%), Gaps = 2/91 (2%)

Query: 4   LNG-SVRFSH-SVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD 61
           LNG +VR     V + R   ++   T L++  L     +  L   FG++G+I++  ++ D
Sbjct: 169 LNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD 228

Query: 62  RVTGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
           ++TG  RG  FV+F     A EAI  ++ ++
Sbjct: 229 KLTGTPRGVAFVRFNKREEAQEAISALNNVI 259

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 = 45.8 bits (108), Expect = 6e-07
 Identities = 17/68 (25%), Positives = 36/68 (52%)

Query: 22  DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
           +A    ++++  +  D +ET +K  F   GEI++ ++         +GYGF+++ +  + 
Sbjct: 200 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQ 259

Query: 82  GEAIKEMD 89
            EAI  M+
Sbjct: 260 SEAIASMN 267

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

 Score = 43.2 bits (101), Expect = 7e-07
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L+ D +E++L   FG  G +  VKVI D  T + +G+GFV   +   A  AI  +
Sbjct: 6  IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 89 DG 90
          +G
Sbjct: 66 NG 67

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

 Score = 43.1 bits (101), Expect = 8e-07
 Identities = 23/62 (37%), Positives = 33/62 (53%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +FI  L  D +E +L   FG  G +  VKVI D  T + +G+GFV   +   A  AI  +
Sbjct: 4  IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 89 DG 90
          +G
Sbjct: 64 NG 65

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

 Score = 42.6 bits (100), Expect = 8e-07
 Identities = 22/59 (37%), Positives = 36/59 (61%)

Query: 33 GLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL 91
          GLS  T E  L++ F ++G +  V V+ D+ TG+SRG+ FV F     + EA++  +G+
Sbjct: 6  GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGM 64

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

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 42.7 bits (100), Expect = 9e-07
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          K+F+GGLS +T    +K  F Q G++ +  ++ D+ T + RG+GFV F +E
Sbjct: 5  KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENE 55

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 23/69 (33%), Positives = 35/69 (50%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LFI  L  +  +T L   F   G +I  KV  D+ T  S+ +GFV + +  +A  AI+ M
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 89 DGLVCRTSK 97
          +G    T +
Sbjct: 67 NGFQIGTKR 75

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

 Score = 42.4 bits (100), Expect = 1e-06
 Identities = 21/65 (32%), Positives = 32/65 (49%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L I  L     +   +  F   G +   K++ D+ TG S G+GFV + S   A  AI+
Sbjct: 1  TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 87 EMDGL 91
           ++GL
Sbjct: 61 TLNGL 65

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

 Score = 42.3 bits (100), Expect = 1e-06
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV---TGQSRGYGFVKFASEAAAGEA 84
          +L+IG L     E  L   F ++G+I +   +  +     GQ RGY FV F ++  A +A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 85 IKEMDG 90
          +K ++G
Sbjct: 61 LKSLNG 66

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

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

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L++  ++  T    L+  FG++G I++V +  D  T + RG+ +V+F     A +A+ 
Sbjct: 1  TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 87 EMDG 90
           +D 
Sbjct: 61 YLDR 64

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 41.5 bits (98), Expect = 2e-06
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 38 TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM-DGLVCRTS 96
          +NE +L+ AF Q GE+    VI D   G+S G G V+F+ +  A  AIK   +G    T+
Sbjct: 12 SNE-LLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKRCSEGCFLLTA 69

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 41.9 bits (98), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GGL+ +  E  +++ FG+ GEI  +++  D  T + RG+ F+ F  E    + +K+
Sbjct: 6  KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEE----DPVKK 61

Query: 88 M 88
          +
Sbjct: 62 V 62

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

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

 Score = 41.3 bits (97), Expect = 3e-06
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +L++     DT+E+ +++ F  +G + EVK+I          + FV+F S  +A  A   
Sbjct: 1  RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 88 MDG 90
          + G
Sbjct: 53 VHG 55

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

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 41.3 bits (97), Expect = 3e-06
 Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+G LS    E  ++  F   G I E  ++     G S+G  FVKF+S A A  AI  
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAINA 61

Query: 88 MDG 90
          + G
Sbjct: 62 LHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 41.1 bits (97), Expect = 4e-06
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR---GYGFVKFASEAAAGEA 84
          K+++G L     +  L+D F ++G +  V V        +R   G+ FV+F     A +A
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWV--------ARNPPGFAFVEFEDPRDAEDA 52

Query: 85 IKEMDGLVCR 94
          ++ +DG    
Sbjct: 53 VRALDGRRIC 62

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

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

 Score = 41.2 bits (96), Expect = 4e-06
 Identities = 25/61 (40%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLFIG +S   NE  ++  F   G+I E +++     G SRG  FV F + A A  AIK 
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRIL-RGPDGLSRGCAFVTFTTRAMAQTAIKA 61

Query: 88 M 88
          M
Sbjct: 62 M 62

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

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

 Score = 41.2 bits (96), Expect = 5e-06
 Identities = 22/63 (34%), Positives = 38/63 (60%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L + GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F +   A EA +  
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 89 DGL 91
          +G+
Sbjct: 72 NGM 74

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

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

 Score = 40.8 bits (96), Expect = 5e-06
 Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          ++ +++  L +      L   F ++G++++V ++ D+ T +S+G  F+ F     A + +
Sbjct: 1  KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 86 KEMDG--LVCRTSK 97
          K ++   L  RT K
Sbjct: 61 KALNNKELFGRTLK 74

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

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

 Score = 40.6 bits (95), Expect = 6e-06
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L     E +LK  F   G +  VK+I D+   +   YGFV++     A  A++ +
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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

 Score = 42.7 bits (100), Expect = 7e-06
 Identities = 18/63 (28%), Positives = 38/63 (60%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           ++++G +S++  E  ++ AF   G I  + +  D  TG+ +G+ FV++    AA  A+++
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 88  MDG 90
           M+G
Sbjct: 169 MNG 171

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T L+IG LS    E  LK+ F ++GEI  + +I        RG  +V   +   A  A
Sbjct: 2  STT-LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRA 54

Query: 85 IKEMDGL 91
          ++++  +
Sbjct: 55 LQKLRNV 61

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.3 bits (94), Expect = 8e-06
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++FIG L  D  E  L     + G+I E++++ D   G +RGY FV F+++  A  AIK+
Sbjct: 3  EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQ 61

Query: 88 MDGLVCRTSK 97
          ++    R  +
Sbjct: 62 LNNYEIRNGR 71

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 40.2 bits (94), Expect = 8e-06
 Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G + Y +    L+  F   G I  V ++CD+ +G  +GY +++FA+  +   A+  +
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-AL 60

Query: 89 DGLVCR 94
          D    R
Sbjct: 61 DESSFR 66

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 39.9 bits (93), Expect = 9e-06
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 6/67 (8%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R +LF+G L  D  E   K  F ++GE  EV +       + RG+GF++  S   A  A 
Sbjct: 1  RCRLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAK 54

Query: 86 KEMDGLV 92
           E+DG +
Sbjct: 55 AELDGTI 61

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 40.0 bits (94), Expect = 9e-06
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 40 ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          + +L+D F + G +I+V ++  +       YG+ K+A   +A  AI  + G
Sbjct: 13 DYILEDVFCRFGGLIDVYLVPGK------NYGYAKYADRESAERAITTLHG 57

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

 Score = 39.9 bits (94), Expect = 9e-06
 Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TKL +  + ++  +  L++ F   G++  V+ +  +  G  RG+ FV+F ++  A  A++
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 87 EM 88
           +
Sbjct: 60 AL 61

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

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

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L+     +G++I  +++ D   GQSRG GF +  S     + I 
Sbjct: 1  TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDS-KGQSRGVGFARMESREKCEDIIS 59

Query: 87 EMDGLVCRTSKD 98
          + +G   +   +
Sbjct: 60 KFNGKYLKGEGE 71

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

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

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 25 SRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          SR  LF+  L     + ++L+  F Q G+    ++      GQ RG+ FV++A+   A E
Sbjct: 2  SRC-LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEE 59

Query: 84 AIKEMDGLVCRTSK 97
          A + ++G   + S 
Sbjct: 60 AQQALNGHSLQGSP 73

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQH-GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          ++L +  L     E  LK+ F +H GEI +VK++     G+SR   F+ + +E  A +A 
Sbjct: 1  SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAK 59

Query: 86 KEMDGLVCRTSK 97
             +     TSK
Sbjct: 60 DYFNNTYINTSK 71

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 9/67 (13%)

Query: 28 KLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          ++F+G L+ D  ++  L++ F ++G+I+ + +         +GYGFV+F +E  A  A+ 
Sbjct: 2  RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 87 EMDGLVC 93
            +G   
Sbjct: 54 GENGREI 60

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

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 6/62 (9%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          ++ GG++    E +++  F   G+I+EV+V  D      +GY FV+F S  +A  AI  +
Sbjct: 3  VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56

Query: 89 DG 90
          +G
Sbjct: 57 NG 58

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

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

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          +LF+G L +D +E+ LK+ F   G ++E+++    V G+   +GFV F
Sbjct: 7  QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVF 54

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

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 39.9 bits (93), Expect = 1e-05
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+G +  D  E  L   F   G I E++++ D   G++RGY FV +  +  A  A++E
Sbjct: 3  EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRE 61

Query: 88 MDGLVCRTSK 97
          ++    R  +
Sbjct: 62 LNNYEIRPGR 71

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.9 bits (93), Expect = 1e-05
 Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT-GQSRGYGFVKFASEAA 80
          D  +   LF+G L     ET L+ AF + G I EV +   R   GQ+  YGF+KF +   
Sbjct: 3  DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDI--KRPGRGQTSTYGFLKFENLDM 60

Query: 81 AGEAIKEMDGLVCR 94
          A  A   M G V R
Sbjct: 61 AHRAKLAMSGKVLR 74

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 36/63 (57%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + LF+  ++ DT    L+  FG++G I++V V  D  T + RG+ +V+F     A +A+ 
Sbjct: 1  SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 87 EMD 89
           +D
Sbjct: 61 NLD 63

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

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

 Score = 39.7 bits (92), Expect = 1e-05
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++ GLS  T  T LK+ F ++G+++  KV+ +  +  +R YGFV  ++   A + I  +
Sbjct: 4  LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

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

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           ++F+G +  D  E  L   F + G I E++++ D  +G +RGY FV + ++ AA  A+K
Sbjct: 2  CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVK 60

Query: 87 EMDGLVCRTSK 97
          ++     R  K
Sbjct: 61 QLHNYEIRPGK 71

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.4 bits (92), Expect = 1e-05
 Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 5/67 (7%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          ++RT LF+  L Y+     LK+ F      +++++   +  G S+G  +++F +EA A +
Sbjct: 2  DART-LFVKNLPYNITVDELKEVFED---AVDIRLPSGK-DGSSKGIAYIEFKTEAEAEK 56

Query: 84 AIKEMDG 90
          A++E  G
Sbjct: 57 ALEEKQG 63

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, 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.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 40 ETVLKDAFGQHGEIIEVKV-ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          + VL+  F + G    V + +    TG+++GY FV+FA+   A EA+K ++G
Sbjct: 21 KKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 17/56 (30%), Positives = 32/56 (57%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          F+  LS    E  L + F + G++ +V++I DR + +S+G  +V+F  E +   A+
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58

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

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

 Score = 39.2 bits (92), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +++IG L Y   E  ++  F  +G I E+ +          G+GFV+F     A +A+ E
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52

Query: 88 MDG 90
          ++G
Sbjct: 53 LNG 55

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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 39.1 bits (91), Expect = 2e-05
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +++IG LSY   E  ++  FG +G+++E+ +          GYGFV+F     A +A+ E
Sbjct: 1  RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52

Query: 88 MDG 90
          ++G
Sbjct: 53 LNG 55

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that 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. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 33 GLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD 89
          GL     E  +++A   HG E  +V+++  + TG SRG+ FV+F S     EA + M+
Sbjct: 9  GLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMS---LEEATRWME 63

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 38.9 bits (90), Expect = 2e-05
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++ GLS +T    LK+ FG++G+++  KV+ +  +  ++ YG V  +S A     I  +
Sbjct: 2  LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 89 D 89
           
Sbjct: 62 H 62

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 20/63 (31%), Positives = 32/63 (50%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LFI  L  +  +  L   F   G ++  KV  D+ T  S+ +GFV + +  +A  AI+ M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 89 DGL 91
          +G 
Sbjct: 70 NGF 72

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

 Score = 38.8 bits (90), Expect = 2e-05
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G L     E +L + F Q G + +V  IC    G+ + +GFV F    +   AI  +
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKV-TICKDKEGKPKSFGFVCFKHSESVPYAIALL 62

Query: 89 DGL 91
          +G+
Sbjct: 63 NGI 65

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%)

Query: 42 VLKDAFGQHGEIIEVKVICDR------VTGQSRGYGFVKFASEAAA 81
          V + A  +  +I +VK++ D         G+S+GYGFV+F +   A
Sbjct: 25 VSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHA 70

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

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 38.8 bits (90), Expect = 3e-05
 Identities = 26/69 (37%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D  +   LFIG L ++ +E  L+ AF ++G I EV VI     GQ   Y F+KF +   A
Sbjct: 4  DQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMA 62

Query: 82 GEAIKEMDG 90
            A   M G
Sbjct: 63 HRAKVAMSG 71

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 38.5 bits (89), Expect = 4e-05
 Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 6/62 (9%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          ++ GG++    E +++  F   G+I+E++V  ++      GY F++F++  +A  AI  +
Sbjct: 3  VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEK------GYSFIRFSTHESAAHAIVSV 56

Query: 89 DG 90
          +G
Sbjct: 57 NG 58

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.5 bits (90), Expect = 4e-05
 Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          +RT LF+G L     E  L+ AF ++G + +V  I     GQ   Y FVKF +   A  A
Sbjct: 2  TRT-LFVGNLEITITEEELRRAFERYGVVEDV-DIKRPPRGQGNAYAFVKFLNLDMAHRA 59

Query: 85 IKEMDG 90
             M G
Sbjct: 60 KVAMSG 65

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 38.5 bits (89), Expect = 4e-05
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+++G L  + N+T L+ AFG +G +  V      V     G+ FV+F     A +A++E
Sbjct: 6  KVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVRE 60

Query: 88 MDG 90
          +DG
Sbjct: 61 LDG 63

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that 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. SRSF3 can shuttle between the nucleus and cytoplasm. It contains 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 = 81

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

 Score = 38.1 bits (89), Expect = 4e-05
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L Y      LK+ F   G+++   +  D+  G+SRG G V+F     A +AI   
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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

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

 Score = 37.9 bits (88), Expect = 5e-05
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+G +  DT++  L+  F  +G ++   V+        R + FV    EAAA  AI+E
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 88 MDG 90
          ++G
Sbjct: 54 LNG 56

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

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

 Score = 37.5 bits (88), Expect = 5e-05
 Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 5/48 (10%)

Query: 43 LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          L   F   G + ++K++         G+ FV+F++E AA +A++ ++G
Sbjct: 1  LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNG 43

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

 Score = 38.3 bits (89), Expect = 5e-05
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+G L     E ++ + F Q G +I+VK+  D+  G+ + + FV F  E +   A+  +
Sbjct: 4  LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 89 DGL 91
          +G+
Sbjct: 63 NGI 65

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 38.3 bits (89), Expect = 6e-05
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD---RVTGQ--SRGYGFVKFASEAAAGE 83
          LF+  L++ T    L DAF      +  +V      +  GQ  S G+GFV F ++  A  
Sbjct: 3  LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 84 AIKEMDGLV 92
          A+K MDG V
Sbjct: 63 ALKAMDGFV 71

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

 Score = 37.8 bits (88), Expect = 6e-05
 Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 43 LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          L + F   GEI  V +  DR TG S+G+ +++F S     +A  E+DG
Sbjct: 20 LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA-LELDG 66

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 37.6 bits (87), Expect = 8e-05
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          +F+G L ++  E  L   FG+ G I  V+++ D  T   +G+ +V+F  E A  +A+
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL 58

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

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

 Score = 37.5 bits (88), Expect = 8e-05
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF-ASEAAAGEAIK 86
          LF+GGLS    E+ L++ F + G + +V++I  +  G  RG+ ++    SEA   +   
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

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

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

 Score = 37.6 bits (87), Expect = 9e-05
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+  L +D    +LKD F + G ++   +  +   G+S+G G V+F S   A  A + 
Sbjct: 1  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRM 58

Query: 88 MDGL 91
          M+G 
Sbjct: 59 MNGY 62

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

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 37.6 bits (87), Expect = 1e-04
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+G +  D  E  L   F + G+I E +++ +  +G++RGY FV + ++  A  AI+ 
Sbjct: 3  EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAIRI 61

Query: 88 MDGLVCRTSK 97
          ++    R  K
Sbjct: 62 LNNYEIRPGK 71

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 6/57 (10%)

Query: 36 YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
          Y   E +LK AF   G II + +       + +  GFV F    +A  AI E++G  
Sbjct: 12 YGLTEEILKKAFSPFGNIINISM------EKEKNCGFVTFEKMESADRAIAELNGTT 62

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

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 3/48 (6%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
          +LF+G L +D +++ LK+ F Q+G ++E+++      G+   +GFV F
Sbjct: 5  QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVF 49

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

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

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++GG+ Y + E  ++  F   GEI E+ ++    TG+ RG  F+ F +E AA  A+  +
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-AL 59

Query: 89 DG 90
          DG
Sbjct: 60 DG 61

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

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

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFAS 77
           K+F+G L+ D  E  L+  F Q GE+ +V +         R + FV FA 
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFAD 46

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

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

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 8/62 (12%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L+    E +L+ AFGQ G++  VK + D        Y F+ F     A +A++EM
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 89 DG 90
          +G
Sbjct: 56 NG 57

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

>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +F+ GL Y  +E  +K+ F  HG  +E  +   R  G++ G   VKFA+   A EA+K
Sbjct: 2  VFLHGLPYTADEHDVKEFF--HGLDVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALK 57

This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L  +T + +L+  F Q     EV+++        RG  FV+F +E  A  A++ +
Sbjct: 5  LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58

Query: 89 DG 90
           G
Sbjct: 59 QG 60

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 36.4 bits (84), Expect = 2e-04
 Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R++LF+G L  D  E  ++  F ++G+  E+ +  D      +G+GF++  +   A  A 
Sbjct: 1  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAK 54

Query: 86 KEMDGLVCR 94
           E+D +  R
Sbjct: 55 AELDNMPLR 63

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 10/64 (15%)

Query: 29  LFIGGLSYDTNETVLKDAFGQ--HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           L++  L   T E +++ +F +   G++  VK I        R Y FV F     A +A+ 
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMD 287

Query: 87  EMDG 90
           E++G
Sbjct: 288 ELNG 291

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 36.1 bits (84), Expect = 3e-04
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 19/82 (23%)

Query: 25 SRTKLFIGGLSYDTN----ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVK------ 74
          +RT L++GG+   +     E +L+  FG+ G+I +++V+       S+G  FV+      
Sbjct: 1  NRT-LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVL------PSKGIAFVRYKYRAS 53

Query: 75 --FASEAAAGEAIKEMDGLVCR 94
            FA EA A +++   + L  R
Sbjct: 54 AEFAKEAMADQSLDGGEVLNVR 75

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 36.1 bits (83), Expect = 3e-04
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T LF+  ++  T    L+  FG++G I++V V  D  T + RG+ +++F     A +A+ 
Sbjct: 1  TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 87 EMD 89
           ++
Sbjct: 61 NLN 63

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

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          ++IG L    +E  L++   + G I ++K++ +      +   FV F S A A + +  +
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.2 bits (83), Expect = 3e-04
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++F+  L +D     LK+ F Q G ++  ++  +   G+S+G G V+F S  +A +A + 
Sbjct: 1  QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRL 58

Query: 88 MDGL 91
          M+G+
Sbjct: 59 MNGI 62

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G LS D  E ++   F Q G     K+I D  T  +  Y FV+F     A  ++  M
Sbjct: 2  LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 89 DG 90
          +G
Sbjct: 60 NG 61

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

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G L  D  E  ++D F ++G I+++ +   ++  +  GY F++F     A +AI+  
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 89 DG 90
          DG
Sbjct: 59 DG 60

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 35.6 bits (83), Expect = 4e-04
 Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 47 FGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          F Q G ++++       T + RG  FV F    +A  A++ + G
Sbjct: 24 FSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNALRALQG 64

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

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

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVIC-DRVTGQSRGYGFVKFASEAAAGEAIK 86
          +L +  + +   +  L+  FGQ G I++V++I  +R    S+G+GFV FA+ A A  A +
Sbjct: 2  RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFANSADADRARE 58

Query: 87 EMDGLV 92
          ++ G V
Sbjct: 59 KLHGTV 64

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 8/62 (12%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L+    E +L+ +F + G++  VK + D        Y FV F    AA  A+ EM
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 89 DG 90
          +G
Sbjct: 56 NG 57

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.7 bits (82), Expect = 4e-04
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 8/63 (12%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +++IG LSY   E  ++  F  +G+I+EV +          GYGFV+F     A +A+ E
Sbjct: 1  RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52

Query: 88 MDG 90
          ++G
Sbjct: 53 LNG 55

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 35.5 bits (81), Expect = 6e-04
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 3/62 (4%)

Query: 36 YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE-MDGLVCR 94
          Y +NE +L++AF Q G +    VI D   G+S G G V+FAS+ AA +A +   +G+   
Sbjct: 10 YVSNE-LLEEAFSQFGPVERAVVIVDD-RGRSTGKGIVEFASKPAARKAFERCTEGVFLL 67

Query: 95 TS 96
          T+
Sbjct: 68 TT 69

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>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 = 35.0 bits (81), Expect = 8e-04
 Identities = 24/68 (35%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA-----SEAAAGE 83
          + I GLS  T    ++  F   GEI E ++  D  TGQS G   V F        AA   
Sbjct: 1  ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 84 AIKEMDGL 91
          A   +DGL
Sbjct: 61 AKAAVDGL 68

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|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

 Score = 34.7 bits (80), Expect = 8e-04
 Identities = 16/55 (29%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          L++G L++ T +  L +A    G  +++E+K   +R  GQS+G+  +   SE+++
Sbjct: 2  LYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSS 56

This subgroup corresponds to the RRM of CFIm68. 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. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 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. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 77

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + +F+  L Y      LK+ F   G ++   ++ D+  G+SRG G V F     A +AI 
Sbjct: 1  STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAIS 59

Query: 87 EMDG 90
            +G
Sbjct: 60 MFNG 63

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 8/64 (12%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQS-RGYGFVKFASEAAAGEAIKE 87
          L++GGL   T+   L+  F + G I        R+     R Y ++++ S  AA  A + 
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAI-------RRIDYDPGRNYAYIEYESIEAAQAAKEA 53

Query: 88 MDGL 91
          + G 
Sbjct: 54 LRGF 57

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

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 34.3 bits (79), Expect = 0.001
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 28 KLFIGGLSYDTNETVLKDAF-GQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          ++FI  + YD     LKD F  + GE+  V++  D   G+SRG G V+F  + +  +A++
Sbjct: 1  RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDE-EGKSRGCGVVEFKDKESVQKALE 59

Query: 87 EM 88
           M
Sbjct: 60 TM 61

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 34.3 bits (79), Expect = 0.001
 Identities = 20/49 (40%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 43 LKDAFGQHGEIIEVKVICDRVTGQSRG-YGFVKFASEAAAGEAIKEMDG 90
          L  AF Q G +  VKV        + G Y FVKF S  AA  A K  +G
Sbjct: 21 LCSAFSQFGLLYSVKV-FPNAAVATPGFYAFVKFYSARAASRAQKACNG 68

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F G   YD  ++ ++  FG++G +       DRV  +S G+ FV    E  A +AI+ +
Sbjct: 3  VFCGNFEYDARQSEIERLFGKYGRV-------DRVDMKS-GFAFVYMEDERDAEDAIRGL 54

Query: 89 D 89
          D
Sbjct: 55 D 55

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

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

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           K+F+G +S       L+  F + G ++E    CD+V    + Y FV    E  A  AI+
Sbjct: 1  WKIFVGNVSATCTSDELRGLFEEFGRVVE----CDKV----KDYAFVHMEREEEALAAIE 52

Query: 87 EMDG 90
           ++G
Sbjct: 53 ALNG 56

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L++     G +I  +++ D   G SRG GF +  S       I+
Sbjct: 2  TNLYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQ 60

Query: 87 EMDGLVCRT 95
            +G   +T
Sbjct: 61 HFNGKYLKT 69

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK-- 86
          L++G LS+ T E  + + F + G+I  + +  DR T    G+ FV++ +   A  A+K  
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 87 ---EMDGLVCRTSKD 98
             ++D  + R   D
Sbjct: 61 NGTKLDDRIIRVDWD 75

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

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

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++++G L  D  E  ++D F ++G I  +  + +R  G    + FV+F     A +A++ 
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAID-LKNRRRGP--PFAFVEFEDPRDAEDAVRG 57

Query: 88 MDG 90
           DG
Sbjct: 58 RDG 60

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

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +++FIG +  D  E  L   F   G + E +++    +G +RG+ + K++    A  AI 
Sbjct: 2  SEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKYSDRRGASAAIA 60

Query: 87 EMDG---------LVCRT 95
           +           LVCR+
Sbjct: 61 TLHNYELPEGCCLLVCRS 78

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

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

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++G L     E +L + F Q G I   K+I +     +  Y FV++    +A  A++ M
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57

Query: 89 DG 90
          +G
Sbjct: 58 NG 59

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          ++L +  L     E  L+  F   G I +V++   +  G+ R +GFV + +E  A +A+K
Sbjct: 1  SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59

Query: 87 EMDGLVCRTSK 97
            +     TSK
Sbjct: 60 HFNNSFIDTSK 70

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 33.6 bits (77), Expect = 0.002
 Identities = 13/65 (20%), Positives = 33/65 (50%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G + Y      L+  F   G +  V ++CD+ +G  +G+ +++F+ + +   A+   
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 89 DGLVC 93
          + L  
Sbjct: 62 ESLFR 66

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

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          L++G L    +E  +K  +   G E + VKVI  R +G + GY FV+F S  AA  A+
Sbjct: 2  LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNAL 59

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 33.9 bits (77), Expect = 0.003
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L++     G++I  +++ D  +G SRG GF +  S       I 
Sbjct: 1  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIS 59

Query: 87 EMDGLVCRT 95
            +G   +T
Sbjct: 60 HFNGKFIKT 68

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 33.5 bits (76), Expect = 0.003
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          L +  LS   +  +L+ AF Q G +    VI D   G+  G GFV+FA++ AA +A++
Sbjct: 2  LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDD-RGRPTGKGFVEFAAKPAARKALE 58

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 33.2 bits (76), Expect = 0.003
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++ G   +T    L   F ++G ++   +   R T QSR + FV++ S   A +A +EM
Sbjct: 2  LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEEM 60

Query: 89 DGLVCRTSKDT 99
           G     + DT
Sbjct: 61 HGRRFPDTGDT 71

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 16/62 (25%), Positives = 31/62 (50%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +    L+ + +E  LKD   ++GE+ EVK+     T +  G   V F S  +A   ++++
Sbjct: 5  VTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKL 64

Query: 89 DG 90
          + 
Sbjct: 65 NQ 66

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR------GYGFVKFASEAAA 81
          +++I  LSY ++E  L++      E + V +    V G         G  + +F+S   A
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 82 GEAIKEMDG 90
           + +K+++G
Sbjct: 60 EKVVKDLNG 68

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 12/43 (27%), Positives = 26/43 (60%)

Query: 43  LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
           L + F + G++ +V+ I DR + +S+G  +V+F    +  +A+
Sbjct: 106 LYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL 148

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|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B")

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+  L  +TNE +L   F Q     EV+++  R         FV+F +EA AG A   +
Sbjct: 8  LFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFENEAQAGAARDAL 62

Query: 89 DGL 91
           G 
Sbjct: 63 QGF 65

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 80

>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          L   G+   T+   LK+AF + GE+  V    D   GQ+ GY  V+F  E AA EA++
Sbjct: 4  LHFSGVGEQTSREDLKEAFEEFGEVAWV----DFARGQTEGY--VRFKEENAAKEALE 55

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 33.5 bits (76), Expect = 0.004
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L+      G++I  +++ D  +G SRG GF +  S       I 
Sbjct: 1  TNLYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIIT 59

Query: 87 EMDGLVCRT 95
            +G   +T
Sbjct: 60 HFNGKYIKT 68

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 32.8 bits (75), Expect = 0.004
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 6/64 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T +++G +   T +  L   F   G I+E +   DR      G+ FVK  +   A  AI 
Sbjct: 1  TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIV 54

Query: 87 EMDG 90
          ++ G
Sbjct: 55 QLQG 58

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.82
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.81
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.79
KOG0122	270	consensus Translation initiation factor 3, subunit	99.78
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.78
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.77
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.76
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.76
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.75
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.75
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.75
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.74
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.73
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.73
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.71
PLN03120	260	nucleic acid binding protein; Provisional	99.71
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.7
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.7
smart00362	72	RRM_2 RNA recognition motif.	99.69
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.68
PLN03213	759	repressor of silencing 3; Provisional	99.67
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.67
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.67
smart00360	71	RRM RNA recognition motif.	99.66
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.66
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.65
PLN03121	243	nucleic acid binding protein; Provisional	99.65
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.64
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.64
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.64
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.63
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.62
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.59
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.59
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.58
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.57
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.57
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.56
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.55
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.54
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.54
smart00361	70	RRM_1 RNA recognition motif.	99.52
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.52
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.51
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.51
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.5
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.49
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.49
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.48
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.48
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.48
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.46
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.46
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.45
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.44
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.44
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.43
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.41
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.36
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.27
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.25
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.23
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.23
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.22
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.21
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.18
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.17
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.16
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.16
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.13
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.12
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.08
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	99.06
KOG0226	290	consensus RNA-binding proteins [General function p	99.02
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.01
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.99
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.98
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.97
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.92
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.84
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.84
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.68
KOG0151	877	consensus Predicted splicing regulator, contains R	98.66
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.6
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.55
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.51
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.49
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.48
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.43
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.4
KOG3152	278	consensus TBP-binding protein, activator of basal	98.39
KOG2314	698	consensus Translation initiation factor 3, subunit	98.36
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.3
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.21
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.2
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.16
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.02
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.98
KOG4210	285	consensus Nuclear localization sequence binding pr	97.96
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.95
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.95
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.9
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.75
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.7
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.66
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.63
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.6
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.54
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.51
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.47
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.46
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.45
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.38
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.29
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.13
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.0
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.98
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.92
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.81
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.76
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.73
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.59
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.48
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.45
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.23
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.21
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.78
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.74
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.65
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.37
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.31
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.98
KOG2135	526	consensus Proteins containing the RNA recognition	94.3
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.81
KOG4483	528	consensus Uncharacterized conserved protein [Funct	92.58
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	92.02
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	91.86
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.72
KOG4210	285	consensus Nuclear localization sequence binding pr	90.55
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	89.8
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	84.05
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.68
KOG2318	650	consensus Uncharacterized conserved protein [Funct	83.53

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

Probab=99.87  E-value=5.4e-21  Score=113.99  Aligned_cols=82  Identities=46%  Similarity=0.719  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|.+||.|..+.++.+..++++++||||+|.+.++|+.|++.|++..+.|+.++|..
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45677999999999999999999999999999999999998999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       111 a~  112 (144)
T PLN03134        111 AN  112 (144)
T ss_pred             CC
Confidence            64

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.82  E-value=1.8e-19  Score=120.54  Aligned_cols=79  Identities=35%  Similarity=0.470  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...|||+|||+.+++++|+++|++||.|.+++++.+..++.++|||||+|.+.++|..|+..|||..++|+.|+|...+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            4479999999999999999999999999999999999899999999999999999999999999999999999998754

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.81  E-value=3.1e-19  Score=93.96  Aligned_cols=70  Identities=39%  Similarity=0.658  Sum_probs=66.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      |||+|||+++++++|+++|.+||.+..+.+..+ .++..+++|||+|.+.++|+.|++.|+|..+.|+.++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 4888999999999999999999999999999999875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=5.2e-19  Score=118.34  Aligned_cols=79  Identities=30%  Similarity=0.495  Sum_probs=75.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +.++|||+|||..+++++|+++|..||+|..++++.+..+|+++|||||+|.+.++|+.|++.|+|..+.|+.++|..+
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a   80 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA   80 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence            3678999999999999999999999999999999999889999999999999999999999999999999999998764

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=7.6e-19  Score=117.45  Aligned_cols=82  Identities=33%  Similarity=0.460  Sum_probs=77.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||++||+++++++|+++|..||+|..++++.+..++++++||||+|.+.++|+.|++.|++..+.++.++|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999987


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus       183 ~a  184 (346)
T TIGR01659       183 YA  184 (346)
T ss_pred             cc
Confidence            65

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.79  E-value=1.2e-18  Score=116.45  Aligned_cols=102  Identities=25%  Similarity=0.414  Sum_probs=83.7

Q ss_pred             cCCCceecccccccccc--ccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHH
Q 034039            3 WLNGSVRFSHSVRFTRL--LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA   80 (105)
Q Consensus         3 ~~~~~~~~~~~~~~~~~--~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~   80 (105)
                      .+++..+..+.+.....  ..+....++|||+|||+.+++++|+++|.+||.|..+.++.+..+++++++|||+|.+.++
T Consensus       168 ~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~  247 (346)
T TIGR01659       168 NLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREE  247 (346)
T ss_pred             HcCCCccCCceeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHH
Confidence            45666666655543322  2233356789999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHcCCceeee--eeeeeccCC
Q 034039           81 AGEAIKEMDGLVCRT--SKDTDMLST  104 (105)
Q Consensus        81 a~~a~~~l~g~~~~~--~~~~v~~~~  104 (105)
                      |++|++.||+..+.+  +.++|.++.
T Consensus       248 A~~Ai~~lng~~~~g~~~~l~V~~a~  273 (346)
T TIGR01659       248 AQEAISALNNVIPEGGSQPLTVRLAE  273 (346)
T ss_pred             HHHHHHHhCCCccCCCceeEEEEECC
Confidence            999999999998876  567777653

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

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

Probab=99.78  E-value=3.3e-18  Score=107.33  Aligned_cols=83  Identities=28%  Similarity=0.386  Sum_probs=78.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...+..+|-|.||+.++++.+|+++|.+||.+.++.+..++.||.++|||||.|.++++|.+||..|||+-++.-.|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            34467889999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus       265 wsk  267 (270)
T KOG0122|consen  265 WSK  267 (270)
T ss_pred             ecC
Confidence            765

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

Probab=99.78  E-value=3.3e-18  Score=120.44  Aligned_cols=79  Identities=20%  Similarity=0.325  Sum_probs=74.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||+.+++++|+++|+.||.|..+++..+..+++++|||||+|.+.++|..|+..||+..++|+.|+|..+
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            4478999999999999999999999999999999999888899999999999999999999999999999999999754

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.

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

Probab=99.77  E-value=2.6e-18  Score=103.12  Aligned_cols=77  Identities=31%  Similarity=0.469  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...+.|||+||+..+++.+|...|..||++..+.+..+     +.|||||+|++..+|+.|+..|+|..|.|.+++|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            34679999999999999999999999999999988765     4589999999999999999999999999999999998


Q ss_pred             CC
Q 034039          104 TG  105 (105)
Q Consensus       104 ~~  105 (105)
                      +|
T Consensus        83 ~G   84 (195)
T KOG0107|consen   83 TG   84 (195)
T ss_pred             cC
Confidence            75

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

Probab=99.76  E-value=1.1e-17  Score=117.48  Aligned_cols=100  Identities=25%  Similarity=0.379  Sum_probs=84.9

Q ss_pred             CCcCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHH
Q 034039            1 MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA   80 (105)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~   80 (105)
                      |.++|+.+.+..+++.|... .....++|||+|||+++++++|.++|.+||.|..++++.+ .+|.++|||||+|.+.++
T Consensus        34 ~~~~~g~r~~g~Pp~~~~~~-~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~  111 (578)
T TIGR01648        34 LVQENGQRKYGGPPPGWSGV-QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEE  111 (578)
T ss_pred             ccccCCcccCCCCCCcccCC-CCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHH
Confidence            34677778888777765432 3445789999999999999999999999999999999999 599999999999999999


Q ss_pred             HHHHHHHcCCceee-eeeeeecc
Q 034039           81 AGEAIKEMDGLVCR-TSKDTDML  102 (105)
Q Consensus        81 a~~a~~~l~g~~~~-~~~~~v~~  102 (105)
                      |+.|++.||+..+. ++.+.|..
T Consensus       112 A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648       112 AKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             HHHHHHHcCCCeecCCccccccc
Confidence            99999999999885 66665543

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.

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

Probab=99.76  E-value=3.4e-18  Score=98.08  Aligned_cols=82  Identities=22%  Similarity=0.368  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..+++|||+||+..+++++|.++|+.+|+|.++.+-.++.+-.+-|||||+|.+.++|+.|++.++|..++.+.|++..+
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            46789999999999999999999999999999999999877778899999999999999999999999999999999876


Q ss_pred             CC
Q 034039          104 TG  105 (105)
Q Consensus       104 ~~  105 (105)
                      .|
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            43

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

Probab=99.75  E-value=5.6e-18  Score=105.74  Aligned_cols=78  Identities=41%  Similarity=0.672  Sum_probs=70.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .-++|||+||+|.+..++|++.|++||+|....++.|+.+|+++|||||+|.+.++|.+|++. ..-.|+||+..+.|+
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            457899999999999999999999999999999999999999999999999999999999944 556778888776654

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

Probab=99.75  E-value=5.8e-18  Score=104.19  Aligned_cols=83  Identities=31%  Similarity=0.472  Sum_probs=78.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +-+.-..|.|-||...++.++|..+|++||.|-++.|+.+..|..++|||||.|.+..+|+.|++.|+|..|+|+.|+|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        89 ~ar   91 (256)
T KOG4207|consen   89 MAR   91 (256)
T ss_pred             hhh
Confidence            876

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.75  E-value=2.8e-17  Score=86.82  Aligned_cols=70  Identities=33%  Similarity=0.544  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      |||+|||+++++++|.++|..+|.|..+.+..++. +..+++|||+|.+.++|..|++.+++..++|+.++
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999875 88999999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.74  E-value=1.4e-17  Score=108.17  Aligned_cols=79  Identities=24%  Similarity=0.470  Sum_probs=73.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +..++|+|+|+|+...+.||+..|.+||.|.+++|+.+. . .++|||||+|++..+|++|-++|||..+.||+|.|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-R-GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-R-GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-C-CCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            355799999999999999999999999999999999885 3 38999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       172 T  172 (376)
T KOG0125|consen  172 T  172 (376)
T ss_pred             c
Confidence            4

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

Probab=99.73  E-value=3.5e-17  Score=115.32  Aligned_cols=79  Identities=23%  Similarity=0.454  Sum_probs=74.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+.+++++|+++|..||.|.++.+..++.+|+++|||||+|.+.++|+.|++.|||..+.|+.++|..
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            3457899999999999999999999999999999999998999999999999999999999999999999999998864

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

Probab=99.73  E-value=2.3e-19  Score=108.35  Aligned_cols=100  Identities=23%  Similarity=0.353  Sum_probs=87.8

Q ss_pred             CcCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            2 QWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      +.+|..+++..-........+-..+.-|||+|||...|+.+|.-+|++||.+..+.+++|..||+++||||+-|++..+.
T Consensus        11 ~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRST   90 (219)
T KOG0126|consen   11 QKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRST   90 (219)
T ss_pred             HHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccce
Confidence            34555555555554455555667788999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCceeeeeeeeec
Q 034039           82 GEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        82 ~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ..|+..|||..|.|+.|+|.
T Consensus        91 ILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   91 ILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             EEEEeccCCceecceeEEee
Confidence            99999999999999999986

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

Probab=99.71  E-value=1.2e-16  Score=102.83  Aligned_cols=82  Identities=30%  Similarity=0.580  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++-.+|||+-|+..+++..|+..|+.||+|+.+.++.+..||+++|||||+|++..+...|.+.-+|..|+|+.+.|.+.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q 034039          104 TG  105 (105)
Q Consensus       104 ~~  105 (105)
                      .|
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            43

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.71  E-value=1.3e-16  Score=101.97  Aligned_cols=75  Identities=17%  Similarity=0.217  Sum_probs=68.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+.+++++|+++|+.||.|.++.++.+..   .+|||||+|.+.++|+.|+ .|+|..+.|+.++|..+.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEecc
Confidence            46899999999999999999999999999999988753   4689999999999999999 599999999999998653

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

Probab=99.70  E-value=1.7e-16  Score=112.01  Aligned_cols=76  Identities=34%  Similarity=0.472  Sum_probs=73.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|+++|..||.|..+++.++..+++++|||||+|.+.++|++|+..+++..+.|+.++++.+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s   77 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS   77 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecc
Confidence            6999999999999999999999999999999999988999999999999999999999999999999999999765

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

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

Probab=99.70  E-value=3.4e-16  Score=109.18  Aligned_cols=79  Identities=24%  Similarity=0.425  Sum_probs=74.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||..+++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|..|+..|+|..+.|+.|.|..+
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4578999999999999999999999999999999999889999999999999999999999999999999999998765

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

>smart00362 RRM_2 RNA recognition motif

Probab=99.69  E-value=7.8e-16  Score=80.51  Aligned_cols=72  Identities=36%  Similarity=0.542  Sum_probs=66.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +|||+|||+.++.++|+++|..||++..+.+..+.  +.++++|||+|.+.+.|+.|+..+++..+.|+.++|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999888765  6788999999999999999999999999999988763

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

Probab=99.68  E-value=4.5e-16  Score=107.39  Aligned_cols=78  Identities=29%  Similarity=0.524  Sum_probs=74.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..+|||+|||..+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|+..|+|..+.|+.++|.++
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            578999999999999999999999999999999999888899999999999999999999999999999999999874

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.68  E-value=3.1e-16  Score=105.46  Aligned_cols=101  Identities=27%  Similarity=0.373  Sum_probs=86.8

Q ss_pred             CcCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            2 QWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      +.-+|.+....+++.|.... ....+.|||+.||.++.+++|..+|++.|+|..+++..++-+|.++|||||+|.+++.|
T Consensus        60 ~ve~gqrk~ggPpP~weg~~-p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~A  138 (506)
T KOG0117|consen   60 VVENGQRKYGGPPPGWEGPP-PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEA  138 (506)
T ss_pred             EEeccccccCCCCCcccCCC-CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHH
Confidence            34566677777766654443 36788999999999999999999999999999999999988999999999999999999


Q ss_pred             HHHHHHcCCceee-eeeeeeccC
Q 034039           82 GEAIKEMDGLVCR-TSKDTDMLS  103 (105)
Q Consensus        82 ~~a~~~l~g~~~~-~~~~~v~~~  103 (105)
                      +.|++.||++.|. |+.|.|-++
T Consensus       139 q~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen  139 QEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             HHHHHHhhCccccCCCEeEEEEe
Confidence            9999999999884 777777554

>PLN03213 repressor of silencing 3; Provisional

Probab=99.67  E-value=4.7e-16  Score=106.21  Aligned_cols=77  Identities=17%  Similarity=0.344  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCH--HHHHHHHHHcCCceeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE--AAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~--~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ....+||||||++.+++++|...|..||.|.++.+++  .+|  +|||||+|...  .++.+|+..|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            4567999999999999999999999999999999984  466  89999999976  78999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        84 KAK   86 (759)
T PLN03213         84 KAK   86 (759)
T ss_pred             ecc
Confidence            765

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

Probab=99.67  E-value=8.8e-17  Score=97.16  Aligned_cols=82  Identities=28%  Similarity=0.432  Sum_probs=77.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +.+...+|||+||+..++++.|+++|.+.|+|.+++++.++.+..++||||++|.++++|+.|++.||...|-|+.|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        85 ka   86 (203)
T KOG0131|consen   85 KA   86 (203)
T ss_pred             ec
Confidence            54

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

Probab=99.67  E-value=3.2e-17  Score=101.93  Aligned_cols=82  Identities=30%  Similarity=0.490  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||++|...+++.-|..-|-+||+|..++++.|..+++++||+||+|...++|.+|+..||+..|-|+.|+|-+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        87 Ak   88 (298)
T KOG0111|consen   87 AK   88 (298)
T ss_pred             cC
Confidence            74

>smart00360 RRM RNA recognition motif

Probab=99.66  E-value=2e-15  Score=78.67  Aligned_cols=71  Identities=31%  Similarity=0.538  Sum_probs=65.8

Q ss_pred             EcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           31 IGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        31 v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      |+|||..+++++|+++|..||.+..+.+..+..++.++++|||+|.+.++|..|+..+++..+.++.++|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57899999999999999999999999998887778899999999999999999999999999999888763

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

Probab=99.66  E-value=1.3e-15  Score=107.63  Aligned_cols=79  Identities=30%  Similarity=0.500  Sum_probs=74.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...+|||+||++.+++++|+++|..||.|..+++..+. +|.++|||||.|.+.++|.+|+..|||..+.|+.+.|.++.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~-~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC-CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            45689999999999999999999999999999999984 89999999999999999999999999999999999998764

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

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

Probab=99.65  E-value=2.1e-15  Score=104.15  Aligned_cols=79  Identities=22%  Similarity=0.307  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||..+++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|..|+ .|+|..+.|+.+.|..+
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEeec
Confidence            34679999999999999999999999999999999999889999999999999999999999 59999999999988754

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.65  E-value=2.6e-15  Score=94.89  Aligned_cols=74  Identities=19%  Similarity=0.173  Sum_probs=67.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...+|||+||++.+++++|+++|+.||.|.+++++.+.   ...++|||+|.+..+++.|+ .|+|..|.++.+++..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~   77 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITR   77 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEe
Confidence            45789999999999999999999999999999999874   34479999999999999999 8999999999988764

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

Probab=99.64  E-value=8.6e-16  Score=97.90  Aligned_cols=79  Identities=35%  Similarity=0.583  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .....+||+.|.+.++.++|++-|.+||+|.++++++|..|++++||+||.|.++++|+.||..|||.-|.+|.|+.--
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            3456899999999999999999999999999999999999999999999999999999999999999999999988643

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

Probab=99.64  E-value=6.8e-16  Score=89.50  Aligned_cols=81  Identities=23%  Similarity=0.369  Sum_probs=76.2

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +.+.....|||.++.+..+++++.+.|..||+|+.+.+..++.+|..+||++|+|++...|++|+..+||..|-+..+.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            34556789999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             c
Q 034039          101 M  101 (105)
Q Consensus       101 ~  101 (105)
                      .
T Consensus       147 D  147 (170)
T KOG0130|consen  147 D  147 (170)
T ss_pred             E
Confidence            6

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

Probab=99.64  E-value=2.4e-16  Score=100.19  Aligned_cols=103  Identities=30%  Similarity=0.496  Sum_probs=88.9

Q ss_pred             CCcCCCceecccccc--ccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCH
Q 034039            1 MQWLNGSVRFSHSVR--FTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE   78 (105)
Q Consensus         1 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~   78 (105)
                      |..+||.+++.+++.  +.++..+......|||++||..++..+|+.+|++||.|-..++..|..+|.++|.+||.|..+
T Consensus       100 intlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  100 INTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             HhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence            356899999999865  566666777888999999999999999999999999998888888888999999999999999


Q ss_pred             HHHHHHHHHcCCceeee--eeeeeccC
Q 034039           79 AAAGEAIKEMDGLVCRT--SKDTDMLS  103 (105)
Q Consensus        79 ~~a~~a~~~l~g~~~~~--~~~~v~~~  103 (105)
                      .+|+.||..|||..-.|  ..|.|.++
T Consensus       180 ~EAe~AIk~lNG~~P~g~tepItVKFa  206 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTEPITVKFA  206 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCCCeEEEec
Confidence            99999999999987654  34555543

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

Probab=99.63  E-value=4.7e-15  Score=94.86  Aligned_cols=78  Identities=36%  Similarity=0.616  Sum_probs=75.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..+|||+|||..+++++|.++|..||.+..+.+..++.++.++|+|||.|.+.+++..|+..++|..+.|+.+.|..+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecc
Confidence            589999999999999999999999999999999999889999999999999999999999999999999999999874

>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=99.62  E-value=1.8e-14  Score=75.61  Aligned_cols=73  Identities=27%  Similarity=0.523  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +|+|+|||+.+++++++++|+.+|.+..+.+..+. .+.+++++||+|.+.++|..|++.+++..+.|+.+.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            48999999999999999999999999999998876 33678999999999999999999999999999998875

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=99.59  E-value=1.9e-14  Score=100.24  Aligned_cols=76  Identities=18%  Similarity=0.218  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....+|||+|||+ .+++++|+++|+.||.|.++++..+.     +|+|||+|.+.++|..|++.|||..+.|+.++|..
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3567999999998 69999999999999999999988763     48999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       348 s~  349 (481)
T TIGR01649       348 SK  349 (481)
T ss_pred             cc
Confidence            64

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).

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

Probab=99.59  E-value=6.7e-15  Score=100.45  Aligned_cols=78  Identities=27%  Similarity=0.584  Sum_probs=75.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..+||+|+|+++++++|..+|...|.|..++++.|+.+|+++||||++|.+.+++..|++.|||..+.|+.++|..+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccc
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999998754

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

Probab=99.58  E-value=2.2e-14  Score=79.73  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....|||.|||..+|.++..++|.+||.|..+++-...   ..+|.|||.|++..+|..|+++|+|..+.++.+.|.+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            45689999999999999999999999999999986544   3568999999999999999999999999999998864

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

Probab=99.57  E-value=8.5e-15  Score=97.01  Aligned_cols=102  Identities=20%  Similarity=0.328  Sum_probs=89.8

Q ss_pred             CCcCCCceecccccccccccc-------------CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCc
Q 034039            1 MQWLNGSVRFSHSVRFTRLLS-------------DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQS   67 (105)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~   67 (105)
                      ++++||..+.++++....+..             +...-++|||..+.++.++.+|+..|+.||+|..|.+.+....+.+
T Consensus       172 lEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~H  251 (544)
T KOG0124|consen  172 LEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGH  251 (544)
T ss_pred             HHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCc
Confidence            468888888888877655553             2234479999999999999999999999999999999999988889


Q ss_pred             cceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           68 RGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        68 ~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      +||+|++|.+..+...|+..||-+.+.|..++|--
T Consensus       252 kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  252 KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             cceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            99999999999999999999999999999999853

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

Probab=99.57  E-value=7.1e-15  Score=89.43  Aligned_cols=79  Identities=23%  Similarity=0.366  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||.++.+.+++++|-+||.|..+.+...+   ...+||||+|++..+|+.|+.--+|+.++|.+|+|++.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            346789999999999999999999999999999875432   24579999999999999999999999999999999987


Q ss_pred             CC
Q 034039          104 TG  105 (105)
Q Consensus       104 ~~  105 (105)
                      .+
T Consensus        81 rg   82 (241)
T KOG0105|consen   81 RG   82 (241)
T ss_pred             cC
Confidence            54

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

Probab=99.56  E-value=2.7e-14  Score=91.13  Aligned_cols=73  Identities=27%  Similarity=0.493  Sum_probs=67.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +.+.++||++|++...+++.+++.|..||+|..+++-.++      ||+||.|.+++.|..||..+|+.++.|...+..
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            3467899999999999999999999999999999988765      899999999999999999999999999887753

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

Probab=99.55  E-value=5.3e-14  Score=97.97  Aligned_cols=73  Identities=19%  Similarity=0.170  Sum_probs=66.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc--CCceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM--DGLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~~~~~~v~~~  103 (105)
                      +++|||+|||+.+++++|+++|+.||.|..+.++.+      +++|||+|.+.++|+.|++.+  ++..+.|+.+.|..+
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            578999999999999999999999999999988753      379999999999999999864  788999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        76 ~   76 (481)
T TIGR01649        76 T   76 (481)
T ss_pred             C
Confidence            3

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

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

Probab=99.54  E-value=6.2e-14  Score=98.78  Aligned_cols=72  Identities=28%  Similarity=0.453  Sum_probs=66.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQH--GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..++|||+||++++++++|+++|..|  |.|.++.++        ++||||+|++.++|++|++.|||..+.|+.|+|.+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  999998764        35899999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       304 Ak  305 (578)
T TIGR01648       304 AK  305 (578)
T ss_pred             cc
Confidence            64

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.

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

Probab=99.54  E-value=4.4e-14  Score=90.02  Aligned_cols=81  Identities=32%  Similarity=0.531  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...+.|.|.=||..+|+++++.+|...|+|+.|++++|+.+|.+.||+||.|-++.+|++|+..|||..+..+.|+|.++
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            34567888889999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       119 R  119 (360)
T KOG0145|consen  119 R  119 (360)
T ss_pred             c
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=99.52  E-value=1.5e-13  Score=72.59  Aligned_cols=61  Identities=20%  Similarity=0.371  Sum_probs=54.5

Q ss_pred             HHHHHHHHh----ccCCeEEEE-EEecCCC--CCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           40 ETVLKDAFG----QHGEIIEVK-VICDRVT--GQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        40 ~~~l~~~f~----~~g~v~~~~-~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +++|+++|+    .||.+.++. +..+..+  +.++|++||.|.+.++|..|+..|||..+.|+.+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            467888898    999999985 6666656  889999999999999999999999999999999876

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

Probab=99.52  E-value=1.3e-14  Score=96.17  Aligned_cols=77  Identities=23%  Similarity=0.475  Sum_probs=74.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      -+++||+.+.+...++.|+.-|..||+|+.+.+.+|+.|++++||+||+|+-.+.|+.|++.|||..+.|+.++|-.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.51  E-value=2.3e-14  Score=98.43  Aligned_cols=75  Identities=27%  Similarity=0.576  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .+||+||.+++++++|+.+|++||.|..+.+..+..+|.++||+||+|.+.+.|..|+..|||..|.|+.++|-.
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            399999999999999999999999999999999988999999999999999999999999999999999999754

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

Probab=99.51  E-value=1e-13  Score=93.47  Aligned_cols=72  Identities=31%  Similarity=0.376  Sum_probs=66.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ....|||.||+.++|++.|++.|..||.|.+++-++        .||||.|.++++|-+|++.+||+.|+|..|.|.|++
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--------DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--------DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--------ceeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            347899999999999999999999999999997664        489999999999999999999999999999999876

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

Probab=99.50  E-value=3.7e-14  Score=90.69  Aligned_cols=84  Identities=31%  Similarity=0.447  Sum_probs=78.7

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+..+.+.|||=-||.+..+.+|...|..||.|...++-.|+.|..++||+||.|.+..++++||..|||+.|..++++|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            45678899999999999999999999999999999998889889999999999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+.+
T Consensus       360 QLKR  363 (371)
T KOG0146|consen  360 QLKR  363 (371)
T ss_pred             hhcC
Confidence            9864

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

Probab=99.49  E-value=9.8e-14  Score=91.60  Aligned_cols=82  Identities=27%  Similarity=0.398  Sum_probs=77.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .++.+.|||-.|.+-++.++|.-+|+.||.|..|.++++..+|.+..||||+|++.++++.|.-+|++..|+.++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       316 SQ  317 (479)
T KOG0415|consen  316 SQ  317 (479)
T ss_pred             hh
Confidence            53

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

Probab=99.49  E-value=2.6e-14  Score=86.58  Aligned_cols=99  Identities=27%  Similarity=0.459  Sum_probs=82.5

Q ss_pred             CCceeccccccccccc---cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEecCCCCCccceEEEEeCCHHH
Q 034039            5 NGSVRFSHSVRFTRLL---SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEAA   80 (105)
Q Consensus         5 ~~~~~~~~~~~~~~~~---~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~~fv~f~~~~~   80 (105)
                      |...++.++++.....   ........+||+||.+.+++..|.+.|+.||++.. .++.++..+|.+++++|+.|++.+.
T Consensus        72 n~VkLYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfea  151 (203)
T KOG0131|consen   72 NMVKLYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEA  151 (203)
T ss_pred             HHHHhcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHH
Confidence            4445566666554444   23345578999999999999999999999998855 4778888889999999999999999


Q ss_pred             HHHHHHHcCCceeeeeeeeeccC
Q 034039           81 AGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        81 a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +.+|+.+++|..+.++++.|.++
T Consensus       152 sd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen  152 SDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             HHHHHHHhccchhcCCceEEEEE
Confidence            99999999999999999999865

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

Probab=99.48  E-value=1.1e-13  Score=95.47  Aligned_cols=79  Identities=23%  Similarity=0.364  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..+|||++||++++.++|.++|+.+|+|..|.++.+..++.++||+||.|...++++.|+....+..+.|+.++|..++
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            3789999999999999999999999999999999999888999999999999999999999999999999999998764

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

Probab=99.48  E-value=7.2e-14  Score=90.01  Aligned_cols=70  Identities=31%  Similarity=0.550  Sum_probs=65.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..+||+|||..+++.+|+.+|++||.|..|.|+++        ||||..++...++.|++.|+|..|+|..|.|+-++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSk   72 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASK   72 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecc
Confidence            36899999999999999999999999999999875        79999999999999999999999999999998765

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

Probab=99.48  E-value=6.4e-14  Score=90.25  Aligned_cols=95  Identities=27%  Similarity=0.392  Sum_probs=83.2

Q ss_pred             CcCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            2 QWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      ..+++..+.+-.+........+..+++++|+|+.+.++.++|+..|.+||++..|.++.+        |+||.|.-.++|
T Consensus        54 rNLhgYtLhg~nInVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda  125 (346)
T KOG0109|consen   54 RNLHGYTLHGVNINVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDA  125 (346)
T ss_pred             hhcccceecceEEEEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccch
Confidence            456777777777665555555667889999999999999999999999999999998754        799999999999


Q ss_pred             HHHHHHcCCceeeeeeeeeccCC
Q 034039           82 GEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        82 ~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..|++.|++.++.|++++|++++
T Consensus       126 ~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen  126 VEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             HHHHhcccccccccceeeeeeec
Confidence            99999999999999999999876

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

Probab=99.46  E-value=3.1e-13  Score=90.95  Aligned_cols=74  Identities=32%  Similarity=0.536  Sum_probs=67.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc-eeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL-VCRTSK   97 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-~~~~~~   97 (105)
                      .+.-++||+.+|..++|.+|+.+|++||.|..|.+++|+.++.++|||||.|.+.++|.+|+..|++. .+.|..
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~  106 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMH  106 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCC
Confidence            34568999999999999999999999999999999999999999999999999999999999999875 455544

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

Probab=99.46  E-value=3.3e-13  Score=91.19  Aligned_cols=77  Identities=22%  Similarity=0.352  Sum_probs=72.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHh-ccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFG-QHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~-~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..+.+||.|+|.++.+++|+++++ +-|.|.+|++..|. +|+++|++.|+|++++.+++|++.||.+.+.|+.+.|.=
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            445699999999999999999996 68999999999997 999999999999999999999999999999999999864

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

Probab=99.45  E-value=9.3e-13  Score=90.94  Aligned_cols=81  Identities=31%  Similarity=0.505  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc-----CC-ceeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM-----DG-LVCRTSK   97 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-----~g-~~~~~~~   97 (105)
                      ....+|||.|||+++++++|...|++||.|....++.++.|+.+.|.|||.|.+...|..||..-     .| ..|+|+.
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~  369 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRL  369 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccE
Confidence            34589999999999999999999999999999999999999999999999999999999999765     34 6789999


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      +.|+++.
T Consensus       370 Lkv~~Av  376 (678)
T KOG0127|consen  370 LKVTLAV  376 (678)
T ss_pred             Eeeeecc
Confidence            9999764

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

Probab=99.44  E-value=1.1e-13  Score=93.18  Aligned_cols=67  Identities=36%  Similarity=0.594  Sum_probs=63.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      ..++|||+.|+..+++.+++++|.+||.|++|.+.++. .+.++||+||.|..++.|..|++.|||..
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccce
Confidence            36789999999999999999999999999999999997 89999999999999999999999999975

>PF13893 RRM_5: RNA recognition motif

Probab=99.44  E-value=7.5e-13  Score=66.97  Aligned_cols=56  Identities=29%  Similarity=0.485  Sum_probs=49.1

Q ss_pred             HHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           43 LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        43 l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      |.++|++||.|..+.+..+.     ++++||+|.+.++|+.|++.|||..+.|+.++|.+|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999886543     579999999999999999999999999999999764

(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 ....

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

Probab=99.43  E-value=7.3e-13  Score=89.45  Aligned_cols=94  Identities=32%  Similarity=0.476  Sum_probs=78.9

Q ss_pred             cCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHH
Q 034039            3 WLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG   82 (105)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   82 (105)
                      .+|...+..+.++..+...+..   .+||.||+++++..+|.++|..||.|..|++..+. +| ++|| ||.|++.++|+
T Consensus        56 ~~n~~~~~~~~~rim~s~rd~~---~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~  129 (369)
T KOG0123|consen   56 TMNFDVLKGKPIRIMWSQRDPS---LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAK  129 (369)
T ss_pred             HcCCcccCCcEEEeehhccCCc---eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHH
Confidence            4555566666666555444332   29999999999999999999999999999999987 56 8999 99999999999


Q ss_pred             HHHHHcCCceeeeeeeeecc
Q 034039           83 EAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        83 ~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .|+..+||..+.++.+-|-+
T Consensus       130 ~ai~~~ng~ll~~kki~vg~  149 (369)
T KOG0123|consen  130 KAIEKLNGMLLNGKKIYVGL  149 (369)
T ss_pred             HHHHHhcCcccCCCeeEEee
Confidence            99999999999999887754

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

Probab=99.41  E-value=1.4e-12  Score=80.35  Aligned_cols=81  Identities=22%  Similarity=0.338  Sum_probs=72.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhcc-CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQH-GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +......+|+..+|..+.+.++..+|.++ |.+.+.++.++..||.++|||||+|++.+.|+-|.+.||++.+.++.+.+
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34456789999999999999999999887 78888899899999999999999999999999999999999999988876


Q ss_pred             cc
Q 034039          101 ML  102 (105)
Q Consensus       101 ~~  102 (105)
                      .+
T Consensus       125 ~v  126 (214)
T KOG4208|consen  125 HV  126 (214)
T ss_pred             EE
Confidence            54

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

Probab=99.36  E-value=8.9e-12  Score=87.17  Aligned_cols=72  Identities=17%  Similarity=0.355  Sum_probs=59.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhcc------------CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQH------------GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~------------g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ....++|||+|||+.+++++|.++|..+            +.|..+.+      +..++||||+|.+.++|..|+ .|+|
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al-~l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAM-ALDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhh-cCCC
Confidence            3456799999999999999999999875            23333333      235689999999999999999 6999


Q ss_pred             ceeeeeeeeec
Q 034039           91 LVCRTSKDTDM  101 (105)
Q Consensus        91 ~~~~~~~~~v~  101 (105)
                      ..+.|..+++.
T Consensus       245 ~~~~g~~l~v~  255 (509)
T TIGR01642       245 IIYSNVFLKIR  255 (509)
T ss_pred             eEeeCceeEec
Confidence            99999998875

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

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

Probab=99.27  E-value=2.1e-11  Score=82.45  Aligned_cols=72  Identities=32%  Similarity=0.474  Sum_probs=67.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..+|||   +.+++..|.+.|+.+|++..+++.++. +  +.|||||.|.+..+|++|++.+|...+.|+.+++|.+.
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~   73 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ   73 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc
Confidence            368998   899999999999999999999999998 6  99999999999999999999999999999999999753

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

Probab=99.25  E-value=3.9e-11  Score=76.63  Aligned_cols=79  Identities=28%  Similarity=0.392  Sum_probs=72.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      +...+.|+|.|||..+.+++|+++|..||.+..+.+.+++ +|.+.|.|-|.|....+|..|++.++|..++|+.+++.+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999999888887 899999999999999999999999999999999988765

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

Probab=99.23  E-value=4e-11  Score=83.72  Aligned_cols=81  Identities=25%  Similarity=0.370  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...+.+||++|...+...+|+.+|++||.|.-.+++.+..+...+||+||++.+..+|..+|..|+.+.|.|+-|.|.-+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            45578999999999888999999999999999999999888889999999999999999999999999999999998866


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            5

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

Probab=99.23  E-value=4.6e-11  Score=81.05  Aligned_cols=77  Identities=23%  Similarity=0.348  Sum_probs=68.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|+|.|||.++|++.|++-|..||.+.+..+.   ++|++++  .|.|.++++|+.|+..|+|..++|+.|+|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            34456789999999999999999999999999988873   3677775  899999999999999999999999999997


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      +.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            63

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

Probab=99.22  E-value=6.7e-11  Score=77.95  Aligned_cols=75  Identities=29%  Similarity=0.453  Sum_probs=64.4

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHH-HcCCceeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK-EMDGLVCRTSKDT   99 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~-~l~g~~~~~~~~~   99 (105)
                      ++.....+|||++|...+++.+|+++|-+||+++.+.+....      ++|||+|.++.+|+.|.. .++...++|.++.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            344567899999999999999999999999999999887654      589999999999999885 5666778898888


Q ss_pred             ec
Q 034039          100 DM  101 (105)
Q Consensus       100 v~  101 (105)
                      +.
T Consensus       297 i~  298 (377)
T KOG0153|consen  297 IK  298 (377)
T ss_pred             EE
Confidence            75

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

Probab=99.21  E-value=6.5e-11  Score=83.79  Aligned_cols=77  Identities=32%  Similarity=0.535  Sum_probs=68.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCC----CccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG----QSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      +.|||.||++..+.+++...|...|.|..+.|...+ .+    .+.|||||+|.+.++|+.|++.|+|+.|+|+.+.+.+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkk-d~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKK-DPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccc-cccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            449999999999999999999999999998877654 22    2559999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            64

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

Probab=99.18  E-value=1.8e-10  Score=71.98  Aligned_cols=77  Identities=25%  Similarity=0.393  Sum_probs=68.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----HHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKD----AFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +..+|||.||+..+..++|+.    +|++||.+..+...   .+.+.+|=|||.|.+.+.|-.|++.|+|..+-|+.+++
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344999999999999988776    99999999888654   36778999999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ++++
T Consensus        85 qyA~   88 (221)
T KOG4206|consen   85 QYAK   88 (221)
T ss_pred             eccc
Confidence            8875

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

Probab=99.18  E-value=3e-11  Score=85.42  Aligned_cols=79  Identities=18%  Similarity=0.340  Sum_probs=72.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+.|.|.|+|+..+-.+++.+|..||++..++++.....+.++|||||+|-++.+|..|+..|..+.+-|+++..+-++
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            5789999999999999999999999999999998875567789999999999999999999999999999999876543

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

Probab=99.17  E-value=7.5e-11  Score=75.73  Aligned_cols=68  Identities=35%  Similarity=0.544  Sum_probs=63.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      .++++|||+.|.+.-.|++++.+|..||.+..|.+.+.. .|.++|++||.|.+..+|+.||..|+|..
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSq   84 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQ   84 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccc
Confidence            367899999999999999999999999999999998887 89999999999999999999999999974

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

Probab=99.16  E-value=1.2e-10  Score=83.30  Aligned_cols=72  Identities=22%  Similarity=0.405  Sum_probs=65.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      -+++|||++|+.++++.+|...|+.||+|..+.+...      ++||||.+..+.+|++|+.+|+...+..+.+++.-
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            4589999999999999999999999999999987654      48999999999999999999999999999887754

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

Probab=99.16  E-value=2.6e-10  Score=75.23  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEII--------EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ...+.|||+|||.++|.+++.++|.+||-|.        .|++..+. .|..+|-|++.|-..++.+.|+..|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            4456799999999999999999999999663        47777776 69999999999999999999999999999999


Q ss_pred             eeeeeccC
Q 034039           96 SKDTDMLS  103 (105)
Q Consensus        96 ~~~~v~~~  103 (105)
                      +.++|.-+
T Consensus       211 ~~~rVerA  218 (382)
T KOG1548|consen  211 KKLRVERA  218 (382)
T ss_pred             cEEEEehh
Confidence            99999865

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

Probab=99.13  E-value=6.8e-10  Score=69.70  Aligned_cols=82  Identities=17%  Similarity=0.193  Sum_probs=65.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCC-CccceEEEEeCCHHHHHHHHHHcCCceee---eeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG-QSRGYGFVKFASEAAAGEAIKEMDGLVCR---TSKD   98 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~-~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---~~~~   98 (105)
                      ....++|||++||.++...+|..+|+.|-..+.+.+......+ ..+.+||++|.+..+|.+|+..|||..++   +..+
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            4457899999999999999999999998777666654433222 24579999999999999999999999886   4556


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +.++++
T Consensus       111 hiElAK  116 (284)
T KOG1457|consen  111 HIELAK  116 (284)
T ss_pred             Eeeehh
Confidence            666654

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

Probab=99.12  E-value=9.5e-11  Score=77.41  Aligned_cols=75  Identities=36%  Similarity=0.603  Sum_probs=63.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +...+||++|+|.++++.|+..|.+||.+..|.+.+++.++.+++|+||+|++.+...+++.. .-..++|+.+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~   79 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEP   79 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccc
Confidence            678999999999999999999999999999999999999999999999999998888887732 233444444443

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

Probab=99.08  E-value=1.7e-10  Score=79.89  Aligned_cols=77  Identities=22%  Similarity=0.264  Sum_probs=65.9

Q ss_pred             ccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           18 RLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        18 ~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      .+.......++|+|-|||..+++++|..+|+.||+|+.++..     -..++..||+|.|..+|++|++.|++..+.|++
T Consensus        67 np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~  141 (549)
T KOG4660|consen   67 NPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKR  141 (549)
T ss_pred             CCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhh
Confidence            333334567899999999999999999999999999886543     335689999999999999999999999999988


Q ss_pred             ee
Q 034039           98 DT   99 (105)
Q Consensus        98 ~~   99 (105)
                      ++
T Consensus       142 ~k  143 (549)
T KOG4660|consen  142 IK  143 (549)
T ss_pred             hc
Confidence            76

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

Probab=99.06  E-value=3.1e-10  Score=72.39  Aligned_cols=81  Identities=23%  Similarity=0.359  Sum_probs=73.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .......+||+|+...++.+++..+|+.||.+..+.++.+.-++.+++|+||+|.+.+.++.++. |+|..+.++.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            34567799999999999999999999999999999999998787899999999999999999997 99999999999887


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      ..
T Consensus       176 ~~  177 (231)
T KOG4209|consen  176 LK  177 (231)
T ss_pred             ee
Confidence            53

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

Probab=99.02  E-value=4.8e-10  Score=71.40  Aligned_cols=81  Identities=33%  Similarity=0.495  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...+.+||.+.|.-+++.+-|...|.+|-....-+++++..+|+++||+||.|.+..++..|++.|+|..++.+.|+..-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            34678999999999999999999999998888888999999999999999999999999999999999999999887654


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus       267 S  267 (290)
T KOG0226|consen  267 S  267 (290)
T ss_pred             h
Confidence            3

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

Probab=99.01  E-value=1.2e-09  Score=72.23  Aligned_cols=75  Identities=33%  Similarity=0.516  Sum_probs=64.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...+||++||..+++.++++.|.+||.|....+..+..+..+++|+||.|.+.++++.++ ...-+.+.++...|.
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevk  171 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVK  171 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec-ccceeeecCceeeEe
Confidence            458999999999999999999999999999999999999999999999999999999987 334445555555444

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

Probab=98.99  E-value=2.3e-09  Score=73.34  Aligned_cols=77  Identities=26%  Similarity=0.320  Sum_probs=62.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....|||.|||.+++.++|+++|..||.|....|......++..+||||+|.+...++.++.+= -..++++++.|+-
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Vee  363 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEE  363 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEe
Confidence            3456999999999999999999999999988876554334555599999999999999999653 5567777777764

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

Probab=98.98  E-value=9.4e-09  Score=57.31  Aligned_cols=68  Identities=22%  Similarity=0.255  Sum_probs=61.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhc--cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQ--HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~--~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ++|.|.|+|...+.++|.+++..  .|....+.++.|..++...|||||.|.+...+....+.++|..+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~   71 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWP   71 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccc
Confidence            68999999999999999888753  467788889999989999999999999999999999999999886

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

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

Probab=98.97  E-value=6.8e-10  Score=69.76  Aligned_cols=69  Identities=25%  Similarity=0.466  Sum_probs=62.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+||++||+.+.+.++..+|..||.+.++.+.        .+|+||+|.+..+|..|+..+++..+.+..+.|+.++
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            58999999999999999999999999888763        2688999999999999999999999999988887765

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

Probab=98.92  E-value=6.8e-10  Score=69.46  Aligned_cols=78  Identities=17%  Similarity=0.271  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ....+|||+|+...++++-|.++|-+.|+|.++.++.++ .++.+ |+||.|.++.+...|++-+||..+.+..+++.+-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            446789999999999999999999999999999988776 66666 9999999999999999999999999998887653

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

Probab=98.84  E-value=2.6e-08  Score=67.29  Aligned_cols=74  Identities=20%  Similarity=0.322  Sum_probs=66.6

Q ss_pred             CceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...|.|.||... +|.+.|..+|..||+|.++++.+++.     .-|+|+|.+...|+.|+..|+|..+.|+.|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            467888888765 89999999999999999999988753     459999999999999999999999999999999876

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

Probab=98.84  E-value=2.4e-08  Score=68.69  Aligned_cols=78  Identities=21%  Similarity=0.340  Sum_probs=62.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +......|-+.+|||++|+++|.+||+.++ |..+.++  +.+|+..|-|||+|.+.++++.|+ +.+...+..+.|.|.
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Al-kkdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKAL-KKDRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHH-HhhHHHhCCceEEEE
Confidence            345566788899999999999999999985 6665444  447999999999999999999999 446666667777776


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        82 ~~   83 (510)
T KOG4211|consen   82 TA   83 (510)
T ss_pred             cc
Confidence            54

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

Probab=98.68  E-value=2.7e-08  Score=69.23  Aligned_cols=81  Identities=23%  Similarity=0.477  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ......+||++||...++.++.+++..||++....++.+..+|-++||+|.+|.+......|+..|||..+.++.+.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34567899999999999999999999999999999999988899999999999999999999999999999999999876


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus       366 A  366 (500)
T KOG0120|consen  366 A  366 (500)
T ss_pred             h
Confidence            4

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

Probab=98.66  E-value=1e-07  Score=68.30  Aligned_cols=76  Identities=30%  Similarity=0.538  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC---CCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR---VTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ..+.+||+||++.++++.|...|..||++..+++...+   +....+-++||.|-+..++++|++.|+|..+.+..++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            45789999999999999999999999999998877654   22335568999999999999999999999998887664

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

Probab=98.61  E-value=9.8e-08  Score=63.46  Aligned_cols=82  Identities=24%  Similarity=0.259  Sum_probs=72.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE--------VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      .....++||-+||..++++++.++|.++|.|..        +.+.++.+|+++++-|.|.|.+...|++|+..+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            345568999999999999999999999997632        566778889999999999999999999999999999999


Q ss_pred             eeeeeeccCC
Q 034039           95 TSKDTDMLST  104 (105)
Q Consensus        95 ~~~~~v~~~~  104 (105)
                      +..++|.++.
T Consensus       143 gn~ikvs~a~  152 (351)
T KOG1995|consen  143 GNTIKVSLAE  152 (351)
T ss_pred             CCCchhhhhh
Confidence            9888887653

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

Probab=98.60  E-value=6.8e-07  Score=55.03  Aligned_cols=67  Identities=22%  Similarity=0.353  Sum_probs=59.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ...+...|.|++||++.++++|+++...-|.+++..+.++       +++.|+|...++.+.|+++|+...+..
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccC
Confidence            3456789999999999999999999999999999988766       378999999999999999999876543

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

Probab=98.55  E-value=1.2e-07  Score=59.79  Aligned_cols=65  Identities=22%  Similarity=0.308  Sum_probs=55.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ..++||.||.+++++++|+.+|..|.....+++...  +|  .+.+|++|++.+.|..|+..|+|..+.
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            358999999999999999999999987777766432  33  357999999999999999999998774

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

Probab=98.51  E-value=5.1e-07  Score=62.29  Aligned_cols=76  Identities=17%  Similarity=0.216  Sum_probs=59.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....|-+.+||+.|++++|.+||+..-.+.. +.++.+. .+++.|-|||.|++.+.|+.|+.. |...+..+.|.|..
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            5678999999999999999999998755544 4456665 788999999999999999999954 44455555555543

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

Probab=98.49  E-value=1.7e-06  Score=46.74  Aligned_cols=67  Identities=22%  Similarity=0.350  Sum_probs=45.3

Q ss_pred             ceEEEcCCCCCCCHHHHH----HHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           27 TKLFIGGLSYDTNETVLK----DAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~----~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ..|||.|||.+.+...++    .++.-|| .|..+          ..+.|++.|.+.+.|.+|.+.|+|..+-|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999998887654    4555666 44443          12569999999999999999999999999999987


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      ..
T Consensus        73 ~~   74 (90)
T PF11608_consen   73 FS   74 (90)
T ss_dssp             SS
T ss_pred             Ec
Confidence            65

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

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

Probab=98.48  E-value=6.8e-08  Score=67.18  Aligned_cols=81  Identities=23%  Similarity=0.339  Sum_probs=73.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ++...+++|+-.++...++.+|.++|..+|.|..+.++.++.++.++|.+||+|.+..+...|+ .|.|..+.|..+.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            3445678888888888999999999999999999999999999999999999999999999999 999999999999887


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      ++
T Consensus       254 ~s  255 (549)
T KOG0147|consen  254 LS  255 (549)
T ss_pred             cc
Confidence            64

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

Probab=98.43  E-value=3.4e-07  Score=61.17  Aligned_cols=79  Identities=22%  Similarity=0.381  Sum_probs=68.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +.....+||+||-|++|.++|.+.+...|  ++..+++-.++.+|.++||+++...+..+.+..++.|..+.|.|..-.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34556899999999999999988887766  6677788888889999999999999999999999999999999887766


Q ss_pred             c
Q 034039          101 M  101 (105)
Q Consensus       101 ~  101 (105)
                      .
T Consensus       157 ~  157 (498)
T KOG4849|consen  157 L  157 (498)
T ss_pred             e
Confidence            4

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.40  E-value=1.2e-06  Score=49.66  Aligned_cols=59  Identities=29%  Similarity=0.420  Sum_probs=38.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL   91 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~   91 (105)
                      ..|.+.+++..++.++|+..|..||.|.++.+....      ..|+|.|.+.+.|+.|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhc
Confidence            468888999999999999999999999999886543      36999999999999998765543

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

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=98.39  E-value=1.9e-07  Score=59.76  Aligned_cols=75  Identities=16%  Similarity=0.237  Sum_probs=62.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCC--------CCc----cceEEEEeCCHHHHHHHHHHcCCce
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT--------GQS----RGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--------~~~----~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      ....||++++|+.+...-|+++|..||.|-++.+.....+        |..    ..-|.|+|.+...|..+...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4578999999999999999999999999999988655423        222    2347899999999999999999999


Q ss_pred             eeeeeee
Q 034039           93 CRTSKDT   99 (105)
Q Consensus        93 ~~~~~~~   99 (105)
                      |.|+.-.
T Consensus       153 Iggkk~S  159 (278)
T KOG3152|consen  153 IGGKKKS  159 (278)
T ss_pred             cCCCCCC
Confidence            9988643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=98.36  E-value=2.9e-06  Score=59.77  Aligned_cols=80  Identities=23%  Similarity=0.339  Sum_probs=62.9

Q ss_pred             ccCCCCCceEEEcCCCCCCCH------HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           20 LSDANSRTKLFIGGLSYDTNE------TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        20 ~~~~~~~~~l~v~~l~~~~~~------~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      ..++.....|.|.|.|---..      ..|..+|+++|++....++.+.. |+.+||.|++|++..+|+.|+++|||+.+
T Consensus        52 ~~~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~l  130 (698)
T KOG2314|consen   52 VTAEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRL  130 (698)
T ss_pred             CccCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhccccee
Confidence            334466778999999864322      23577899999999999998874 45999999999999999999999999988


Q ss_pred             e-eeeeee
Q 034039           94 R-TSKDTD  100 (105)
Q Consensus        94 ~-~~~~~v  100 (105)
                      + ++...|
T Consensus       131 dknHtf~v  138 (698)
T KOG2314|consen  131 DKNHTFFV  138 (698)
T ss_pred             cccceEEe
Confidence            6 333443

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.30  E-value=2.3e-06  Score=57.89  Aligned_cols=81  Identities=16%  Similarity=0.270  Sum_probs=68.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccC-CeEE--EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHG-EIIE--VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~--~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      .......|.+.+||...+.++|.+||..|. .+..  ++++.+. .|.+.|-|||+|.+.++|.+|..+.+.+.-+.+.+
T Consensus       276 ~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYi  354 (508)
T KOG1365|consen  276 PTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYI  354 (508)
T ss_pred             CCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceE
Confidence            344567899999999999999999998876 3444  6778776 78899999999999999999999988888788888


Q ss_pred             eeccC
Q 034039           99 TDMLS  103 (105)
Q Consensus        99 ~v~~~  103 (105)
                      .|..+
T Consensus       355 Evfp~  359 (508)
T KOG1365|consen  355 EVFPC  359 (508)
T ss_pred             EEeec
Confidence            88754

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

Probab=98.21  E-value=1.5e-05  Score=50.32  Aligned_cols=77  Identities=23%  Similarity=0.389  Sum_probs=65.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-eeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-TSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-~~~~~v~  101 (105)
                      ..+...+++.|+|..++.+.+..+|.+|.....++++...     .+.+||+|.+...+..|...++|..+. ...+++.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            4567789999999999999999999999998888877543     368999999999999999999999887 6666666


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            554

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.20  E-value=7.1e-06  Score=59.18  Aligned_cols=75  Identities=17%  Similarity=0.200  Sum_probs=64.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      +.|-+.|+|+.++-+++.+||..|-.. ..+.+.++ ..|+..|.|.|.|++.++|.+|...|++..|.++.+.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            478889999999999999999999755 34444444 4799999999999999999999999999999998887654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.16  E-value=8e-06  Score=54.56  Aligned_cols=77  Identities=17%  Similarity=0.298  Sum_probs=59.2

Q ss_pred             CceEEEcCCCCCCCHHH----H--HHHHhccCCeEEEEEEecCC--CCCccce-EEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           26 RTKLFIGGLSYDTNETV----L--KDAFGQHGEIIEVKVICDRV--TGQSRGY-GFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~----l--~~~f~~~g~v~~~~~~~~~~--~~~~~g~-~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      .+-+||-+||+.+..++    |  .++|.+||.|..+.+.+...  +.....+ .||+|...++|.++|...+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45789999998876655    2  56899999999987754431  1111112 39999999999999999999999999


Q ss_pred             eeeecc
Q 034039           97 KDTDML  102 (105)
Q Consensus        97 ~~~v~~  102 (105)
                      .++..+
T Consensus       194 ~lkatY  199 (480)
T COG5175         194 VLKATY  199 (480)
T ss_pred             eEeeec
Confidence            998754

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

Probab=98.02  E-value=4.9e-06  Score=52.58  Aligned_cols=72  Identities=25%  Similarity=0.388  Sum_probs=61.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....+.+.+.+++..+.+++|.++|..+|++.....        ..+++||.|...+++..|+..|+|..+.++.+.++.
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            446678999999999999999999999999833322        235799999999999999999999999999998754

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

Probab=97.98  E-value=3.5e-05  Score=38.36  Aligned_cols=52  Identities=25%  Similarity=0.443  Sum_probs=40.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHH
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI   85 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~   85 (105)
                      +.|-|.|.++...+. +..+|..||+|....+...      ....++.|.+..+|+.|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            457788888776655 4558889999999887522      247899999999999885

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.96  E-value=6.4e-06  Score=54.36  Aligned_cols=76  Identities=22%  Similarity=0.403  Sum_probs=66.0

Q ss_pred             CCceEE-EcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           25 SRTKLF-IGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        25 ~~~~l~-v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...++| +++++..++.++|+..|..+|.+..++++.+..++...|++++.|.+...+..++.. +...+.+..+.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  259 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLE  259 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccc
Confidence            344555 999999999999999999999999999999999999999999999999999988876 7777777766554

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.95  E-value=5e-05  Score=53.04  Aligned_cols=65  Identities=25%  Similarity=0.336  Sum_probs=59.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHh-ccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHH
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFG-QHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK   86 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~-~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~   86 (105)
                      .-++.++||||+||.-++.++|..+|. -||.|..+-|-.|++-..++|-|=|+|.+..+-.+||.
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            345778999999999999999999998 69999999999997788899999999999999999985

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

Probab=97.95  E-value=0.00012  Score=49.70  Aligned_cols=76  Identities=18%  Similarity=0.212  Sum_probs=66.3

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .+...+.|-+|... ++.+.|..+|-.||.|.++++.+..     .|-|.|++.+....++|+..||+..+-|.+|.+-.
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            35678889999876 6778899999999999999988765     25799999999999999999999999999998877


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       360 Sk  361 (494)
T KOG1456|consen  360 SK  361 (494)
T ss_pred             cc
Confidence            65

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

Probab=97.90  E-value=8e-05  Score=49.85  Aligned_cols=76  Identities=18%  Similarity=0.244  Sum_probs=57.1

Q ss_pred             CCCceEEEcCCCC----CCC-------HHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           24 NSRTKLFIGGLSY----DTN-------ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        24 ~~~~~l~v~~l~~----~~~-------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      ...++|.+.|+=.    ..+       .++|..-..+||++..+.+.-..    +.|.+-|.|.+.+.|..+|+.|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h----PdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH----PDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC----CCceeEEEeCChHHHHHHHHHhcCee
Confidence            3456777777521    122       23455567889999998765333    45788899999999999999999999


Q ss_pred             eeeeeeeeccC
Q 034039           93 CRTSKDTDMLS  103 (105)
Q Consensus        93 ~~~~~~~v~~~  103 (105)
                      ++|++|.+.+.
T Consensus       339 fdgRql~A~i~  349 (382)
T KOG1548|consen  339 FDGRQLTASIW  349 (382)
T ss_pred             ecceEEEEEEe
Confidence            99999998764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.75  E-value=0.00015  Score=50.73  Aligned_cols=64  Identities=27%  Similarity=0.512  Sum_probs=47.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC---CCCCccc---eEEEEeCCHHHHHHHHHH
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR---VTGQSRG---YGFVKFASEAAAGEAIKE   87 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~~g---~~fv~f~~~~~a~~a~~~   87 (105)
                      ...++.||||+||++++++.|...|..||.+. +.++...   ....++|   |.|+.|+++.+...-+..
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            34678999999999999999999999999752 2333111   1122456   999999999888876644

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.70  E-value=0.00055  Score=46.72  Aligned_cols=61  Identities=26%  Similarity=0.414  Sum_probs=49.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhc----cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHH
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQ----HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE   87 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~----~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   87 (105)
                      .-.|...+||.++++.++.+||..    -|....+.++... +|+..|-||+.|...++|+.|+.+
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH
Confidence            446777899999999999999963    1244566666665 789999999999999999999954

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.66  E-value=9.8e-05  Score=54.67  Aligned_cols=71  Identities=23%  Similarity=0.325  Sum_probs=61.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      .....+.+++++|++++....|...|..||.+..+.+-..      ..|++|.|++...++.|++.|-|..+.+..-
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~  521 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPR  521 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCc
Confidence            4456789999999999999999999999999998876433      2689999999999999999999999976543

>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=97.63  E-value=0.00036  Score=39.23  Aligned_cols=72  Identities=17%  Similarity=0.201  Sum_probs=45.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEE-EEecC------CCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVK-VICDR------VTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~-~~~~~------~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      ..+.|.|-|.|+. ....+...|++||.|.... +..+.      .......+-.|.|.++.+|.+|+ .-||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcE
Confidence            3456778899988 4566788999999986653 10000      00112247889999999999999 66888887654


Q ss_pred             e
Q 034039           98 D   98 (105)
Q Consensus        98 ~   98 (105)
                      +
T Consensus        83 m   83 (100)
T PF05172_consen   83 M   83 (100)
T ss_dssp             E
T ss_pred             E
Confidence            3

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.

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

Probab=97.60  E-value=0.00031  Score=48.16  Aligned_cols=76  Identities=16%  Similarity=0.164  Sum_probs=60.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeee-eeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTS-KDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~-~~~v~  101 (105)
                      .+..++..+|+|+++++++++..|..-|.. .-..+     -++.+.++++.+.+.+.|-.|+..++.+.+... .++|.
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf-----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF-----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee-----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            345688899999999999999999887754 33333     233456999999999999999999999988654 78888


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       487 FSk  489 (492)
T KOG1190|consen  487 FSK  489 (492)
T ss_pred             eec
Confidence            765

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

Probab=97.54  E-value=0.00045  Score=41.23  Aligned_cols=53  Identities=26%  Similarity=0.350  Sum_probs=43.9

Q ss_pred             HHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           42 VLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        42 ~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|.+.|..||.+.-++++.+        .-+|+|.+-.+|.+|+ .++|..+.|+.+++.+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LK  104 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLK  104 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE-
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeC
Confidence            56777889998887777643        3689999999999999 89999999999998864

; PDB: 1UFW_A 2DNR_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.51  E-value=0.00017  Score=49.61  Aligned_cols=69  Identities=17%  Similarity=0.233  Sum_probs=55.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEec---CC--CCCc--------cceEEEEeCCHHHHHHHHHHcCC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD---RV--TGQS--------RGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~---~~--~~~~--------~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      -..++|.+-|||.+..-+.|.++|..+|.|..+++...   +.  .+..        +-+|+|+|..-+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36788999999999988999999999999999988654   21  1221        45789999999999999988865


Q ss_pred             ce
Q 034039           91 LV   92 (105)
Q Consensus        91 ~~   92 (105)
                      ..
T Consensus       309 e~  310 (484)
T KOG1855|consen  309 EQ  310 (484)
T ss_pred             hh
Confidence            43

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

Probab=97.47  E-value=0.0021  Score=32.96  Aligned_cols=55  Identities=20%  Similarity=0.254  Sum_probs=43.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhcc---CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQH---GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM   88 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~---g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l   88 (105)
                      ...|+|.|+. +.+.++++.+|..|   ....+++++-|.       -|-|.|.+...|.+|+..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4579999986 47778899999988   235678887665       3779999999999999765

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

Probab=97.46  E-value=0.00075  Score=36.56  Aligned_cols=58  Identities=14%  Similarity=0.207  Sum_probs=41.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ...+..+++ +|......+|.++|+.||.|.-- ++-+       .-|||...+++.+..++..+.-
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~Vs-Wi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVS-WIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEEEE-EECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEEEE-EEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            345566665 99999999999999999987443 3333       2599999999999999877763

; 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.

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

Probab=97.45  E-value=0.00065  Score=47.96  Aligned_cols=59  Identities=17%  Similarity=0.251  Sum_probs=47.0

Q ss_pred             HHHHHhccCCeEEEEEEecCCCCC---ccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           43 LKDAFGQHGEIIEVKVICDRVTGQ---SRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        43 l~~~f~~~g~v~~~~~~~~~~~~~---~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ++.-+.+||.|..|.++.+...+.   ..|--||+|.+.++++.|.+.|+|.++.++.+...
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvts  487 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVAS  487 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEE
Confidence            444567899999999887722222   34667999999999999999999999999987654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.38  E-value=0.00027  Score=45.64  Aligned_cols=63  Identities=24%  Similarity=0.390  Sum_probs=55.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ..|||.||+..+..+.+..-|+.||++..-.+..|. .+++.+-++|.|.....+..|++.+..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhcc
Confidence            689999999999999999999999999887666665 788888999999999999999988743

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.29  E-value=0.00034  Score=48.27  Aligned_cols=70  Identities=24%  Similarity=0.351  Sum_probs=53.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc-eeeeeeeeecc
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL-VCRTSKDTDML  102 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-~~~~~~~~v~~  102 (105)
                      +.+|++||.+..+..+|..+|...---..-.+...      .||+|+.+.+..-|..|++.++|. .+.|++..+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~   72 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEH   72 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccc
Confidence            36899999999999999999976421112222222      279999999999999999999987 57788877654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.13  E-value=0.00021  Score=46.05  Aligned_cols=61  Identities=25%  Similarity=0.239  Sum_probs=47.0

Q ss_pred             HHHHHHh-ccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           42 VLKDAFG-QHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        42 ~l~~~f~-~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++...+. +||.+..+.+-.+. ..-..|-.||.|...++|++|++.||+..+.|+++...++
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            4444455 78988887554332 2224567899999999999999999999999999988764

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.00  E-value=0.0003  Score=51.94  Aligned_cols=75  Identities=19%  Similarity=0.337  Sum_probs=62.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...++|+|.|+..|.+.++.++..+|.+....++..+ .|+++|.+++.|.+..++..+..+.+...+.-..+.+.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~  810 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQ  810 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCcccc
Confidence            3579999999999999999999999999888887776 89999999999999999999887766655544444443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.98  E-value=0.0021  Score=44.08  Aligned_cols=76  Identities=14%  Similarity=0.122  Sum_probs=59.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCC---CCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV---TGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...|.|.||.++++.++++.+|.-.|.|..+.+..+..   -......|||-|.+...+..|. .|-++.+-++.+.|..
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            34899999999999999999999999998887654221   1223457999999988887776 7888888777766643

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.92  E-value=0.0018  Score=40.07  Aligned_cols=74  Identities=16%  Similarity=0.135  Sum_probs=45.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhc-cCCe---EEEEEEecCCCCC--ccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQ-HGEI---IEVKVICDRVTGQ--SRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~v---~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      .....|.|++||+..+++++...+.. +++-   ....-......-.  ...-|||.|.+.+++......++|..+...+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999998876665 5544   2332112211111  2345899999999999999999998775443

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=96.81  E-value=0.0012  Score=47.30  Aligned_cols=76  Identities=16%  Similarity=0.198  Sum_probs=58.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhc-cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee---eee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQ-HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR---TSK   97 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---~~~   97 (105)
                      ....++.|+|.||-.-+|..+|+.++.. +|.|....|  |    +-+.+|||.|.+.++|-+....|||..+.   .+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            3456789999999999999999999984 555554432  2    13468999999999999999999998763   455


Q ss_pred             eeeccC
Q 034039           98 DTDMLS  103 (105)
Q Consensus        98 ~~v~~~  103 (105)
                      |.+.+.
T Consensus       514 L~adf~  519 (718)
T KOG2416|consen  514 LIADFV  519 (718)
T ss_pred             eEeeec
Confidence            555543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.76  E-value=0.00083  Score=49.01  Aligned_cols=76  Identities=14%  Similarity=-0.003  Sum_probs=60.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      -...|||..||..+++..+.+.|...-.|.+ +.+.+.. +++.++.|||.|...+.+..|...-+...+..+.|+|.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            4579999999999999999999987666655 7776666 78888999999999888888875555556666777765

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

Probab=96.73  E-value=0.041  Score=31.51  Aligned_cols=67  Identities=19%  Similarity=0.181  Sum_probs=45.6

Q ss_pred             ceEEEcCCCCC-CCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           27 TKLFIGGLSYD-TNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        27 ~~l~v~~l~~~-~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ..+.+-..|+. .+.+.|..+...+- .+..+++.++.  ...+-..++.|.+..+|......+||+.+..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34444444555 45455655545443 56778887764  2245568999999999999999999987653

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

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.59  E-value=0.015  Score=38.65  Aligned_cols=60  Identities=15%  Similarity=0.118  Sum_probs=46.8

Q ss_pred             HHHHHHHhccCCeEEEEEEecCCCCCcc-ceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           41 TVLKDAFGQHGEIIEVKVICDRVTGQSR-GYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        41 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~-g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ++..+-..+||.|.+|.+.......... ---||+|...++|..|+-.|||..+.|+....
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A  361 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSA  361 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeh
Confidence            3567778899999988766554332222 23699999999999999999999999998764

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

Probab=96.48  E-value=0.023  Score=39.06  Aligned_cols=64  Identities=20%  Similarity=0.298  Sum_probs=49.8

Q ss_pred             ceEEEcCC--CCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           27 TKLFIGGL--SYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        27 ~~l~v~~l--~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ..|.+.=|  -..+|.+.|..+....|+|.++.+...  +|.   -|.|+|++.+.|++|.+.|||..|-.
T Consensus       121 ~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYs  186 (494)
T KOG1456|consen  121 KVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYS  186 (494)
T ss_pred             eEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccc
Confidence            34444433  345788899999999999999977654  443   38999999999999999999987743

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.45  E-value=0.0013  Score=44.05  Aligned_cols=77  Identities=21%  Similarity=0.348  Sum_probs=56.6

Q ss_pred             CceEEEcCCCCCCCHHHH---HHHHhccCCeEEEEEEecCC---CCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           26 RTKLFIGGLSYDTNETVL---KDAFGQHGEIIEVKVICDRV---TGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l---~~~f~~~g~v~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      .+-+||-+|+.....+.+   ...|.+||.+..+....+..   .....+-++|+|...++|..+|...+|..++|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            356788889887655443   34688999998887766441   111223489999999999999999999999998865


Q ss_pred             ecc
Q 034039          100 DML  102 (105)
Q Consensus       100 v~~  102 (105)
                      ..+
T Consensus       157 a~~  159 (327)
T KOG2068|consen  157 ASL  159 (327)
T ss_pred             Hhh
Confidence            543

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.23  E-value=0.011  Score=42.38  Aligned_cols=71  Identities=15%  Similarity=0.183  Sum_probs=55.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhc--cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC--ceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQ--HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG--LVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~--~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~~~~~~v  100 (105)
                      ..+.+.++-+|..+..++++.+|..  |-.+..|++..+..       =||+|++..+|+.|.+.|..  +.+.|+.|++
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4567778999999999999999975  77889998877652       48999999999999877664  3566666655


Q ss_pred             cc
Q 034039          101 ML  102 (105)
Q Consensus       101 ~~  102 (105)
                      .+
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            44

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.21  E-value=0.00018  Score=53.04  Aligned_cols=63  Identities=29%  Similarity=0.453  Sum_probs=53.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD   89 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   89 (105)
                      .++|++||+..+.+.+|...|..+|.+..+++..-..+++.+|+||+.|.+.+.+.+|+....
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d  730 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRD  730 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhh
Confidence            578999999999999999999999988777665444578899999999999999999985433

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

Probab=95.78  E-value=0.02  Score=40.80  Aligned_cols=44  Identities=20%  Similarity=0.193  Sum_probs=38.7

Q ss_pred             cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           50 HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        50 ~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      .|...++.++.|..+....|||||.|.+.+.+..+.+++||..+
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W  456 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKW  456 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCch
Confidence            56667788888888888899999999999999999999999864

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.74  E-value=0.086  Score=37.03  Aligned_cols=68  Identities=21%  Similarity=0.256  Sum_probs=55.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhcc-CCeEEEEEEecCCCCCccc-eEEEEeCCHHHHHHHHHHcCCceee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQH-GEIIEVKVICDRVTGQSRG-YGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~g-~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      .+++.|.|-.+|-.++-.+|..|...+ ..|..++++++   |.+.. ..+|.|.+..+|......+||..+.
T Consensus        72 ~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd---~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   72 SSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRD---GMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeec---CCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            347889999999999999999888754 46788998884   33333 4689999999999999999998765

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

Probab=95.65  E-value=0.045  Score=34.16  Aligned_cols=59  Identities=15%  Similarity=0.084  Sum_probs=43.3

Q ss_pred             CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC--CceeeeeeeeeccC
Q 034039           39 NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD--GLVCRTSKDTDMLS  103 (105)
Q Consensus        39 ~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~~~~~~~v~~~  103 (105)
                      ..+.|+++|..++.+.........      +-..|.|.+.+.|.+|...|+  +..+.|..+++.++
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~   68 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFG   68 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE--
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEc
Confidence            347789999999988776655433      347899999999999999999  99999999888654

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

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

Probab=95.37  E-value=0.089  Score=27.76  Aligned_cols=67  Identities=18%  Similarity=0.289  Sum_probs=37.5

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhccC-----CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           28 KLFIG-GLSYDTNETVLKDAFGQHG-----EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        28 ~l~v~-~l~~~~~~~~l~~~f~~~g-----~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ++||. |--..++..+|..++...+     .|-.+.+..        .|+|++.. .+.+..++..|++..+.|+.++++
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~-~~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVP-EEVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE--TT-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEEC-HHHHHHHHHHhcCCCCCCeeEEEE
Confidence            34552 2234578888888887654     455666532        36888877 457888999999999999999987


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            54

; PDB: 2G0C_A 3MOJ_B.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.31  E-value=0.12  Score=30.99  Aligned_cols=63  Identities=16%  Similarity=0.212  Sum_probs=44.1

Q ss_pred             CCCCCceEEEcCCCCCCCH-HH---HHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc
Q 034039           22 DANSRTKLFIGGLSYDTNE-TV---LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL   91 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~-~~---l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~   91 (105)
                      .+.+-.+|.|.=|..++.. ++   +...++.||+|..+-.-     |  +.-|.|.|.+..+|=.|+.+++..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s~  148 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQSR  148 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcCC
Confidence            3445567778766655433 34   45556789999887542     2  235999999999999999888753

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.98  E-value=0.0047  Score=46.25  Aligned_cols=75  Identities=21%  Similarity=0.343  Sum_probs=60.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ...+||++||+..+++.+++..|..+|.+..+.+-... -+....|+|+.|.+-..+..|+..+.+..|....++.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            45799999999999999999999999999888775543 2333458999999999999998888887776544443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.30  E-value=0.021  Score=40.12  Aligned_cols=67  Identities=25%  Similarity=0.258  Sum_probs=49.2

Q ss_pred             eEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           28 KLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        28 ~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .+-+.-.|+. .+.++|..+|.+||.|..|.+-+..      -.|.|+|.+..+|-.|. ..++..|+++-+++.
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~  441 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLF  441 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchh-ccccceecCceeEEE
Confidence            4444444555 3568899999999999999886552      36899999999987666 566777777776664

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.81  E-value=0.051  Score=39.67  Aligned_cols=70  Identities=20%  Similarity=0.289  Sum_probs=58.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++||+|+...+..+-+..++..||-|..+...         -|||..|........|+..+.-..+++..+.+.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            4466789999999999999999999999988766432         289999999999999999998888888776554

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.58  E-value=1.2  Score=31.26  Aligned_cols=68  Identities=18%  Similarity=0.140  Sum_probs=52.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGE-IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      +..-.+.|-|-++|.....++|...|..|+. -.++.++-+.       ++|-.|.+...|..|+. |....+.-+.
T Consensus       387 e~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt-~kh~~lKiRp  455 (528)
T KOG4483|consen  387 ESDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALT-LKHDWLKIRP  455 (528)
T ss_pred             cccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhh-ccCceEEeee
Confidence            4445678889999999999999999999874 4777777664       79999999999999994 4544554444

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=92.02  E-value=0.1  Score=39.42  Aligned_cols=68  Identities=13%  Similarity=0.161  Sum_probs=52.5

Q ss_pred             EcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee--eeeeeeeccCC
Q 034039           31 IGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC--RTSKDTDMLST  104 (105)
Q Consensus        31 v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~--~~~~~~v~~~~  104 (105)
                      +.|.+-..+-..|..++..||.+...+..++-      -++.|.|..-+.|..|+.+++|+++  .|-..+|++++
T Consensus       303 ~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  303 LENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            33344455666788999999999888776654      3689999999999999999999976  46667776654

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=91.86  E-value=1.5  Score=29.58  Aligned_cols=63  Identities=16%  Similarity=0.320  Sum_probs=43.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      .=|-|-++|+.-. ..+..+|.+||.|.+....  + +|   -+-+|.|.++.+|++|| .-||..|++..
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~--~-ng---NwMhirYssr~~A~KAL-skng~ii~g~v  260 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP--S-NG---NWMHIRYSSRTHAQKAL-SKNGTIIDGDV  260 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC--C-CC---ceEEEEecchhHHHHhh-hhcCeeeccce
Confidence            3344457776533 4567789999988665433  1 33   37789999999999999 45676666543

>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=91.72  E-value=1.1  Score=23.28  Aligned_cols=54  Identities=19%  Similarity=0.196  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           37 DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        37 ~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      .++-++++..+..|+ ..++  ..++ +|     =||.|.+..+|+++....+|..+-+-++.
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I--~~d~-tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~   64 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRI--RDDR-TG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQ   64 (66)
T ss_pred             CccHHHHHHHHhcCC-cceE--EecC-CE-----EEEEECChHHHHHHHHhcCCCEEEEEEEE
Confidence            357788999999985 3333  3343 32     48999999999999999999988777654

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=90.55  E-value=0.2  Score=33.38  Aligned_cols=73  Identities=22%  Similarity=0.203  Sum_probs=55.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      ...+.|++++.+...+.+...++..+|......+.........++++++.|+..+.+..++.......+.+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~  159 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNK  159 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhcccccccc
Confidence            4678899999998888877788888887766666555557778899999999999999999544333444333

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=89.80  E-value=0.007  Score=42.08  Aligned_cols=73  Identities=16%  Similarity=0.178  Sum_probs=57.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEE-ecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVI-CDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~-~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .++.+-|.|+|+...++.|..++..||.+..|..+ .+..+    ...-++|...+.++-|+.+++|..+....+++-
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence            45678899999999999999999999999888643 33322    122367888999999999999998877766654

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=84.05  E-value=5.5  Score=26.87  Aligned_cols=62  Identities=11%  Similarity=0.121  Sum_probs=47.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC-------CCCCccceEEEEeCCHHHHHHH
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-------VTGQSRGYGFVKFASEAAAGEA   84 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-------~~~~~~g~~fv~f~~~~~a~~a   84 (105)
                      +-..+.|...|+..+++-..+...|..||+|+.+.+..+.       ...+......+.|-+++.+...
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdF   80 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDF   80 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHH
Confidence            3456678889999999988889999999999999987654       1223345677888888887664

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.68  E-value=9.9  Score=25.73  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=34.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEEecCCCCCccceEEEEeCCH
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASE   78 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~g~~fv~f~~~   78 (105)
                      -.+-||++||+.+..-.+|+.-+++-+-+ .++.+      ..+.+-||+.|.+.
T Consensus       329 ~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~  377 (396)
T KOG4410|consen  329 AKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNR  377 (396)
T ss_pred             cccceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCc
Confidence            34679999999999999999999876532 23322      22556799999653

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.53  E-value=15  Score=27.23  Aligned_cols=77  Identities=23%  Similarity=0.342  Sum_probs=55.7

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHHhcc----CCeEEEEEEecC----------CCCC---------------------
Q 034039           23 ANSRTKLFIGGLSYD-TNETVLKDAFGQH----GEIIEVKVICDR----------VTGQ---------------------   66 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~----g~v~~~~~~~~~----------~~~~---------------------   66 (105)
                      ....++|-|-|+.|. +...+|.-+|..|    |.|..+.|....          ..|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456778999999998 6778888887765    466776664321          1121                     


Q ss_pred             ----------------ccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           67 ----------------SRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        67 ----------------~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                                      -.=||.|+|.+...|.+....++|..+......
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~  299 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANK  299 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccce
Confidence                            012788999999999999999999988755444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	105
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-13
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-12
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-11
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-11
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		1e-10
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-10
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		5e-10
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-09
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-09
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-09
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		9e-09
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-08
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-08
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		4e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		4e-08
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		5e-08
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		7e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-07
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-07
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-07
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-07
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-07
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		5e-07
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		9e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		9e-07
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		1e-06
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-06
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		3e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		4e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		4e-06
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		5e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		5e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		5e-06
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		5e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		5e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		6e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		8e-06
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		1e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-05
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		3e-05
2khc_A	118	Bruno Rrm3+ Length = 118		3e-05
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		4e-05
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		4e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		4e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		5e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		5e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		6e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		7e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		1e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-04
3p5t_L	90	Cfim25-Cfim68 Complex Length = 90		2e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		2e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		3e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		3e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		3e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		3e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		3e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		3e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		4e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		4e-04
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		4e-04
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		4e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		5e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		7e-04
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		7e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		8e-04
3q2s_C	229	Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Lengt		8e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-04

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 48/69 (69%), Gaps = 1/69 (1%)
Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +A+   KLFIGGL+ +TNE +LK  FG+HG I EV +I DR T +SRG+ F+ F + A A
Sbjct: 3  EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 82 GEAIKEMDG 90
            A K+M+G
Sbjct: 62 KNAAKDMNG 70

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 47/68 (69%)
Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A+   KLF+GGLS+DTNE  L+  F ++G+I EV V+ DR T +SRG+GFV F +   A 
Sbjct: 9  ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 83 EAIKEMDG 90
          +A+  M+G
Sbjct: 69 DAMMAMNG 76

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 42/66 (63%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TK+F+GGL Y T +  L+  F   G+I E  VI DR TG+SRGYGFV  A  AAA  A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 87 EMDGLV 92
          + + ++
Sbjct: 78 DPNPII 83

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 47/68 (69%), Gaps = 3/68 (4%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+FIGGL++DT E  L++ FG++G + ++K++ D  TG+SRG+GF+ F   ++  E +K 
Sbjct: 5  KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 88 ---MDGLV 92
             +DG V
Sbjct: 65 QHILDGKV 72

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 43/70 (61%)
Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          +S+ N    +++GGL    +E +L + F Q G ++   +  DRVTGQ +GYGFV+F SE 
Sbjct: 9  ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 80 AAGEAIKEMD 89
           A  AIK MD
Sbjct: 69 DADYAIKIMD 78

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 37/58 (63%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          KLF+GGL + T +  L+  F Q+GE+++  ++ D+ T QSRG+GFVKF      G  +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 46/78 (58%)
Query: 14  VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           +  T++  + +    L +  +    +E  L+  F ++G I  VK++CDR T QSRGYGFV
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Query: 74  KFASEAAAGEAIKEMDGL 91
           KF S ++A +AI  ++G 
Sbjct: 90  KFQSGSSAQQAIAGLNGF 107

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
           +S  K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A   
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 83 EAIKE 87
          + + +
Sbjct: 82 KVLAQ 86

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 7   SVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ 66
           +++ S++   +  + DAN    L++ GL     +  L+  F Q+G II  +++ D+VTG 
Sbjct: 73  TIKVSYARPSSASIRDAN----LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV 128
Query: 67  SRGYGFVKFASEAAAGEAIKEMDG 90
           SRG GF++F     A EAIK ++G
Sbjct: 129 SRGVGFIRFDKRIEAEEAIKGLNG 152

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 40/60 (66%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A   + + +
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 39/59 (66%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +FIGGLS+DT +  LKD F + GE+++  +  D +TG+SRG+GFV F    +  + + +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K F+GGLS+DT++  LKD F + GE+++  +  D  TG+SRG+GF+ F   A+  + + +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 88 ----MDGLVCRTSK 97
              +DG V    K
Sbjct: 73 KEHRLDGRVIDPKK 86

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +S+T L +  L  +  +   K  FG  G+I   K++ D++TGQS GYGFV ++    A +
Sbjct: 2  DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 84 AIKEMDGLVCRT 95
          AI  ++GL  +T
Sbjct: 62 AINTLNGLKLQT 73

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 7   SVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ 66
           +++ S++   +  + DAN    L++ GL    ++  ++  F Q+G II  +++ D+ TG 
Sbjct: 75  TIKVSYARPSSASIRDAN----LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGV 130
Query: 67  SRGYGFVKFASEAAAGEAIKEMDG 90
           SRG GF++F     A EAIK ++G
Sbjct: 131 SRGVGFIRFDKRIEAEEAIKGLNG 154

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 39/62 (62%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+G + Y+  E  LKD F + G ++  +++ DR TG+ +GYGF ++  +  A  A++ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 89 DG 90
          +G
Sbjct: 71 NG 72

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 44/81 (54%)
Query: 13  SVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGF 72
           S+ + R   D    T L +  L+Y T+   L+  F ++G + +V +  DR T +SRG+ F
Sbjct: 34  SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93
Query: 73  VKFASEAAAGEAIKEMDGLVC 93
           V+F  +  A +A+  MDG V 
Sbjct: 94  VRFHDKRDAEDAMDAMDGAVL 114

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 10/96 (10%)
Query: 1   MQWLNG------SVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEII 54
           +  LNG      +++ S++   + ++ DAN    L+I GL     +  ++D F + G II
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDAN----LYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 55  EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
             +V+ D+ TG SRG  F++F   + A EAI   +G
Sbjct: 117 NSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 10/96 (10%)
Query: 1   MQWLNG------SVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEII 54
           +  LNG      +++ S++   + ++ DAN    L+I GL     +  ++D F + G II
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDAN----LYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 55  EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
             +V+ D+ TG SRG  F++F   + A EAI   +G
Sbjct: 117 NSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          DAN    L++ GL    ++  ++  F Q+G II  +++ D+ TG SRG GF++F     A
Sbjct: 1  DAN----LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEA 56
Query: 82 GEAIKEMDG 90
           EAIK ++G
Sbjct: 57 EEAIKGLNG 65

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFAS----EAAAGE 83
           KLFIGGLS++T E  L++ + Q G++ +  V+ D  + +SRG+GFV F+S    +AA   
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 84  AIKEMDGLVCRTSK 97
               +DG V    +
Sbjct: 89  RPHSIDGRVVEPKR 102

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 48/79 (60%), Gaps = 12/79 (15%)
Query: 21 SDANSRTK----LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
          S  N+R++    LF+ GLS DT E  LK++F      +  +++ DR TG S+G+GFV F 
Sbjct: 6  SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFN 62
Query: 77 SE---AAAGEAIK--EMDG 90
          SE    AA EA++  E+DG
Sbjct: 63 SEEDAKAAKEAMEDGEIDG 81

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  AI++M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 89  DGLVCRTSK 97
           +G++    K
Sbjct: 159 NGMLLNDRK 167

>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 = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D ++   +F+G LS +     +K AF   G I + +V+ D  TG+S+GYGFV F ++  A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 82 GEAIKEMDG 90
            AI++M G
Sbjct: 71 ENAIQQMGG 79

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  AI++M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 89  DGLVCRTSK 97
           +G++    K
Sbjct: 164 NGMLLNDRK 172

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%)
Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D ++   +F+G LS +     +K AF   G+I + +V+ D  TG+S+GYGFV F ++  A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 82 GEAIKEMDG 90
            AI  M G
Sbjct: 71 ENAIVHMGG 79

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  AI++M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 89 DGLVCRTSK 97
          +G++    K
Sbjct: 72 NGMLLNDRK 80

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 41/64 (64%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +L++G L ++  E +L+  F   G I  ++++ D  TG+S+GYGF+ F+    A +A+++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 88 MDGL 91
          ++G 
Sbjct: 88 LNGF 91

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 22  DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
           D    T L +  L+Y T+   L+  F ++G + +V +  DR T +SRG+ FV+F  +  A
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 82  GEAIKEMDGLVC 93
            +A+  MDG V 
Sbjct: 126 EDAMDAMDGAVL 137

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKF 75
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  AI++M
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 89 DGLVCRTSK 97
          +G++    K
Sbjct: 66 NGMLLNDRK 74

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 35/63 (55%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           LF+G L+ + ++  L++AF      +   V+ D  TG SRGYGFV F S+  A  A+  
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 88 MDG 90
          M G
Sbjct: 63 MQG 65

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 1   MQWLNGSVRFSHSVR----FTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV 56
           +Q LNG    ++ V+    F    S ++    LF+G L+ + ++  L++AF      +  
Sbjct: 58  LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117
Query: 57  KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
            V+ D  TG SRGYGFV F S+  A  A+  M G
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 151

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +FIG L  + +E +L D F   G I++  K++ D  TG S+GY F+ FAS  A+  AI+ 
Sbjct: 8  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 88 MDG 90
          M+G
Sbjct: 68 MNG 70

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G L Y      +K+ F Q G++  VK+I DR T + +G+GFV+   E+ + EAI ++
Sbjct: 4  IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAKL 62
Query: 89 DG 90
          D 
Sbjct: 63 DN 64

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           LF+  ++YDT E+ L+  F  +G I  + ++  + +G+ RGY F+++  E     A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 89  DG 90
           DG
Sbjct: 165 DG 166

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%)
Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          RT L +  L  +  +  L+  F   GE+   K+I D+V G S GYGFV + +   A  AI
Sbjct: 4  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 86 KEMDGL 91
            ++GL
Sbjct: 64 NTLNGL 69

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          +F+GG+    +ET ++  F ++G + EVK+I DR TG S+GYGFV F ++ 
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +++G + YD  E  + D     G +I +K++ D  TG+S+GY F++F    ++  A++ +
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 89  DG-------LVCRTSKDTDM 101
           +G       L C  S ++D+
Sbjct: 65  NGYQLGSRFLKCGYSSNSDI 84

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +++G + YD  E  + D     G +I +K++ D  TG+S+GY F++F    ++  A++ +
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 89  DG-------LVCRTSKDTDM 101
           +G       L C  S ++D+
Sbjct: 66  NGYQLGSRFLKCGYSSNSDI 85

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          +F+GG+    +ET ++  F ++G + EVK+I DR TG S+GYGFV F ++ 
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          +F+GG+    +ET ++  F ++G + EVK+I DR TG S+GYGFV F ++ 
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 62

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 50/94 (53%), Gaps = 2/94 (2%)
Query: 1   MQWLNG-SVRFSH-SVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKV 58
           ++ LNG +VR     V + R   ++   T L++  L     +  L   FG++G I++  +
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 59  ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
           + D++TG+ RG  FV++     A EAI  ++ ++
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 2/95 (2%)
Query: 1   MQWLNG-SVRFSH-SVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKV 58
           ++ LNG +VR     V + R   ++   T L++  L     +  L   FG++G I++  +
Sbjct: 73  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 59  ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC 93
           + D++TG+ RG  FV++     A EAI  ++ ++ 
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 167

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 36/59 (61%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
           K+F+GG+ ++  ET L++ F + G + EV +I D    + RG+GF+ F  E +  +A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 37/62 (59%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +++G + YD  E  + D     G +I +K++ D  TG+S+GY F++F    ++  A++ +
Sbjct: 7  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 89 DG 90
          +G
Sbjct: 67 NG 68

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          + KLFI GL +   +  L++    HG + +++++ +R  G+ +G  +V++ +E+ A +A+
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAV 75
Query: 86 KEMDGLVCR 94
           +MDG+  +
Sbjct: 76 MKMDGMTIK 84

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 39/67 (58%)
Query: 23  ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
           A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A 
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 83  EAIKEMD 89
            AI  M+
Sbjct: 120 AAIDNMN 126

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 40/65 (61%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + L++G L ++  E +L+  F   G+I  + ++ D  TG+S+GYGF+ F+    A  A++
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 87 EMDGL 91
          +++G 
Sbjct: 66 QLNGF 70

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 34/65 (52%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L +  L  +  +  L+  F   GE+   K+I D+V G S GYGFV + +   A  AI 
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 87 EMDGL 91
           ++GL
Sbjct: 80 TLNGL 84

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 37/67 (55%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L++  L     +  L   FG++G I++  ++ D++TG+ RG  FV++     A EAI 
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 87 EMDGLVC 93
           ++ ++ 
Sbjct: 74 ALNNVIP 80

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           LF+  ++YDT E+ L+  F  +G I  + ++  + +G+ RGY F+++  E     A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 89  DG 90
           DG
Sbjct: 165 DG 166

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          K+F+GGLS DT E  +++ FG  GE+  +++  D  T + RG+ F+ F  E   
Sbjct: 3  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPV 56

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 40/69 (57%)
Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     
Sbjct: 2  SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 81 AGEAIKEMD 89
          A  AI  M+
Sbjct: 62 AAAAIDNMN 70

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 38/65 (58%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A  A
Sbjct: 1  SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 85 IKEMD 89
          I  M+
Sbjct: 61 IDNMN 65

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 39/67 (58%)
Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A 
Sbjct: 9  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 83 EAIKEMD 89
           AI  M+
Sbjct: 69 AAIDNMN 75

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 37/67 (55%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +LF+  LSY ++E  L+  F  +G + E+    D +T + +G+ FV F     A +A  E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 88 MDGLVCR 94
          +DG V +
Sbjct: 70 VDGQVFQ 76

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE- 87
          L + GL + T E  LK+ F   GE++ V+V  D  TG S+G+GFV+F       + + + 
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 88 --MDGLVC 93
            +DG  C
Sbjct: 78 HMIDGRWC 85

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 39/67 (58%)
Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          + ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A 
Sbjct: 2  STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 83 EAIKEMD 89
           AI  M+
Sbjct: 62 AAIDNMN 68

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L+I GL   T +  L      +G+I+  K I D+ T + +GYGFV F S +AA +A+  +
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +F+GGLS DT E  +++ FG  GE+  +++  D  T + RG+ F+ F  E   
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPV 54

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 35/73 (47%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T L +  L  D  +  L   F   G I   +++ D  TG S GY FV F SE  +  A
Sbjct: 2  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 85 IKEMDGLVCRTSK 97
          IK ++G+  R  +
Sbjct: 62 IKVLNGITVRNKR 74

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 19 LLSDANSRTKLFIG--GLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
          L S AN      +G  GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F 
Sbjct: 3  LGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Query: 77 SEAAAGEAIKEMDGL 91
          +   A EA +  +G+
Sbjct: 63 NVDDAKEAKERANGM 77

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%)
Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A+    + +  LS DT ET L++ F   G I  + +  D+ TGQS+G+ F+ F     A 
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 83 EAIKEMDGL 91
           AI  + G 
Sbjct: 72 RAIAGVSGF 80

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 38/66 (57%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S   +F+G LS +     +  AF   G I + +V+ D  TG+S+GYGFV F ++  A  A
Sbjct: 5  SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 85 IKEMDG 90
          I++M G
Sbjct: 65 IQQMGG 70

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 33/63 (52%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           LFI  L  +  +T L   F   G +I  KV  D+ T  S+ +GFV F +  +A  AIK M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 89  DGL 91
           +G 
Sbjct: 103 NGF 105

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGE-IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          L++G L    +E  +  AF   GE ++ VK+I +R+TG   GY FV+FA  A A + + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 88 MDG 90
          ++G
Sbjct: 72 ING 74

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T+LF+     D  E+ L + FG  G + EVK++         G+ FV+F    +A +A
Sbjct: 3  SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKA 54
Query: 85 IKEMDG 90
          I+E+ G
Sbjct: 55 IEEVHG 60

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 17 TRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
           R   D N    +F  GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F 
Sbjct: 8  NRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Query: 77 SEAAAGEAIKEMDGL 91
          +   A EA +  +G+
Sbjct: 66 NVDDAKEAKERANGM 80

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          +F+GGLS +T    +K  F Q G++ +  ++ D+ T + RG+GFV F SE
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T+LF+     D  E+ L + FG  G + EVK++         G+ FV+F    +A +A
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKA 81
Query: 85 IKEMDG 90
          I+E+ G
Sbjct: 82 IEEVHG 87

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 17  TRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
            R   D N    +F  GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F 
Sbjct: 39  NRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Query: 77  SEAAAGEAIKEMDGL 91
           +   A EA +  +G+
Sbjct: 97  NVDDAKEAKERANGM 111

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 17 TRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
           R   D N    +F  GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F 
Sbjct: 8  NRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Query: 77 SEAAAGEAIKEMDGL 91
          +   A EA +  +G+
Sbjct: 66 NVDDAKEAKERANGM 80

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
           R +LF+G L  D  E   K  F ++GE  EV +  D      RG+GF++  S   A  A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIA 74
Query: 85 IKEMDGLVCRT 95
            E+DG + ++
Sbjct: 75 KAELDGTILKS 85

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 17/67 (25%), Positives = 39/67 (58%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +++++G + Y+  E  ++ AF   G I  + +  D VT + +G+ FV++    AA  A++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 87 EMDGLVC 93
          +M+ ++ 
Sbjct: 89 QMNSVML 95

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 33/57 (57%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          KLFIG +  + +E  LK  F + G+I E+ V+ DR TG  +G  F+ +    +A +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 17/65 (26%), Positives = 38/65 (58%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++++G + Y+  E  ++ AF   G I  + +  D VT + +G+ FV++    AA  A+++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 88 MDGLV 92
          M+ ++
Sbjct: 75 MNSVM 79

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L++  L    ++  L+ AF   G I   KV+ +   G+S+G+GFV F+S   A +A+ EM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 89 DGLVCRT 95
          +G +  T
Sbjct: 76 NGRIVAT 82

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           +++G + Y +    L+  F   G I  + ++CD+ +G  +GY +++FA   +   A+  M
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-M 97
Query: 89  DGLVCR 94
           D  V R
Sbjct: 98  DETVFR 103

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 35/69 (50%)
Query: 23  ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
            +S  KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++       
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 83  EAIKEMDGL 91
           +AI  ++G+
Sbjct: 171 QAIAGLNGM 179

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           K+++G L  + N+T L+ AFG +G +  V      V     G+ FV+F     A +A++E
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVRE 129
Query: 88  MDG 90
           +DG
Sbjct: 130 LDG 132

>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex Length = 90

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          R  L+IG L++ T +  L +A    G  +I+E+K   +R  GQS+G+  V   SEA++  
Sbjct: 1  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK- 59
Query: 84 AIKEMDGLVCR 94
            K MD L  R
Sbjct: 60 --KLMDLLPKR 68

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV--TGQSRGYGFVKFASEAAAGEA 84
          K+F+G +    +E  L++ F Q+G + E+ V+ DR     QS+G  FV F +  AA EA
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/109 (21%), Positives = 58/109 (53%), Gaps = 14/109 (12%)
Query: 5   NGSVRFSHSVRFTRLLSDANSRT-KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV 63
           +GS   +  +RF  +++ ++ +   ++ GG++    + +++  F   G+I+E++V  ++ 
Sbjct: 3   SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK- 61
Query: 64  TGQSRGYGFVKFASEAAAGEAIKEMDG-------LVCRTSKDTDMLSTG 105
                GY FV+F++  +A  AI  ++G       + C   K++  +++G
Sbjct: 62  -----GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSG 105

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++       +AI  
Sbjct: 96  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 88  MDGL 91
           ++G+
Sbjct: 156 LNGM 159

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 DG 90
          +G
Sbjct: 70 NG 71

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 DG 90
          +G
Sbjct: 70 NG 71

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 12  HSVRFTRLLSDANSRT---KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR 68
           H ++     S+ N+     KLFIG +S    E  ++  F   G+I E +++     G SR
Sbjct: 90  HPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL-RGPDGLSR 148
Query: 69  GYGFVKFASEAAAGEAIKEM 88
           G  FV F + A A  AIK M
Sbjct: 149 GCAFVTFTTRAMAQTAIKAM 168

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++       +AI  
Sbjct: 98  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 88  MDGL 91
           ++G+
Sbjct: 158 LNGM 161

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 DG 90
          +G
Sbjct: 70 NG 71

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 12  HSVRFTRLLSDANSRT---KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSR 68
           H ++     S+ N+     KLFIG +S    E  ++  F   G+I E +++     G SR
Sbjct: 78  HPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL-RGPDGLSR 136
Query: 69  GYGFVKFASEAAAGEAIKEM 88
           G  FV F + A A  AIK M
Sbjct: 137 GCAFVTFTTRAMAQTAIKAM 156

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++       +AI  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 88 MDGL 91
          ++G+
Sbjct: 63 LNGM 66

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 89 DG 90
          +G
Sbjct: 72 NG 73

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 89 DG 90
          +G
Sbjct: 86 NG 87

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ-SRGYGFVKFASEAAAGEAI 85
          TK+ IG L+ +  +  + + F  +G+I  + +  +R+    S+GY +V+F +   A +A+
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 86 KEMDG 90
          K MDG
Sbjct: 65 KHMDG 69

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 89 DG 90
          +G
Sbjct: 85 NG 86

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +L +  + +   +  L+  FGQ G+I++V++I +     S+G+GFV F + A A  A ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 88 MDGLVCRTSK 97
          + G V    K
Sbjct: 89 LHGTVVEGRK 98

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +L +  + +   +  L+  FGQ G+I++V++I +     S+G+GFV F + A A  A ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 74
Query: 88 MDGLVCRTSK 97
          + G V    K
Sbjct: 75 LHGTVVEGRK 84

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           K+++G L  + N+T L+ AFG +G +  V      V     G+ FV+F     A +A+++
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVRD 129
Query: 88  MDG 90
           +DG
Sbjct: 130 LDG 132

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++   ++F+  L +D    +LKD F + G ++   +  +   G+S+G G VKF S   
Sbjct: 3  SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEV 60
Query: 81 AGEAIKEMDGL 91
          A  A + M+G+
Sbjct: 61 AERACRMMNGM 71

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 33/63 (52%)
Query: 19 LLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          L SD      +FI  LS+D+ E  L +   Q G++  V+V+    T  S+G  F +F ++
Sbjct: 8  LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67
Query: 79 AAA 81
           AA
Sbjct: 68 EAA 70

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           KLFIG L  +  E  ++  F Q+G+++E  +I        + YGFV    + AA +AI+
Sbjct: 9  VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60
Query: 87 EM 88
           +
Sbjct: 61 NL 62

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          KLF+G +    +E  LK  F + G I E+ V+ DR+TG  +G  F+ + +  +A +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +F+  L +D    +LKD F + G ++   +  +   G+S+G G VKF S   A  A + M
Sbjct: 8  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 89 DGL 91
          +G+
Sbjct: 66 NGM 68

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 29  LFIGGLSYDTNETVLKDAFGQ-HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           LF+G L+ D ++ +L + F + +      KV+ D+ TG S+GYGFVKF  E     A+ E
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 88  MDGLVCRTSKDTDM 101
             G V   SK   +
Sbjct: 71  CQGAVGLGSKPVRL 84

>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Length = 229

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 26  RTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           R  L+IG L++ T +  L +A    G  +I+E+K   +R  GQS+G+  V   SEA+   
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEAS--- 124
Query: 84  AIKEMDGLVCR 94
           + K MD L  R
Sbjct: 125 SKKLMDLLPKR 135

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 38.5 bits (88), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 16/64 (25%), Positives = 35/64 (54%)
Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++++G + Y+  E  ++ AF   G I  +    D VT + +G+ FV++    AA  A+++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 88 MDGL 91
           + +
Sbjct: 74 XNSV 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	105
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-30
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-30
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-30
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-29
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-29
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-29
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-29
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-28
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-28
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-28
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-28
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-28
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-28
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-28
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-28
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-28
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-27
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-27
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-27
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-27
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-27
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-27
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-27
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-26
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-26
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-26
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-26
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-26
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-26
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-26
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-26
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-26
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-26
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-26
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-25
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-25
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-20
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-25
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-25
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-25
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-25
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-25
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-25
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-25
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-25
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	6e-25
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-25
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-25
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-24
2div_A	99	TRNA selenocysteine associated protein; structural	2e-24
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-24
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-24
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-24
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-24
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-24
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-24
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-21
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-22
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-23
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-23
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-22
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-23
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-23
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-23
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-23
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-23
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	9e-23
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-23
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-22
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-22
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-20
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-22
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-22
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-21
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-18
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-20
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-20
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-20
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-20
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-19
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-19
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-19
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-19
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-19
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-18
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-18
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-18
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-18
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-18
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-17
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-17
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-17
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-14
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-14
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	9e-14
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-13
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-13
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-13
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-12
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-11
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	4e-04

>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 =  104 bits (262), Expect = 1e-30
 Identities = 27/71 (38%), Positives = 42/71 (59%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            + +    L +  +    +E  L+  F ++G I  VK++CDR T QSRGYGFVKF S ++
Sbjct: 37  PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 81  AGEAIKEMDGL 91
           A +AI  ++G 
Sbjct: 97  AQQAIAGLNGF 107

>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 =  102 bits (256), Expect = 2e-30
 Identities = 23/70 (32%), Positives = 40/70 (57%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     
Sbjct: 2  SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 81 AGEAIKEMDG 90
          A  AI  M+ 
Sbjct: 62 AAAAIDNMNE 71

>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 =  102 bits (255), Expect = 8e-30
 Identities = 35/69 (50%), Positives = 48/69 (69%), Gaps = 1/69 (1%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +A+   KLFIGGL+ +TNE +LK  FG+HG I EV +I DR T +SRG+ F+ F + A A
Sbjct: 3  EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61

Query: 82 GEAIKEMDG 90
            A K+M+G
Sbjct: 62 KNAAKDMNG 70

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  101 bits (254), Expect = 2e-29
 Identities = 22/70 (31%), Positives = 39/70 (55%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     
Sbjct: 58  GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 117

Query: 81  AGEAIKEMDG 90
           A  AI  M+ 
Sbjct: 118 AAAAIDNMNE 127

>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 =  100 bits (252), Expect = 2e-29
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+GGLS+DTNE  L+  F ++G+I EV V+ DR T +SRG+GFV F +   A +A+  
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 88 MDG 90
          M+G
Sbjct: 74 MNG 76

>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 = 99.6 bits (249), Expect = 4e-29
 Identities = 22/68 (32%), Positives = 39/68 (57%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A 
Sbjct: 9  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68

Query: 83 EAIKEMDG 90
           AI  M+ 
Sbjct: 69 AAIDNMNE 76

>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 = 98.8 bits (247), Expect = 5e-29
 Identities = 22/64 (34%), Positives = 35/64 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + L+I GL   T +  L      +G+I+  K I D+ T + +GYGFV F S +AA +A+ 
Sbjct: 6  SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 87 EMDG 90
           +  
Sbjct: 66 ALKA 69

>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 = 98.3 bits (246), Expect = 1e-28
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            LF+G L+ + ++  L++AF      +   V+ D  TG SRGYGFV F S+  A  A+ 
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 87 EMDG 90
           M G
Sbjct: 62 SMQG 65

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 98.0 bits (245), Expect = 1e-28
 Identities = 25/69 (36%), Positives = 38/69 (55%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
             S   +F+G LS +     +  AF   G I + +V+ D  TG+S+GYGFV F ++  A
Sbjct: 2  PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

Query: 82 GEAIKEMDG 90
            AI++M G
Sbjct: 62 ENAIQQMGG 70

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 99.0 bits (247), Expect = 2e-28
 Identities = 27/86 (31%), Positives = 44/86 (51%)

Query: 5   NGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT 64
            G      S+ + R   D    T L +  L+Y T+   L+  F ++G + +V +  DR T
Sbjct: 26  GGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 85

Query: 65  GQSRGYGFVKFASEAAAGEAIKEMDG 90
            +SRG+ FV+F  +  A +A+  MDG
Sbjct: 86  KESRGFAFVRFHDKRDAEDAMDAMDG 111

>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 = 98.6 bits (246), Expect = 2e-28
 Identities = 24/86 (27%), Positives = 43/86 (50%)

Query: 5   NGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT 64
            G  +     R     ++ +    L + GLS  T E  L++ F ++G I +V ++ D+ +
Sbjct: 25  TGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS 84

Query: 65  GQSRGYGFVKFASEAAAGEAIKEMDG 90
            +SRG+ FV F +   A EA +  +G
Sbjct: 85  RRSRGFAFVYFENVDDAKEAKERANG 110

>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 = 97.3 bits (243), Expect = 3e-28
 Identities = 22/70 (31%), Positives = 40/70 (57%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          ++ +    L + GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F +   
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 81 AGEAIKEMDG 90
          A EA +  +G
Sbjct: 70 AKEAKERANG 79

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 96.9 bits (242), Expect = 6e-28
 Identities = 20/69 (28%), Positives = 34/69 (49%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D +    L +  L+Y T+   L+  F ++G + +V +  +  T   RG+ FV+F     A
Sbjct: 9  DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 82 GEAIKEMDG 90
           +A   MDG
Sbjct: 69 QDAEAAMDG 77

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 98.5 bits (245), Expect = 6e-28
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASE 78
              N R  +++G  S+ T +  L       G  +++E+K   +R  GQS+GY  V  ASE
Sbjct: 50  GLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASE 109

Query: 79  AAAGEAIKEMDG 90
            +  + ++ + G
Sbjct: 110 NSVHKLLELLPG 121

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 97.0 bits (242), Expect = 6e-28
 Identities = 26/69 (37%), Positives = 41/69 (59%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D ++   +F+G LS +     +K AF   G I + +V+ D  TG+S+GYGFV F ++  A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 82 GEAIKEMDG 90
            AI++M G
Sbjct: 71 ENAIQQMGG 79

>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 = 97.0 bits (242), Expect = 8e-28
 Identities = 32/62 (51%), Positives = 39/62 (62%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          TK+F+GGL Y T +  L+  F   G+I E  VI DR TG+SRGYGFV  A  AAA  A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77

Query: 87 EM 88
          + 
Sbjct: 78 DP 79

>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 = 98.0 bits (244), Expect = 1e-27
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            D    T L +  L+Y T+   L+  F ++G + +V +  DR T +SRG+ FV+F  +  
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124

Query: 81  AGEAIKEMDG 90
           A +A+  MDG
Sbjct: 125 AEDAMDAMDG 134

>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 = 99.0 bits (246), Expect = 2e-27
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASE 78
           +    R  L+IG L++ T +  L +A    G  +I+E+K   +R  GQS+G+  V   SE
Sbjct: 63  TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122

Query: 79  AAAGEAIKEMDG 90
           A++ + +  +  
Sbjct: 123 ASSKKLMDLLPK 134

>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 = 95.4 bits (238), Expect = 2e-27
 Identities = 14/68 (20%), Positives = 37/68 (54%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A S++ +++  L +      L   F ++G++++V ++ D+ T +S+G  F+ F  + +A 
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

Query: 83 EAIKEMDG 90
             + ++ 
Sbjct: 73 NCTRAINN 80

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 95.4 bits (238), Expect = 2e-27
 Identities = 22/70 (31%), Positives = 38/70 (54%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++   +LF+  LSY ++E  L+  F  +G + E+    D +T + +G+ FV F     
Sbjct: 3  SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 81 AGEAIKEMDG 90
          A +A  E+DG
Sbjct: 63 AVKAYAEVDG 72

>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 = 95.5 bits (238), Expect = 2e-27
 Identities = 21/66 (31%), Positives = 34/66 (51%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
             KLFIG +  + +E  LK  F + G+I E+ V+ DR TG  +G  F+ +    +A +A
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 85 IKEMDG 90
             +  
Sbjct: 72 QSALHE 77

>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 = 95.4 bits (238), Expect = 3e-27
 Identities = 30/70 (42%), Positives = 42/70 (60%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S+ N    +++GGL    +E +L + F Q G ++   +  DRVTGQ +GYGFV+F SE  
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69

Query: 81 AGEAIKEMDG 90
          A  AIK MD 
Sbjct: 70 ADYAIKIMDM 79

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 94.5 bits (236), Expect = 4e-27
 Identities = 20/64 (31%), Positives = 40/64 (62%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + L++G L ++  E +L+  F   G+I  + ++ D  TG+S+GYGF+ F+    A  A++
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 87 EMDG 90
          +++G
Sbjct: 66 QLNG 69

>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 = 93.4 bits (233), Expect = 1e-26
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV-TGQSRGYGFVKFASEAAAGEAI 85
          TK+ IG L+ +  +  + + F  +G+I  + +  +R+    S+GY +V+F +   A +A+
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 86 KEMDG 90
          K MDG
Sbjct: 65 KHMDG 69

>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 = 93.9 bits (234), Expect = 1e-26
 Identities = 21/74 (28%), Positives = 43/74 (58%)

Query: 17 TRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
            L   +    +L++G L ++  E +L+  F   G I  ++++ D  TG+S+GYGF+ F+
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76

Query: 77 SEAAAGEAIKEMDG 90
              A +A+++++G
Sbjct: 77 DSECAKKALEQLNG 90

>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 = 93.5 bits (233), Expect = 1e-26
 Identities = 21/70 (30%), Positives = 41/70 (58%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +   S   +F+G + Y+  E  LKD F + G ++  +++ DR TG+ +GYGF ++  +  
Sbjct: 3  AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 81 AGEAIKEMDG 90
          A  A++ ++G
Sbjct: 63 ALSAMRNLNG 72

>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 = 93.4 bits (233), Expect = 1e-26
 Identities = 23/70 (32%), Positives = 35/70 (50%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            A+    + +  LS DT ET L++ F   G I  + +  D+ TGQS+G+ F+ F     
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 81 AGEAIKEMDG 90
          A  AI  + G
Sbjct: 70 AARAIAGVSG 79

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 94.0 bits (234), Expect = 1e-26
 Identities = 24/64 (37%), Positives = 33/64 (51%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             LFI  L  +  +T L   F   G +I  KV  D+ T  S+ +GFV F +  +A  AIK
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100

Query: 87  EMDG 90
            M+G
Sbjct: 101 AMNG 104

>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 = 93.0 bits (232), Expect = 1e-26
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          R  L+IG L++ T +  L +A    G  +I+E+K   +R  GQS+G+  V   SEA++ +
Sbjct: 1  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 84 AIKEMDG 90
           +  +  
Sbjct: 61 LMDLLPK 67

>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 = 93.2 bits (232), Expect = 2e-26
 Identities = 21/80 (26%), Positives = 35/80 (43%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           SD      +FI  LS+D+ E  L +   Q G++  V+V+    T  S+G  F +F ++ A
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69

Query: 81  AGEAIKEMDGLVCRTSKDTD 100
           A + +              D
Sbjct: 70  AQKCLAAASLEAEGGGLKLD 89

>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 = 93.2 bits (232), Expect = 2e-26
 Identities = 20/70 (28%), Positives = 33/70 (47%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           +      LFI  L  +  +  L   F   G ++  KV  D+ T  S+ +GFV + +  +
Sbjct: 20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79

Query: 81 AGEAIKEMDG 90
          A  AI+ M+G
Sbjct: 80 AQAAIQSMNG 89

>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 = 92.3 bits (230), Expect = 4e-26
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + L + GL + T E  LK+ F   GE++ V+V  D  TG S+G+GFV+F       + + 
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 87 EM 88
          + 
Sbjct: 76 QR 77

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 91.6 bits (228), Expect = 6e-26
 Identities = 20/70 (28%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S +  + KLFI GL +   +  L++    HG + +++++ +R  G+ +G  +V++ +E+ 
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70

Query: 81 AGEAIKEMDG 90
          A +A+ +MDG
Sbjct: 71 ASQAVMKMDG 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 92.1 bits (229), Expect = 6e-26
 Identities = 18/64 (28%), Positives = 31/64 (48%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           ++    L+ +  ET LKD   ++GE+ EV+++    T +  G   V F S   A E +K
Sbjct: 7  KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 87 EMDG 90
           +  
Sbjct: 67 NLHL 70

>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 = 91.5 bits (228), Expect = 6e-26
 Identities = 18/64 (28%), Positives = 37/64 (57%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            +++G + YD  E  + D     G +I +K++ D  TG+S+GY F++F    ++  A++
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 87 EMDG 90
           ++G
Sbjct: 63 NLNG 66

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 91.2 bits (227), Expect = 1e-25
 Identities = 19/64 (29%), Positives = 35/64 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 87 EMDG 90
           ++G
Sbjct: 84 GLNG 87

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 92.6 bits (231), Expect = 1e-25
 Identities = 21/77 (27%), Positives = 40/77 (51%)

Query: 14  VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           V + R   ++   T L++  L     +  L   FG++G I++  ++ D++TG+ RG  FV
Sbjct: 77  VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136

Query: 74  KFASEAAAGEAIKEMDG 90
           ++     A EAI  ++ 
Sbjct: 137 RYNKREEAQEAISALNN 153

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 91.5 bits (228), Expect = 4e-25
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T L +  L  D  +  L   F   G I   +++ D  TG S GY FV F SE  +  A
Sbjct: 2  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 85 IKEMDG 90
          IK ++G
Sbjct: 62 IKVLNG 67

>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 = 92.6 bits (231), Expect = 1e-25
 Identities = 25/67 (37%), Positives = 38/67 (56%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+T L +  L  +  +   +  FG  GEI   K++ D++TGQS GYGFV +     A +A
Sbjct: 1  SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 85 IKEMDGL 91
          I  ++GL
Sbjct: 61 INTLNGL 67

>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 = 92.3 bits (230), Expect = 2e-25
 Identities = 28/77 (36%), Positives = 43/77 (55%)

Query: 14  VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           V + R  S +     L++ GL     +  L+  F Q+G II  +++ D+VTG SRG GF+
Sbjct: 76  VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135

Query: 74  KFASEAAAGEAIKEMDG 90
           +F     A EAIK ++G
Sbjct: 136 RFDKRIEAEEAIKGLNG 152

>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 = 92.2 bits (230), Expect = 2e-25
 Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 4/97 (4%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSRT----KLFIGGLSYDTNETVLKDAFGQHGEIIEV 56
           +Q LNG    ++ V+         S +     LF+G L+ + ++  L++AF      +  
Sbjct: 58  LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117

Query: 57  KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC 93
            V+ D  TG SRGYGFV F S+  A  A+  M G   
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL 154

>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 = 78.0 bits (193), Expect = 7e-20
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R  L++G L     E +LK  F   G I  +K++ D+   ++  Y FV++     A  A+
Sbjct: 1  RV-LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIAL 58

Query: 86 KEMDG 90
          + ++G
Sbjct: 59 QTLNG 63

>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 = 90.8 bits (226), Expect = 2e-25
 Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 4/74 (5%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             +S  K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A 
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79

Query: 81 AGEAIK----EMDG 90
            + +     E+D 
Sbjct: 80 VDKVLAQSRHELDS 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.5 bits (233), Expect = 2e-25
 Identities = 17/69 (24%), Positives = 37/69 (53%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
               +++++G + Y+  E  ++ AF   G I  + +  D VT + +G+ FV++    AA
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 82 GEAIKEMDG 90
            A+++M+ 
Sbjct: 84 QLALEQMNS 92

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 92.0 bits (229), Expect = 8e-25
 Identities = 16/76 (21%), Positives = 39/76 (51%)

Query: 15  RFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVK 74
              +L  +A +  ++++  +  D ++  +K  F   G+I    +  D  TG+ +GYGF++
Sbjct: 114 IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173

Query: 75  FASEAAAGEAIKEMDG 90
           +    ++ +A+  M+ 
Sbjct: 174 YEKAQSSQDAVSSMNL 189

>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 = 89.5 bits (223), Expect = 3e-25
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           +++G L Y      +K+ F Q G++  VK+I DR T + +G+GFV+   E+ + EAI +
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAK 61

Query: 88 MDG 90
          +D 
Sbjct: 62 LDN 64

>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 = 90.0 bits (224), Expect = 3e-25
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + +     LF+ GLS DT E  LK++F      +  +++ DR TG S+G+GFV F SE  
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEED 66

Query: 81 AGEAIKEMDG 90
          A  A + M+ 
Sbjct: 67 AKAAKEAMED 76

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 89.2 bits (222), Expect = 4e-25
 Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAA 81
          ++  + +FIG L  + +E +L D F   G I++  K++ D  TG S+GY F+ FAS  A+
Sbjct: 2  SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 82 GEAIKEMDG 90
            AI+ M+G
Sbjct: 62 DAAIEAMNG 70

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 88.7 bits (221), Expect = 4e-25
 Identities = 28/67 (41%), Positives = 42/67 (62%), Gaps = 4/67 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
          K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A   + +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 87 ---EMDG 90
             E+D 
Sbjct: 62 SRHELDS 68

>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 = 88.8 bits (221), Expect = 5e-25
 Identities = 24/63 (38%), Positives = 42/63 (66%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           K+F+GGLS+DT++  LKD F + GE+++  +  D  TG+SRG+GF+ F   A+  + + 
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

Query: 87 EMD 89
          + +
Sbjct: 72 QKE 74

>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 = 89.6 bits (223), Expect = 5e-25
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S A+   KLF+GGL + T +  L+  F Q+GE+++  ++ D+ T QSRG+GFVKF     
Sbjct: 11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70

Query: 81 AGEAIK----EMDG 90
           G  +      +DG
Sbjct: 71 VGTVLASRPHTLDG 84

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 88.3 bits (220), Expect = 5e-25
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
          K+F+GGLS +T    +K  F Q G++ +  ++ D+ T + RG+GFV F SE    +  + 
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 87 ---EMDGLVCRTSK 97
             E++  +    K
Sbjct: 61 HFHEINNKMVECKK 74

>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 = 88.8 bits (221), Expect = 6e-25
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S  +   K+F+GG+ ++  ET L++ F + G + EV +I D    + RG+GF+ F  E +
Sbjct: 5  SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64

Query: 81 AGEAIK----EMDGLVCRTSK 97
            +A+     ++ G      +
Sbjct: 65 VDQAVNMHFHDIMGKKVEVKR 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 = 89.7 bits (223), Expect = 7e-25
 Identities = 19/64 (29%), Positives = 35/64 (54%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            LF+ G+  +  E  + D F ++GEI  + +  DR TG  +GY  V++ +   A  A++
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 87 EMDG 90
           ++G
Sbjct: 83 GLNG 86

>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 = 88.8 bits (221), Expect = 9e-25
 Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            +F+GG+    +ET ++  F ++G + EVK+I DR TG S+GYGFV F ++    + ++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68

Query: 87 EM 88
            
Sbjct: 69 SQ 70

>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 = 88.9 bits (221), Expect = 1e-24
 Identities = 18/63 (28%), Positives = 34/63 (53%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           LF+  +  +  E  +++ F  +GEI  + +  DR TG S+GY  V++ +   A  A + 
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 88 MDG 90
          ++G
Sbjct: 88 LNG 90

>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 = 88.1 bits (219), Expect = 2e-24
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEA 79
            +     L++G L    +E  +  AF   GE +  VK+I +R+TG   GY FV+FA  A
Sbjct: 4  GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 80 AAGEAIKEMDG 90
           A + + +++G
Sbjct: 64 TAEKCLHKING 74

>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 = 88.1 bits (219), Expect = 2e-24
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ---SRGYGFVKFASEAAAGE 83
          + LFI  L++ T E  LK  F + G I    +   +       S G+GFV++     A +
Sbjct: 6  SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 84 AIKEMDG 90
          A+K++ G
Sbjct: 66 ALKQLQG 72

>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 = 88.5 bits (220), Expect = 2e-24
 Identities = 27/68 (39%), Positives = 42/68 (61%), Gaps = 4/68 (5%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           KLFIGGLS++T E  L++ + Q G++ +  V+ D  + +SRG+GFV F+S A    A+ 
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87

Query: 87 ----EMDG 90
               +DG
Sbjct: 88 ARPHSIDG 95

>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 = 92.4 bits (230), Expect = 2e-24
 Identities = 15/90 (16%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVIC 60
           +   + S      +     +    +   L +  L     +   ++     G +    ++ 
Sbjct: 74  INAFHQSRLRERELS----VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 61  DRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
              TGQS+GYGF ++  + +A  A  ++ G
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLG 159

>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 = 77.3 bits (191), Expect = 1e-18
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 21  SDANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
                   L +  L     +   L  A          ++ C +  GQ +G+  +++ +  
Sbjct: 179 PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAE 237

Query: 80  AAGEAIKEMDG 90
            A EA ++ DG
Sbjct: 238 MAEEAQQQADG 248

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 71.9 bits (177), Expect = 1e-16
 Identities = 16/81 (19%), Positives = 24/81 (29%), Gaps = 7/81 (8%)

Query: 14 VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           R         +R K+ I GL  D     + D    +  +    V       + +G  FV
Sbjct: 10 KRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFV 62

Query: 74 KFASEAAAGEAIKEMDGLVCR 94
             +   A  AI        R
Sbjct: 63 TLLNGEQAEAAINAFHQSRLR 83

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 87.8 bits (218), Expect = 2e-24
 Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 3/77 (3%)

Query: 15 RFTRLLSDANSR-TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
          R + + ++  S+  +L +  + +   +  L+  FGQ G+I++V++I +     S+G+GFV
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 74

Query: 74 KFASEAAAGEAIKEMDG 90
           F + A A  A +++ G
Sbjct: 75 TFENSADADRAREKLHG 91

>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 = 86.9 bits (216), Expect = 4e-24
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +   +   +F+G L     E +L + F Q G + +V +  DR  G+ + +GFV F    +
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPES 69

Query: 81 AGEAIKEMDG 90
             AI  ++G
Sbjct: 70 VSYAIALLNG 79

>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 = 87.3 bits (217), Expect = 5e-24
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L++     G++I  +++ D  +G SRG GF +  S       I 
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIG 84

Query: 87 EMDG 90
            +G
Sbjct: 85 HFNG 88

>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 = 87.3 bits (217), Expect = 5e-24
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
              +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  A
Sbjct: 4  GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 61

Query: 85 IKEMDG 90
          I++M+G
Sbjct: 62 IEKMNG 67

>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 = 88.8 bits (221), Expect = 5e-24
 Identities = 21/77 (27%), Positives = 34/77 (44%)

Query: 14  VRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFV 73
           +R            KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F 
Sbjct: 82  IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141

Query: 74  KFASEAAAGEAIKEMDG 90
           ++       +AI  ++G
Sbjct: 142 EYVDINVTDQAIAGLNG 158

>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 = 68.4 bits (168), Expect = 4e-16
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVK-----VICDRVTGQSRGYGFVKFAS 77
           ++R +L++G + +   E  + D F     +  +       +      Q + + F++F S
Sbjct: 2  GSAR-RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 78 EAAAGEAIKEMDG 90
               +A+   DG
Sbjct: 61 VDETTQAMA-FDG 72

>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 = 86.6 bits (215), Expect = 5e-24
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           +L +  + +   +  L+  FGQ G+I++V++I +     S+G+GFV F + A A  A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 73

Query: 87 EMDG 90
          ++ G
Sbjct: 74 KLHG 77

>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 = 88.4 bits (220), Expect = 7e-24
 Identities = 25/61 (40%), Positives = 43/61 (70%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+FIGGL++DT E  L++ FG++G + ++K++ D  TG+SRG+GF+ F   ++  E +K 
Sbjct: 5  KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 88 M 88
           
Sbjct: 65 Q 65

>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 = 82.6 bits (205), Expect = 1e-21
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 22  DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
           + +   K+F+GG+  D      ++ F Q G II+ +++ D+ TGQSRG+GFV + S  A 
Sbjct: 83  EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142

Query: 82  GEAIK----EMDGLVCRTSK 97
               +    +         +
Sbjct: 143 DRVCQNKFIDFKDRKIEIKR 162

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 85.8 bits (213), Expect = 9e-24
 Identities = 13/67 (19%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
            + +  ++  T    +  A   +    +  +++I D+ T Q+RG+ FV+ +S   A + 
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 85 IKEMDGL 91
          ++ +  L
Sbjct: 70 LQILQSL 76

>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 = 88.9 bits (221), Expect = 1e-23
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + +     L++G L  D  E +L + F   G I+ ++V  D +T +S GY +V F   A 
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69

Query: 81 AGEAIKEMDGLVC 93
          A  A+  M+  V 
Sbjct: 70 AERALDTMNFDVI 82

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 86.6 bits (215), Expect = 1e-22
 Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 6/97 (6%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSR----TKLFIGGLSYDTNETVLKDAFGQHGEIIEV 56
           +  +N  V     VR      D + R      +FI  L    +   L D F   G I+  
Sbjct: 74  LDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSC 133

Query: 57  KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC 93
           KV+CD     S+GYGFV F ++ AA  AI++M+G++ 
Sbjct: 134 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLL 168

>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 = 85.7 bits (213), Expect = 1e-23
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++  L    ++  L+ AF   G I   KV+ +   G+S+G+GFV F+S   A +A+ 
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73

Query: 87 EMDG 90
          EM+G
Sbjct: 74 EMNG 77

>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 = 87.6 bits (217), Expect = 2e-23
 Identities = 18/64 (28%), Positives = 34/64 (53%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             LF+  +  +  E  +++ F  +GEI  + +  DR TG S+GY  V++ +   A  A +
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 87  EMDG 90
            ++G
Sbjct: 133 ALNG 136

>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 = 84.9 bits (211), Expect = 2e-23
 Identities = 14/69 (20%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +A++R+ +++G + Y      L+  F   G +  V ++CD+ +G  +G+ +++F+ + + 
Sbjct: 3  EADARS-IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

Query: 82 GEAIKEMDG 90
            ++  +D 
Sbjct: 62 RTSL-ALDE 69

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 85.8 bits (213), Expect = 2e-23
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 13 SVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGF 72
          S   +  L      + +F+  L Y      LK+ F   G ++   ++ D+  G+SRG G 
Sbjct: 2  SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGT 60

Query: 73 VKFASEAAAGEAIKEMDG 90
          V F     A +AI   +G
Sbjct: 61 VTFEQSIEAVQAISMFNG 78

>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 = 88.2 bits (219), Expect = 2e-23
 Identities = 21/70 (30%), Positives = 34/70 (48%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
              +S  KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++     
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168

Query: 81  AGEAIKEMDG 90
             +AI  ++G
Sbjct: 169 TDQAIAGLNG 178

>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 = 65.8 bits (161), Expect = 7e-15
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVK-----VICDRVTGQSRGYGFVKFASEAAAG 82
          +L++G + +   E  + D F     +  +       +      Q + + F++F S     
Sbjct: 6  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 83 EAIKEMDG 90
          +A+   DG
Sbjct: 66 QAM-AFDG 72

>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 = 84.1 bits (209), Expect = 3e-23
 Identities = 20/60 (33%), Positives = 36/60 (60%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GGLS DT E  +++ FG  GE+  +++  D  T + RG+ F+ F  E    + +++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 86.9 bits (216), Expect = 3e-23
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG--QSRGYGFVKFASEAAA 81
          +   K+F+G +    +E  L++ F Q+G + E+ V+ DR     QS+G  FV F +  AA
Sbjct: 1  SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 82 GEAIKEMDG 90
           EA   +  
Sbjct: 61 LEAQNALHN 69

>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 = 84.6 bits (210), Expect = 3e-22
 Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            KLFIG +S    E  ++  F   G+I E +++     G SRG  FV F + A A  AIK
Sbjct: 96  RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIK 154

Query: 87  EMDG 90
            M  
Sbjct: 155 AMHQ 158

>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 = 84.6 bits (210), Expect = 4e-23
 Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +   +  KL +  L +  ++  +++ F + G + +  V  DR +G+S G   V F  +A 
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKAD 82

Query: 81 AGEAIKEMDG 90
          A +A+K+ +G
Sbjct: 83 ALKAMKQYNG 92

>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 = 84.6 bits (210), Expect = 4e-23
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L +  LSY   E  L++ F +   I     +     G+S+GY F++FAS   A EA+ 
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 87 EMDG 90
            + 
Sbjct: 72 SCNK 75

>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 = 85.0 bits (211), Expect = 4e-23
 Identities = 16/64 (25%), Positives = 29/64 (45%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++  LS    E  L   F +  E     +    +TG+ RG  F+ F ++  A +A+ 
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 87 EMDG 90
           ++G
Sbjct: 86 LVNG 89

>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 = 84.8 bits (210), Expect = 5e-23
 Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           + + R+ +++G + Y +    L+  F   G I  + ++CD+ +G  +GY +++FA   +
Sbjct: 32 KEIDKRS-VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS 90

Query: 81 AGEAIKEMDG 90
             A+  MD 
Sbjct: 91 VDAAV-AMDE 99

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 84.3 bits (209), Expect = 8e-23
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
              +  KL +  L +  ++  +++ F + G + +  V  DR +G+S G   V F   A 
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 88

Query: 81 AGEAIKEMDG 90
          A +A+K+  G
Sbjct: 89 ALKAMKQYKG 98

>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 = 83.5 bits (207), Expect = 9e-23
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 11 SHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGY 70
          SH +          +   L    LS++  E  LK+ F    EI           G+S+G 
Sbjct: 1  SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGI 55

Query: 71 GFVKFASEAAAGEAIKEMDG 90
           +++F SEA A + ++E  G
Sbjct: 56 AYIEFKSEADAEKNLEEKQG 75

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 87.4 bits (217), Expect = 9e-23
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 5/90 (5%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVIC 60
              L+G++  S  +R    +  A     L +  LS   +  +L+ AF Q G + +  V+ 
Sbjct: 75  KAELDGTILKSRPLR----IRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130

Query: 61  DRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
           D   G++ G GFV+FA++  A +A++    
Sbjct: 131 DD-RGRATGKGFVEFAAKPPARKALERCGD 159

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 79.0 bits (195), Expect = 2e-19
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
              R +LF+G L  D  E   K  F ++GE  EV +  D      RG+GF++  S   A
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71

Query: 82 GEAIKEMDG 90
            A  E+DG
Sbjct: 72 EIAKAELDG 80

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 83.0 bits (206), Expect = 1e-22
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          ++   ++F+  L +D    +LKD F + G ++   +  +   G+S+G G VKF S   A 
Sbjct: 5  SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62

Query: 83 EAIKEMDG 90
           A + M+G
Sbjct: 63 RACRMMNG 70

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 82.7 bits (205), Expect = 2e-22
 Identities = 24/70 (34%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S      KLF+G L+   +E  +   F   G I E  V+     G S+G  FVKF+S   
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTE 68

Query: 81 AGEAIKEMDG 90
          A  AI  + G
Sbjct: 69 AQAAIHALHG 78

>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 = 82.3 bits (204), Expect = 3e-22
 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           D      L++G LS D  E ++   F Q G     K+I +  +     Y FV+F     
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRD 67

Query: 81 AGEAIKEMDG 90
          A  A+  M+G
Sbjct: 68 AAAALAAMNG 77

>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 = 83.7 bits (207), Expect = 4e-22
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             L++G LS+ T E  + + F + G+I ++ +  D++   + G+ FV++ S A A  A++
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 87  EM-----DGLVCRTSKDT 99
            +     D  + RT  D 
Sbjct: 100 YINGTRLDDRIIRTDWDA 117

>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 = 84.7 bits (210), Expect = 4e-22
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +     KLFIGGLS++T +  L+  F Q G + +  V+ D  T +SRG+GFV +A+    
Sbjct: 9  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

Query: 82 GEAIK----EMDG 90
            A+     ++DG
Sbjct: 69 DAAMNARPHKVDG 81

>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 = 80.8 bits (200), Expect = 1e-20
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
           K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F    +  + +  
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

Query: 87  ---EMDGLVCRTSK 97
               ++G  C   K
Sbjct: 166 KYHTVNGHNCEVRK 179

>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 = 82.0 bits (203), Expect = 4e-22
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-VTGQSRGYGFVKFASEA 79
              + +K+ +  + +  N+  +++ F   GE+  V++      TG  RG+GFV F ++ 
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69

Query: 80 AAGEAIKEM 88
           A +A   +
Sbjct: 70 DAKKAFNAL 78

>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 = 82.0 bits (203), Expect = 5e-22
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           +      +F   L+       L+D F   G++ +V++I DR + +S+G  +V+F    +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79

Query: 81 AGEAIKEMDG 90
             AI  + G
Sbjct: 80 VPLAI-GLTG 88

>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 = 80.4 bits (199), Expect = 2e-21
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 11 SHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGY 70
          SH +      S++ +   LFIG L+ + +   LK A  +     ++ V+ D  TG +R +
Sbjct: 2  SHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKF 60

Query: 71 GFVKFASEAAAGEAIKEMDG 90
          G+V F S     +A+ E+ G
Sbjct: 61 GYVDFESAEDLEKAL-ELTG 79

>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 = 79.7 bits (197), Expect = 4e-21
 Identities = 20/89 (22%), Positives = 48/89 (53%), Gaps = 7/89 (7%)

Query: 5  NGSVRFSHSVRFTRLLSDANS-RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV 63
          +GS   +  +RF  +++ ++     ++ GG++    + +++  F   G+I+E++V  +  
Sbjct: 3  SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-- 60

Query: 64 TGQSRGYGFVKFASEAAAGEAIKEMDGLV 92
              +GY FV+F++  +A  AI  ++G  
Sbjct: 61 ----KGYSFVRFSTHESAAHAIVSVNGTT 85

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 78.9 bits (195), Expect = 6e-21
 Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 8/72 (11%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIE--------VKVICDRVTGQSRGYGFVKFASE 78
            +F+ GL  +     + D F Q G I          + +  DR TG+ +G   V F   
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 79 AAAGEAIKEMDG 90
           +A  AI   DG
Sbjct: 74 PSAKAAIDWFDG 85

>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 = 78.8 bits (195), Expect = 7e-21
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 6/65 (9%)

Query: 26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          R++LF+G L  D  E  ++  F ++G+  EV +       + +G+GF++  +   A  A 
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAK 68

Query: 86 KEMDG 90
           E+D 
Sbjct: 69 VELDN 73

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 80.7 bits (200), Expect = 8e-21
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S++ +   LFIG L+ + +   LK A  +     ++ V+ D  TG +R +G+V F S   
Sbjct: 8  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAED 66

Query: 81 AGEAIKEMDG 90
            +A+ E+ G
Sbjct: 67 LEKAL-ELTG 75

>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 = 74.9 bits (185), Expect = 1e-18
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             L    LS++  E  LK+ F    EI           G+S+G  +++F SEA A + ++
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADAEKNLE 154

Query: 87  EMDG 90
           E  G
Sbjct: 155 EKQG 158

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 78.2 bits (193), Expect = 2e-20
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEI--------IEVKVICDRVTGQSRGYGFV 73
          D +    +F+ GL  +     + D F Q G I          + +  DR TG+ +G   V
Sbjct: 3  DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 74 KFASEAAAGEAIKEMDG 90
           F    +A  AI   DG
Sbjct: 63 SFDDPPSAKAAIDWFDG 79

>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 = 76.1 bits (188), Expect = 7e-20
 Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++   KL+IG LS       L+  FG     +              GY FV +  +  
Sbjct: 3  SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNW 56

Query: 81 AGEAIKEMDG 90
          A  AI+ + G
Sbjct: 57 AIRAIETLSG 66

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 76.2 bits (188), Expect = 8e-20
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQH-GEIIEVKVICDRVTGQSRGYGFVKFASEA 79
            +     LF+G L+ D ++ +L + F +        KV+ D+ TG S+GYGFVKF  E 
Sbjct: 4  GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL 62

Query: 80 AAGEAIKEMDG 90
              A+ E  G
Sbjct: 63 EQKRALTECQG 73

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 75.8 bits (187), Expect = 9e-20
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +     T  +IG + +   E  L   F   G I++ K   +      +G  F+K+ +   
Sbjct: 23 APPRVTT-AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQ 75

Query: 81 AGEAIKEMDGLV 92
          A   I  +    
Sbjct: 76 AAVCIVALANFP 87

>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 = 75.8 bits (187), Expect = 1e-19
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S       LF+  L+    E +L+ AF Q G++  VK +        + Y F+ F     
Sbjct: 6  SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDG 57

Query: 81 AGEAIKEMDG 90
          A +A++EM+G
Sbjct: 58 AVKAMEEMNG 67

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 77.6 bits (191), Expect = 1e-19
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
               +  KL +  L +  ++  +++ F + G + +  V  DR +G+S G   V F   A 
Sbjct: 83  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 141

Query: 81  AGEAIKEMDG 90
           A +A+K+  G
Sbjct: 142 ALKAMKQYKG 151

>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 = 74.9 bits (185), Expect = 1e-19
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          +  K+F+G +S       L+  F + G +IE  V+        + Y FV    EA A  A
Sbjct: 8  NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAA 59

Query: 85 IKEMDG 90
          I +++G
Sbjct: 60 IAQLNG 65

>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 = 75.5 bits (186), Expect = 2e-19
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE--------VKVICDRVTGQSRGYGFV 73
          + +  + +++ GL+       L D F Q G +          + +  D+ TG+ +G   V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 74 KFASEAAAGEAIKEMDG 90
           +     A  A++  DG
Sbjct: 71 SYEDPPTAKAAVEWFDG 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 73.8 bits (182), Expect = 4e-19
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S   + TKL +G +S       L+  F ++G +IE  ++        + Y FV       
Sbjct: 5  SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAED 56

Query: 81 AGEAIKEMDG 90
          A EAI+ +D 
Sbjct: 57 AVEAIRGLDN 66

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.3 bits (183), Expect = 4e-19
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             N+  ++++G L  D     ++D F ++G I ++ +   R       + FV+F     
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRD 73

Query: 81 AGEAIKEMDG 90
          A +A+   DG
Sbjct: 74 AEDAVYGRDG 83

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 73.8 bits (182), Expect = 5e-19
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++   KLFIG L  +  E  ++  F Q+G+++E  +I        + YGFV    + A
Sbjct: 3  SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54

Query: 81 AGEAIKEMDG 90
          A +AI+ +  
Sbjct: 55 AEDAIRNLHH 64

>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 = 78.1 bits (193), Expect = 5e-19
 Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           T + +  L    N+  +   F   G II V V       ++  +  ++FA    A  AI 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAIT 99

Query: 87  EMDGLV 92
           +   +V
Sbjct: 100 KTHKVV 105

>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 = 76.2 bits (188), Expect = 3e-18
 Identities = 17/96 (17%), Positives = 40/96 (41%), Gaps = 7/96 (7%)

Query: 1   MQWLNG---SVRFS-HSVRFTRLLSDANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIE 55
              + G     + S    +  R  S      ++ I  LS +  +E +L+++F   G I +
Sbjct: 181 GLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK 240

Query: 56  VKVICDR-VTGQSRGYGFVKFASEAAAGEAIKEMDG 90
           + +   +     +    F+ F ++ +A  A+ +M+ 
Sbjct: 241 INIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNR 275

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 75.8 bits (187), Expect = 4e-18
 Identities = 7/67 (10%), Positives = 24/67 (35%)

Query: 24  NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
            +   L++        +  ++D       +     +       SR + ++   S+  A  
Sbjct: 115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARY 174

Query: 84  AIKEMDG 90
            +++++G
Sbjct: 175 CVEKLNG 181

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 73.5 bits (181), Expect = 9e-19
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
            ++G L ++T +  +   F     I  V+++ D+ T + +G+ +V+F    +  EA+  
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74

Query: 88 MDG 90
           DG
Sbjct: 75 YDG 77

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.1 bits (180), Expect = 1e-18
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 8/70 (11%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
              S T+LF+     D  E+ L + FG  G + EVK++         G+ FV+F    +
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAES 77

Query: 81 AGEAIKEMDG 90
          A +AI+E+ G
Sbjct: 78 AAKAIEEVHG 87

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.9 bits (177), Expect = 3e-18
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             +S   L++  L   T+E +++  F         +V       + R Y FV F++   
Sbjct: 10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNRED 63

Query: 81 AGEAIKEMDG 90
          A EA+K ++G
Sbjct: 64 AVEAMKALNG 73

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 71.5 bits (176), Expect = 4e-18
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + +F+G  + D  E  L++ F Q+G++++V      +    R + FV FA +  A     
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 87 EM---DGLVCRTSK 97
          E     G+    S 
Sbjct: 61 EDLIIKGISVHISN 74

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 71.7 bits (176), Expect = 4e-18
 Identities = 15/61 (24%), Positives = 28/61 (45%)

Query: 30 FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD 89
           I        +  L   F + G+++ ++   D  TG+++G+ FV+  S   A + IK   
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 90 G 90
          G
Sbjct: 76 G 76

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 71.1 bits (175), Expect = 6e-18
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          +K+F+G  + D     L+  F Q+GE+++V +         R + FV FA +  A     
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG 66

Query: 87 EM---DGLVCRTSK 97
          E     G+    S 
Sbjct: 67 EDLIIKGISVHISN 80

>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 = 76.0 bits (186), Expect = 7e-18
 Identities = 20/64 (31%), Positives = 35/64 (54%)

Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           LF+  ++YDT E+ L+  F  +G I  + ++  + +G+ RGY F+++  E     A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 89  DGLV 92
           DG  
Sbjct: 165 DGKK 168

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.2 bits (175), Expect = 7e-18
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+++G L     +  L+ AF  +G +  V +  +       G+ FV+F     A +A++ 
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 88 MDG 90
          +DG
Sbjct: 57 LDG 59

>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 = 70.9 bits (174), Expect = 2e-17
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          L    +R  L+I  L Y      + D FG++G I +++V     T ++RG  +V +    
Sbjct: 3  LPPEVNRI-LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIF 58

Query: 80 AAGEAIKEMDG 90
           A  A+  + G
Sbjct: 59 DAKNAVDHLSG 69

>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 = 70.0 bits (172), Expect = 2e-17
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 6/64 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T+L++GGL  +T+   L   F + G I  +  +      +   + ++++ S  AA  A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

Query: 87 EMDG 90
          +M G
Sbjct: 72 KMRG 75

>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 = 70.0 bits (172), Expect = 2e-17
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 8/64 (12%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++ G   D   T+L+ AF   G II++ +         R   FV +    +A +A+ 
Sbjct: 16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 67

Query: 87 EMDG 90
          E++G
Sbjct: 68 ELNG 71

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 71.1 bits (174), Expect = 2e-17
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            K+++G L  + N+T L+ AFG +G +  V V  +       G+ FV+F     A +A++
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128

Query: 87  EMDG 90
           E+DG
Sbjct: 129 ELDG 132

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 68.5 bits (168), Expect = 5e-17
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           D    T L++GGL     ET L++ F Q GEI  + V+        +   F++FA+  A
Sbjct: 8  EDKTITT-LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQA 60

Query: 81 AGEAIKEM 88
          A  A ++ 
Sbjct: 61 AEVAAEKS 68

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.1 bits (164), Expect = 3e-16
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEII-EVKVICD-RVTGQSRGYGFVKFASEAAAGEA 84
           +LFIGG+        + +   +  E + +V V        ++RG+ FV++ S  AA  A
Sbjct: 9  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 85 IKEMDG 90
           +++  
Sbjct: 69 RRKLMP 74

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 70.3 bits (171), Expect = 4e-16
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 29 LFIGGLSYDTNETVLKDA----FGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          ++I  L+    +  LK +    F Q G+I+++ V     + + RG  FV F   ++A  A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68

Query: 85 IKEMDG 90
          ++ M G
Sbjct: 69 LRSMQG 74

>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 = 56.4 bits (135), Expect = 5e-11
 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 30  FIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD 89
           F+  L  +TNE +L   F Q     EV+++  R         FV+F +E  AG A   + 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

Query: 90  G 90
           G
Sbjct: 266 G 266

>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 = 66.1 bits (162), Expect = 7e-16
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT-GQSRGYGFVKFASEAAAGEAIK 86
            F+G L YD  E  +K+ F     I  V++  +     + +G+G+ +F    +   A+ 
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78

Query: 87 EMDG 90
           ++ 
Sbjct: 79 SLNE 82

>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 = 64.6 bits (158), Expect = 3e-15
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD-RVTGQSRGYGFVKFASEAAAGEAIK 86
            F+G L YD  E  +K+ F     I  V++  +     + +G+G+ +F    +   A+ 
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 87 EMDG 90
           ++ 
Sbjct: 76 -LNE 78

>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 = 65.6 bits (160), Expect = 3e-15
 Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEI--IEVKVICDRV---TGQSRGYGFVKFASEAAA 81
            ++++  L+    E  LK  FG++ +      +++ D      G+ +G  F+   +E AA
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 82  GEAIKEMDG 90
            +A+KE +G
Sbjct: 106 AKALKEANG 114

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 64.6 bits (158), Expect = 3e-15
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 6  GSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDT-NETVLKDAFGQHGEIIEVKVICDRVT 64
          GS    H      +   ++ +++LFIG L     ++  L   F  +G I+++ +      
Sbjct: 2  GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------ 55

Query: 65 GQSRGYGFVKFASEAAAGEAIKEMDG 90
               +GF++F +  +  +AI+    
Sbjct: 56 --KNAFGFIQFDNPQSVRDAIEXESQ 79

>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 = 63.8 bits (156), Expect = 5e-15
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 8/70 (11%)

Query: 25 SRTKLFIGGLSYDTNETVLKDA----FGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + T ++I  L+    +  LK +    F + G+I+++ V     + + RG  FV F   ++
Sbjct: 8  NHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSS 63

Query: 81 AGEAIKEMDG 90
          A  A++ M G
Sbjct: 64 ATNALRSMQG 73

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 65.9 bits (160), Expect = 7e-15
 Identities = 8/62 (12%), Positives = 20/62 (32%)

Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           L       +  E    +   + G      V       +    G +++ S++ A E +  +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 89  DG 90
           + 
Sbjct: 186 NH 187

>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 = 55.5 bits (133), Expect = 5e-11
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 23 ANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          A+S   L + GL     N   + + F  +G + +VK +  +      G   V+ A   A 
Sbjct: 2  ADSPV-LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAV 55

Query: 82 GEAIKEMDGLVCRTSK 97
            AI  ++       K
Sbjct: 56 DRAITHLNNNFMFGQK 71

>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 = 63.2 bits (154), Expect = 1e-14
 Identities = 18/90 (20%), Positives = 44/90 (48%), Gaps = 12/90 (13%)

Query: 5  NGSVRFSHSVRFTRLLSDANSR---TKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVIC 60
          +GS   S  ++ + + +  + +   +++FIG L+     ++ ++  F ++G +    V  
Sbjct: 3  SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-- 60

Query: 61 DRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
                 +GY FV++++E  A  A+   +G
Sbjct: 61 ------HKGYAFVQYSNERHARAAVLGENG 84

>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 = 62.3 bits (152), Expect = 2e-14
 Identities = 12/70 (17%), Positives = 24/70 (34%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S     T + +  + +  +   + D F  +  I     +     G   G   V F S   
Sbjct: 10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69

Query: 81 AGEAIKEMDG 90
          A  A+ +++ 
Sbjct: 70 ATAAVIDLND 79

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 62.1 bits (151), Expect = 2e-14
 Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
              KL I  +       VL     Q+G +   + +             V ++S+  A +
Sbjct: 13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQ 69

Query: 84 AIKEMDG 90
          A+ +++G
Sbjct: 70 ALDKLNG 76

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 62.2 bits (152), Expect = 2e-14
 Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 9/71 (12%)

Query: 21 SDANSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
           +   +++LFIG L   + ++  L   F  +G I+++ +           +GF++F +  
Sbjct: 5  HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQ 56

Query: 80 AAGEAIKEMDG 90
          +  +AI+    
Sbjct: 57 SVRDAIECESQ 67

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 3e-14
 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D  +R+ ++I G   D     +K+     G+++ +++         +G  FV F S  +A
Sbjct: 8  DVKNRS-VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESA 65

Query: 82 GEAIKEMD 89
           + ++   
Sbjct: 66 KKFVETPG 73

>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 = 61.6 bits (150), Expect = 3e-14
 Identities = 12/70 (17%), Positives = 24/70 (34%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S     T + +  + +  +   + D F  +  I     +     G   G   V F S   
Sbjct: 10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69

Query: 81 AGEAIKEMDG 90
          A  A+ +++ 
Sbjct: 70 ATAAVIDLND 79

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 61.8 bits (150), Expect = 5e-14
 Identities = 10/76 (13%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDA----FGQHGEIIEVKVICDRVTGQSRGYGFVKFA 76
                  + I  ++ +  +  L+          G+I+++ V    ++  + G  ++ FA
Sbjct: 24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNSGKAYIVFA 80

Query: 77 SEAAAGEAIKEMDGLV 92
          ++ +A   ++   G  
Sbjct: 81 TQESAQAFVEAFQGYP 96

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 61.3 bits (149), Expect = 6e-14
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 27 TKLFIGGL------SYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + + +  +        +  + V+   F + G+I           G+++GY F+++AS A 
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAH 73

Query: 81 AGEAIKEMDG 90
          A +A+K  DG
Sbjct: 74 AVDAVKNADG 83

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 61.0 bits (148), Expect = 9e-14
 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
            R ++ +  L    +   LKD   ++             T    G G ++F SE    E
Sbjct: 26 AKRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVE 82

Query: 84 AIKEMDG 90
          A++ ++ 
Sbjct: 83 ALERLNN 89

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 60.6 bits (147), Expect = 1e-13
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           S  ++ + GL    +   LKD   + G++    V          G G V+F  +     
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTY 65

Query: 84 AIKEMDG 90
          A++++D 
Sbjct: 66 AVRKLDN 72

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 59.5 bits (144), Expect = 2e-13
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ-SRGYGFVKFASEAA 80
           A     +++G L  D   + LK A  + G       +  R+T Q  R   F+ +   AA
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELG------SVPLRLTWQGPRRRAFLHYPDSAA 68

Query: 81 AGEAIKEMDGL 91
          A +A+  + GL
Sbjct: 69 AQQAVSCLQGL 79

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 59.6 bits (144), Expect = 3e-13
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD--RVTGQSRGYGFVKFASE 78
            + SR K+F+GGL  D +E  +  +F + G ++         +     +GY F+ F  E
Sbjct: 4  GSSGSR-KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62

Query: 79 AAAGEAIKE 87
          ++    I  
Sbjct: 63 SSVQALIDA 71

>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 = 59.0 bits (143), Expect = 3e-13
 Identities = 13/90 (14%), Positives = 31/90 (34%), Gaps = 14/90 (15%)

Query: 23  ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
           ++  + + +  L  D+N   + D    +     +K        +++   FV   +   A 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYD----LKYC---YVDRNKRTAFVTLLNGEQAQ 54

Query: 83  EAIKEMDG-------LVCRTSKDTDMLSTG 105
            AI+           L+ +      +L +G
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTDALLCSG 84

>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 = 59.1 bits (143), Expect = 5e-13
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           S  ++ + GL    +   LKD   + G++    V          G G V+F  +     
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTY 66

Query: 84 AIKEMDG 90
          A++++D 
Sbjct: 67 AVRKLDN 73

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.5 bits (142), Expect = 6e-13
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 5/69 (7%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++    +F+ G     +   L + F   G +  V +  D+  G    +  V+     A
Sbjct: 3  SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKDKG---VFAIVEMGDVGA 57

Query: 81 AGEAIKEMD 89
              + +  
Sbjct: 58 REAVLSQSQ 66

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 57.8 bits (140), Expect = 7e-13
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 27 TKLFIGGL------SYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + + +  +        +  + V+   F + G+I       +   G+++GY F+++AS A 
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59

Query: 81 AGEAIKEMDG 90
          A +A+K  DG
Sbjct: 60 AVDAVKNADG 69

>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 = 59.9 bits (145), Expect = 1e-12
 Identities = 10/64 (15%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             L +  +    +E  LK  F  +G +++      +   + R    ++  S   A +A+ 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQALI 176

Query: 87  EMDG 90
           ++  
Sbjct: 177 DLHN 180

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 55.7 bits (134), Expect = 5e-11
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 29 LFIGGLSYDT-NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          L +  L+ +      L   FG +G++  VK++ +      +    V+ A    A  A+  
Sbjct: 6  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 88 MDG 90
          ++G
Sbjct: 61 LNG 63

>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 = 57.9 bits (140), Expect = 1e-12
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 25 SRTKLFIGGLSYD-TNETVLK--DAFGQHGEIIEVKVICDRVTGQSR---GYGFVKFASE 78
           +  +F+ GLS    +  VLK  + FG+ G+I +V +        S+      +V +   
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 79 AAAGEAIKEMDG 90
            A  AI+ ++ 
Sbjct: 74 EDALRAIQCVNN 85

>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 = 59.6 bits (144), Expect = 2e-12
 Identities = 10/62 (16%), Positives = 24/62 (38%), Gaps = 4/62 (6%)

Query: 29  LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
           L +  +    +E  LK  F  +G +++          + R    ++  S   A +A+ ++
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALIDL 209

Query: 89  DG 90
             
Sbjct: 210 HN 211

>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 = 57.3 bits (138), Expect = 1e-11
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 20 LSDANSRTKLFIGGLSYDT-NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          L+ A +   L +  L+ +      L   FG +G++  VK++ +      +    V+ A  
Sbjct: 29 LAGAGNSV-LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADG 82

Query: 79 AAAGEAIKEMDG 90
            A  A+  ++G
Sbjct: 83 NQAQLAMSHLNG 94

>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 = 57.1 bits (138), Expect = 3e-12
 Identities = 11/66 (16%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+T +    L   T    +++ F + G +  V +              V+F     A +A
Sbjct: 9  SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKA 62

Query: 85 IKEMDG 90
           + +  
Sbjct: 63 FRHLAY 68

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 57.2 bits (138), Expect = 4e-12
 Identities = 16/72 (22%), Positives = 33/72 (45%)

Query: 15 RFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVK 74
          + +R  S   +   +++ GL ++     + D F +   + +   I     G++ G GFV+
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73

Query: 75 FASEAAAGEAIK 86
          F +EA    A+ 
Sbjct: 74 FRNEADYKAALC 85

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 56.8 bits (137), Expect = 6e-12
 Identities = 13/66 (19%), Positives = 28/66 (42%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           +D+ +   + + GL +   +  +   F     +     +     G+  G  FV+FAS+  
Sbjct: 37  ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQEL 96

Query: 81  AGEAIK 86
           A +A+ 
Sbjct: 97  AEKALG 102

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 55.5 bits (134), Expect = 9e-12
 Identities = 15/66 (22%), Positives = 29/66 (43%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           D  +   + + GL +  ++  +   F     +     +     G+S G  FV+FAS+  
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 81 AGEAIK 86
          A +A+K
Sbjct: 70 AEKALK 75

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 55.5 bits (134), Expect = 1e-11
 Identities = 8/66 (12%), Positives = 21/66 (31%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
             +++    I  + +   +  +               +     GQ  G   V+F +E  
Sbjct: 10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDD 69

Query: 81 AGEAIK 86
          A ++ +
Sbjct: 70 ARKSER 75

>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 = 54.7 bits (132), Expect = 1e-11
 Identities = 12/72 (16%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKV-----ICDRVTGQSRGYGFVKFASEAAAG 82
          +L++G + +   E  + D F     +  +       +      Q + + F++F S     
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 83 EAIKEMDGLVCR 94
          +A+   DG++ +
Sbjct: 68 QAM-AFDGIIFQ 78

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 57.5 bits (138), Expect = 2e-11
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 16/78 (20%)

Query: 22  DANSRTKLFIGGLSYDTN---------ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGF 72
              ++T L++GG+    N         E+ ++  F + G+I  ++ +      +S+  GF
Sbjct: 131 RKKNKT-LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGF 183

Query: 73  VKFASEAAAGEAIKEMDG 90
           VKF  +A A  A + M  
Sbjct: 184 VKFKYQANAEFAKEAMSN 201

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.4 bits (128), Expect = 1e-10
 Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          +  GGL    +   L     + G +  + +  ++       Y F ++ +   +  A   +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83

Query: 89 DG 90
          +G
Sbjct: 84 NG 85

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 51.9 bits (125), Expect = 2e-10
 Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S   +   + + G  ++  E  + +        + ++++ +   G   GY FV F++E  
Sbjct: 5  SSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEE 62

Query: 81 AGEAIK 86
            +A+K
Sbjct: 63 VKQALK 68

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 2/86 (2%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVIC 60
           M  + G  +       +     + +   + + GL Y   E  + + F      + V +  
Sbjct: 21  MASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI 79

Query: 61  DRVTGQSRGYGFVKFASEAAAGEAIK 86
               G+  G   V+FA+   A  A+ 
Sbjct: 80  GP-DGRVTGEADVEFATHEEAVAAMS 104

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 50.5 bits (121), Expect = 7e-10
 Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 7/66 (10%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S   + I GL     E  L +A  + G I  V V+        +    V+F     A  A
Sbjct: 21 SPV-VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNA 73

Query: 85 IKEMDG 90
          +     
Sbjct: 74 VNYAAD 79

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 50.5 bits (121), Expect = 1e-09
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           + +    + + G+ +   E  ++D F     +  V ++ D   G++ G G VKF S   
Sbjct: 12 INPDDLY-VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQD 68

Query: 81 AGEAIK 86
            EA+K
Sbjct: 69 TFEALK 74

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.7 bits (119), Expect = 1e-09
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            + +   + + GL Y   E  + + F      + V +      G+  G   V+FA+   
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHED 67

Query: 81 AGEAIK 86
          A  A+ 
Sbjct: 68 AVAAMA 73

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 48.7 bits (116), Expect = 4e-09
 Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 7/70 (10%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S   SR  + I  L  D  E  +       G++  + ++      + +   F++  +E A
Sbjct: 12 SGVPSRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEA 64

Query: 81 AGEAIKEMDG 90
          A   +     
Sbjct: 65 ANTMVNYYTS 74

>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 = 48.3 bits (115), Expect = 7e-09
 Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 7/66 (10%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S   + + GL     E  L +A  + G I  V ++        +    V+F +  +A E 
Sbjct: 15 SPV-VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKEC 67

Query: 85 IKEMDG 90
          +     
Sbjct: 68 VTFAAD 73

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 5  NGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVK---VICD 61
          +GS     S    + LS  N    + + GL +      +   FGQH  I   K   +   
Sbjct: 3  SGSSGGGTSNEVAQFLSKENQVI-VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 62 RVTGQSRGYGFVKFASEAAAGEAIK 86
             G+  G  FV FA E  A  A++
Sbjct: 62 YPDGRPTGDAFVLFACEEYAQNALR 86

>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 = 47.6 bits (113), Expect = 2e-08
 Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 7/64 (10%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          SR  + I  L  D  E  +       G++  + ++        +   F++  +E AA   
Sbjct: 31 SRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTM 83

Query: 85 IKEM 88
          +   
Sbjct: 84 VNYY 87

>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 = 44.8 bits (106), Expect = 1e-07
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A SR  L I  L  +  ET +       G++  + ++      + +   F++ A+E AA 
Sbjct: 13 APSRV-LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAI 65

Query: 83 EAIKEMDG 90
            +     
Sbjct: 66 TMVNYYSA 73

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 44.5 bits (105), Expect = 2e-07
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 40 ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          E V  +   ++GE+ E+ V CD +     G  +VKF  E  A +A+ +++ 
Sbjct: 41 EEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 44.5 bits (105), Expect = 2e-07
 Identities = 10/67 (14%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVI--CDRVTGQSRGYGFVKFASEA 79
          + +    +   GL +      + + F           I       G+ RG   ++  SE 
Sbjct: 7  EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66

Query: 80 AAGEAIK 86
             +A++
Sbjct: 67 DVQKALE 73

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 43.5 bits (102), Expect = 7e-07
 Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 5/91 (5%)

Query: 1  MQWLNGSVRFSHSVRFTRLLSDANSRTKLF-IGGLSYDTNETVLKDAFGQHGEIIEVKVI 59
          +Q  N ++  S +     +     S      +  L Y     VL   F + G ++++   
Sbjct: 2  VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 61

Query: 60 CDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
                Q      +++A   +A  A   +DG
Sbjct: 62 TKNNQFQ----ALLQYADPVSAQHAKLSLDG 88

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 1e-06
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 29 LFIGGLSYDTNETVLKDAFGQ---HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          + + GL +  +   +++       H  +  V  I  R  G+  G  FV+  SE     A+
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78

Query: 86 K 86
          K
Sbjct: 79 K 79

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 43.6 bits (102), Expect = 1e-06
 Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 5/91 (5%)

Query: 1   MQWLNGSVRFSHSVRFTRLLSDANSRTKLF-IGGLSYDTNETVLKDAFGQHGEIIEVKVI 59
           +Q  N ++  S +     +     S      +  L Y     VL   F + G ++++   
Sbjct: 20  VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79

Query: 60  CDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
                 Q      +++A   +A  A   +DG
Sbjct: 80  TKNNQFQ----ALLQYADPVSAQHAKLSLDG 106

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 43.3 bits (101), Expect = 2e-06
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
             ++I G   D     +K+     G+++ +++         +G  FV F S  +A + ++
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 168

Query: 87  EMD 89
              
Sbjct: 169 TPG 171

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 41.9 bits (98), Expect = 3e-06
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQ---HGEIIEVKVICDRVTGQSRGYGFVKFAS 77
            +      + + GL +  +   +++       H     V  I  R  G+  G  FV+  S
Sbjct: 39  PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFVELGS 97

Query: 78  EAAAGEAIK 86
           E     A+K
Sbjct: 98  EDDVKMALK 106

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 43 LKDAFGQHGEIIEVKV--ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          ++D   ++G +  +++    D V     G  FV+F S     +A++ + G
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 36.9 bits (86), Expect = 2e-04
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 43 LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          + +   +HG +I + V  D+ + Q  G  +VK  S AAA  A+  + G
Sbjct: 34 VIEECNKHGGVIHIYV--DKNSAQ--GNVYVKCPSIAAAIAAVNALHG 77

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 43 LKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
          L+    + G+I ++ ++ DR      G   V F     A   I+ +DG
Sbjct: 43 LRVECSKFGQIRKL-LLFDR---HPDGVASVSFRDPEEADYCIQTLDG 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.9
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.9
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.89
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.89
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.89
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.89
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.89
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.89
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.88
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.88
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.88
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.88
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.88
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.88
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.88
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.88
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.88
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.88
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.88
2div_A	99	TRNA selenocysteine associated protein; structural	99.88
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.87
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.87
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.87
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.87
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.87
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.87
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.87
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.87
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.87
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.87
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.87
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.87
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.87
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.87
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.86
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.86
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.86
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.86
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.86
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.85
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.85
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.85
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.85
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.85
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.84
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.84
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.84
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.84
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.84
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.84
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.84
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.84
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.84
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.84
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.84
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.84
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.84
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.83
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.83
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.83
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.83
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.83
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.83
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.83
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.83
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.83
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.82
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.82
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.82
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.82
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.82
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.82
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.82
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.82
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.81
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.81
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.81
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.81
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.81
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.81
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.81
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.8
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.8
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.8
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.8
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.79
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.79
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.79
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.78
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.78
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.77
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.76
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.76
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.76
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.74
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.74
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.74
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.74
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.74
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.73
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.72
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.7
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.68
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.67
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.67
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.67
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.66
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.62
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.59
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.51
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.43
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.36
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.18
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.16
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.78
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.29
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.24
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.12
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.73
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.7
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.55
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.0
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.47
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.35
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.69
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.67

>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=99.92  E-value=9.3e-25  Score=122.15  Aligned_cols=80  Identities=29%  Similarity=0.482  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..+.|+.|+|..++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999998774

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.91  E-value=8.7e-24  Score=120.23  Aligned_cols=81  Identities=23%  Similarity=0.233  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++|++.|||..+.|+.++|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34678999999999999999999999999999999999989999999999999999999999999999999999999987


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        84 ~   84 (110)
T 3s8s_A           84 I   84 (110)
T ss_dssp             S
T ss_pred             C
Confidence            5

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.90  E-value=5.8e-23  Score=111.50  Aligned_cols=82  Identities=28%  Similarity=0.455  Sum_probs=77.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999999887999999999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.90  E-value=9.6e-23  Score=113.69  Aligned_cols=83  Identities=25%  Similarity=0.334  Sum_probs=77.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE--------VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      .....++|||+|||+++++++|+++|.+||.+..        +.+..++.+|.++|||||+|.+.++|+.|++.|+|..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456789999999999999999999999999999        99999988999999999999999999999999999999


Q ss_pred             eeeeeeeccCC
Q 034039           94 RTSKDTDMLST  104 (105)
Q Consensus        94 ~~~~~~v~~~~  104 (105)
                      .|+.++|..++
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999998874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.7e-22  Score=111.68  Aligned_cols=83  Identities=27%  Similarity=0.378  Sum_probs=78.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        91 ~a~   93 (95)
T 2cqc_A           91 GPS   93 (95)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=1.3e-22  Score=112.07  Aligned_cols=82  Identities=17%  Similarity=0.354  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.+++||||+|.+.++|+.|++.|||..+.|+.++|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            45678999999999999999999999999999999999988899999999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.89  E-value=2.2e-22  Score=108.75  Aligned_cols=78  Identities=31%  Similarity=0.489  Sum_probs=74.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+|||+|||+++++++|+++|..||.+..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|..++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   79 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA   79 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecC
Confidence            579999999999999999999999999999999998899999999999999999999999999999999999998875

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.89  E-value=2.5e-22  Score=114.74  Aligned_cols=83  Identities=25%  Similarity=0.402  Sum_probs=78.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       101 ~a~  103 (115)
T 2cpz_A          101 LKR  103 (115)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            865

>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=99.89  E-value=1.8e-22  Score=110.03  Aligned_cols=81  Identities=32%  Similarity=0.507  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|..+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        84 ~   84 (87)
T 3bs9_A           84 T   84 (87)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.89  E-value=1.1e-22  Score=116.58  Aligned_cols=83  Identities=31%  Similarity=0.440  Sum_probs=77.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            864

>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=99.89  E-value=1.1e-22  Score=118.57  Aligned_cols=83  Identities=28%  Similarity=0.396  Sum_probs=78.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       122 ~a~  124 (129)
T 2kxn_B          122 FSI  124 (129)
T ss_dssp             CCS
T ss_pred             Eec
Confidence            875

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.89  E-value=3.5e-23  Score=113.74  Aligned_cols=78  Identities=27%  Similarity=0.415  Sum_probs=72.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+|||+|||+++++++|+++|..||  .+..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.++|..+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999998899999999999999999999999999999999999998764

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=2.4e-22  Score=113.07  Aligned_cols=84  Identities=36%  Similarity=0.504  Sum_probs=78.5

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34567789999999999999999999999999999999998888999999999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        90 ~~a~   93 (105)
T 1x5u_A           90 NKAS   93 (105)
T ss_dssp             EETT
T ss_pred             EECC
Confidence            8764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=5.2e-22  Score=110.82  Aligned_cols=82  Identities=24%  Similarity=0.561  Sum_probs=77.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        92 ~a~   94 (100)
T 2do4_A           92 ISN   94 (100)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.89  E-value=3.7e-22  Score=113.07  Aligned_cols=83  Identities=25%  Similarity=0.537  Sum_probs=78.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus       102 ~a~  104 (108)
T 2jrs_A          102 HVT  104 (108)
T ss_dssp             CSC
T ss_pred             Ecc
Confidence            875

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.89  E-value=6.8e-22  Score=112.87  Aligned_cols=83  Identities=33%  Similarity=0.512  Sum_probs=78.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        91 ~a~   93 (115)
T 2dgo_A           91 WAT   93 (115)
T ss_dssp             ESS
T ss_pred             Ecc
Confidence            764

>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=99.88  E-value=3e-22  Score=111.07  Aligned_cols=79  Identities=24%  Similarity=0.492  Sum_probs=75.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||..+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|++.|+|..+.|+.++|..++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            5789999999999999999999999999999999998889999999999999999999999999999999999998875

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.8e-22  Score=112.49  Aligned_cols=83  Identities=28%  Similarity=0.397  Sum_probs=78.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        91 ~a~   93 (103)
T 2cq0_A           91 WAK   93 (103)
T ss_dssp             ESS
T ss_pred             ECC
Confidence            764

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=3.8e-22  Score=110.37  Aligned_cols=81  Identities=26%  Similarity=0.518  Sum_probs=76.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            35679999999999999999999999999999999999888999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        83 ~   83 (95)
T 2dnz_A           83 T   83 (95)
T ss_dssp             S
T ss_pred             c
Confidence            4

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=4.1e-23  Score=114.65  Aligned_cols=82  Identities=16%  Similarity=0.259  Sum_probs=75.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCC--eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc----eeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGE--IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL----VCRTS   96 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~--v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~----~~~~~   96 (105)
                      ...-.+|||+|||+.+|+++|+++|++||.  +..++++.++.+|.++|||||+|.+.++|++|++.|||.    .++|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            345678999999999999999999999995  578999999989999999999999999999999999996    58999


Q ss_pred             eeeeccCC
Q 034039           97 KDTDMLST  104 (105)
Q Consensus        97 ~~~v~~~~  104 (105)
                      .+.|.+++
T Consensus        86 ~i~V~~Ak   93 (95)
T 2lkz_A           86 TIGVDFAK   93 (95)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEEcc
Confidence            99999886

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=1.1e-22  Score=114.10  Aligned_cols=84  Identities=24%  Similarity=0.362  Sum_probs=78.6

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ++....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        88 ~~a~   91 (103)
T 2dnm_A           88 QVAR   91 (103)
T ss_dssp             EECS
T ss_pred             EECC
Confidence            8875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.88  E-value=2.4e-23  Score=114.70  Aligned_cols=79  Identities=23%  Similarity=0.346  Sum_probs=73.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC-CceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD-GLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~-g~~~~~~~~~v~~~  103 (105)
                      +++|||+|||+++++++|+++|++|| .|..++++.++.+|.++|||||+|.+.++|++|++.++ +..+.|+.++|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 79999999998899999999999999999999998875 56799999999886


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        81 ~   81 (91)
T 2lxi_A           81 D   81 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.88  E-value=3.5e-22  Score=111.28  Aligned_cols=82  Identities=29%  Similarity=0.429  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999999888999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        85 a~   86 (99)
T 1whw_A           85 ST   86 (99)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=4.6e-22  Score=112.08  Aligned_cols=82  Identities=23%  Similarity=0.332  Sum_probs=77.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|+..|+|..+.|+.++|..
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       100 a~  101 (106)
T 1p27_B          100 CF  101 (106)
T ss_dssp             SE
T ss_pred             ec
Confidence            63

>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=99.88  E-value=5.1e-22  Score=109.82  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            4567899999999999999999999999999999999988 588999999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.88  E-value=5.9e-22  Score=111.78  Aligned_cols=83  Identities=24%  Similarity=0.381  Sum_probs=77.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+. +|.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             cCCC
Q 034039          102 LSTG  105 (105)
Q Consensus       102 ~~~~  105 (105)
                      ++++
T Consensus       104 ~a~s  107 (107)
T 3ulh_A          104 LVTS  107 (107)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            8753

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.88  E-value=7.4e-23  Score=114.50  Aligned_cols=80  Identities=20%  Similarity=0.304  Sum_probs=75.8

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee-e
Q 034039           24 NSRTKLFIGGLSY------DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT-S   96 (105)
Q Consensus        24 ~~~~~l~v~~l~~------~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~-~   96 (105)
                      ...++|||+|||.      .+++++|+++|.+||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4467999999999      99999999999999999999999999889999999999999999999999999999999 9


Q ss_pred             eeeeccC
Q 034039           97 KDTDMLS  103 (105)
Q Consensus        97 ~~~v~~~  103 (105)
                      .++|..+
T Consensus        84 ~l~V~~a   90 (100)
T 3ns6_A           84 RLFLYTM   90 (100)
T ss_dssp             BCEEEES
T ss_pred             EEEEEEC
Confidence            9999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.88  E-value=5.7e-22  Score=118.87  Aligned_cols=80  Identities=28%  Similarity=0.412  Sum_probs=75.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..++|||+|||+++++++|+++|..||  .|..+.++.+..+|.++|||||+|.+.++|+.|++.|||..+.|+.++|..
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999988999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       134 a~  135 (156)
T 3n9u_C          134 AT  135 (156)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=6.2e-22  Score=110.34  Aligned_cols=82  Identities=27%  Similarity=0.461  Sum_probs=76.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++ |++..+.|+.++|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999998 99999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .+.
T Consensus        85 ~a~   87 (99)
T 2dgs_A           85 RAE   87 (99)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=9.3e-22  Score=111.57  Aligned_cols=83  Identities=27%  Similarity=0.427  Sum_probs=77.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC------Cceeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD------GLVCRT   95 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------g~~~~~   95 (105)
                      +....++|||+|||+.+++++|+.+|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            44567899999999999999999999999999999999998889999999999999999999999999      999999


Q ss_pred             eeeeeccCC
Q 034039           96 SKDTDMLST  104 (105)
Q Consensus        96 ~~~~v~~~~  104 (105)
                      +.++|..+.
T Consensus        91 ~~l~v~~a~   99 (111)
T 1x4h_A           91 RQLKVDLAV   99 (111)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEEEECC
Confidence            999998764

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.88  E-value=6.5e-22  Score=113.15  Aligned_cols=77  Identities=34%  Similarity=0.590  Sum_probs=71.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|..||.|..++++.+.  +.++|||||+|.+.++|+.|++.|+|..+.|+.++|..++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            5689999999999999999999999999999999885  3478999999999999999999999999999999998653

>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=99.88  E-value=1.2e-21  Score=106.78  Aligned_cols=81  Identities=30%  Similarity=0.525  Sum_probs=74.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+.+++++|+++|.+||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..+.|+.++|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999994 58889999999987


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            54

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=9.1e-22  Score=109.61  Aligned_cols=82  Identities=29%  Similarity=0.458  Sum_probs=76.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeE-EEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee----
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEII-EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK----   97 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~----   97 (105)
                      ....++|||+|||+++++++|+++|.+||.|. .+.+..++.++.++|||||+|.+.++|+.|++.|||..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34578999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      ++|..++
T Consensus        86 l~v~~a~   92 (99)
T 2div_A           86 FKLNYAT   92 (99)
T ss_dssp             CCEEETT
T ss_pred             EEEeecC
Confidence            8887664

>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=99.87  E-value=7.1e-22  Score=112.00  Aligned_cols=82  Identities=22%  Similarity=0.305  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|+..|+|..+.|+.++|..
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999888999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       103 a~  104 (110)
T 1oo0_B          103 CF  104 (110)
T ss_dssp             SE
T ss_pred             cc
Confidence            63

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=8.4e-22  Score=109.56  Aligned_cols=81  Identities=27%  Similarity=0.424  Sum_probs=74.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCC---CCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRV---TGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+.++|||+|||+++++++|+++|..||.|..+.+..+..   ++.++|||||+|.+.++|+.|++.|+|..+.|+.++|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3567899999999999999999999999999999988765   5588999999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        83 ~~a~   86 (98)
T 2cpf_A           83 RISE   86 (98)
T ss_dssp             ECSS
T ss_pred             EEcc
Confidence            8865

>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=99.87  E-value=1.9e-21  Score=109.38  Aligned_cols=81  Identities=30%  Similarity=0.389  Sum_probs=75.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee---eeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT---SKDT   99 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~---~~~~   99 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|||..+.+   +.++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3457899999999999999999999999999999999988 89999999999999999999999999999998   9999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.++.
T Consensus        91 V~~a~   95 (105)
T 2dnh_A           91 VKFAD   95 (105)
T ss_dssp             EEESC
T ss_pred             EEECc
Confidence            98764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.87  E-value=1.4e-21  Score=114.92  Aligned_cols=83  Identities=34%  Similarity=0.557  Sum_probs=78.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|.+|++.|||..+.|+.++|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       118 ~a~  120 (139)
T 1u6f_A          118 LAA  120 (139)
T ss_dssp             ESS
T ss_pred             ECC
Confidence            765

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4e-22  Score=110.44  Aligned_cols=81  Identities=33%  Similarity=0.525  Sum_probs=76.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+ .+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356899999999999999999999999999999 9999877999999999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        83 a~   84 (96)
T 1x5t_A           83 AF   84 (96)
T ss_dssp             SC
T ss_pred             ec
Confidence            64

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.87  E-value=8.1e-22  Score=112.97  Aligned_cols=82  Identities=43%  Similarity=0.648  Sum_probs=76.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999988 89999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        82 ~a~   84 (116)
T 2fy1_A           82 QAK   84 (116)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=1.3e-21  Score=110.30  Aligned_cols=83  Identities=19%  Similarity=0.396  Sum_probs=77.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEec-CCCCCccceEEEEeCCHHHHHHHHHHc-CCceeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICD-RVTGQSRGYGFVKFASEAAAGEAIKEM-DGLVCRTSKDT   99 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~~~~~~   99 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+ ..++.++|||||+|.+.++|+.|++.| |+..+.|+.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4456789999999999999999999999999999999888 678999999999999999999999999 99999999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.+++
T Consensus        91 v~~a~   95 (107)
T 2cph_A           91 LEWAD   95 (107)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            98764

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=1.6e-21  Score=109.46  Aligned_cols=82  Identities=30%  Similarity=0.455  Sum_probs=76.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhc-cCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce-eeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQ-HGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV-CRTSKDT   99 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~-~~~~~~~   99 (105)
                      +....++|||+|||+.+++++|+++|.. ||.|..+.+..+. ++.++|||||+|.+.++|..|++.|+|.. +.|+.++
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999998 99999999999999999999999999999 9999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |..+.
T Consensus        84 v~~a~   88 (104)
T 2dhg_A           84 LSVAI   88 (104)
T ss_dssp             CCBCC
T ss_pred             EEEcc
Confidence            98764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4.2e-22  Score=111.54  Aligned_cols=82  Identities=28%  Similarity=0.455  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45678999999999999999999999999999999999888899999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        89 a~   90 (102)
T 2cqb_A           89 AK   90 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=5.1e-22  Score=110.46  Aligned_cols=82  Identities=16%  Similarity=0.142  Sum_probs=76.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|+.|++.|||..+.|+.++|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34568999999999999999999999999998887788877999999999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        92 a~   93 (98)
T 2cqp_A           92 GS   93 (98)
T ss_dssp             SS
T ss_pred             cC
Confidence            75

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4.9e-22  Score=111.26  Aligned_cols=82  Identities=40%  Similarity=0.601  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999888899999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        89 a~   90 (102)
T 1x5s_A           89 AG   90 (102)
T ss_dssp             EE
T ss_pred             CC
Confidence            54

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.87  E-value=1.4e-21  Score=106.78  Aligned_cols=78  Identities=17%  Similarity=0.521  Sum_probs=74.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|++|+ .|+|..+.|+.++|..++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            568999999999999999999999999999999999889999999999999999999999 999999999999998764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4.3e-22  Score=108.15  Aligned_cols=80  Identities=28%  Similarity=0.433  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.+++...
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            35679999999999999999999999999999999999888999999999999999999999999999999999998754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.87  E-value=2.1e-21  Score=113.99  Aligned_cols=82  Identities=28%  Similarity=0.457  Sum_probs=76.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            64

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=2.1e-21  Score=108.86  Aligned_cols=80  Identities=30%  Similarity=0.503  Sum_probs=75.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+  ++.+++||||+|.+.++|+.|++.|||..+.|+.++|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            446789999999999999999999999999999999887  788999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        90 a~   91 (103)
T 2d9p_A           90 AQ   91 (103)
T ss_dssp             CS
T ss_pred             ec
Confidence            64

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=2.2e-21  Score=110.97  Aligned_cols=83  Identities=41%  Similarity=0.621  Sum_probs=77.1

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ......++|||+|||+.+++++|+++|..||.|..+.+..+..++.+++||||+|.+.++|++|++.+++ .+.|+.++|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            3455678999999999999999999999999999999999988899999999999999999999999998 899999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .++.
T Consensus        91 ~~a~   94 (116)
T 2cqd_A           91 NLAY   94 (116)
T ss_dssp             EEST
T ss_pred             EEcc
Confidence            8763

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.3e-21  Score=111.38  Aligned_cols=83  Identities=23%  Similarity=0.342  Sum_probs=77.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEII--------EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      +....++|||+|||+.+++++|+++|..||.|.        .+.+..+..++.++|||||+|.+.++|+.|++.|||..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        699999877999999999999999999999999999999


Q ss_pred             eeeeeeeccCC
Q 034039           94 RTSKDTDMLST  104 (105)
Q Consensus        94 ~~~~~~v~~~~  104 (105)
                      .|+.++|.+++
T Consensus        91 ~g~~l~V~~a~  101 (113)
T 2cpe_A           91 QGSKLKVSLAR  101 (113)
T ss_dssp             TTEECEEECSS
T ss_pred             CCCEEEEEECC
Confidence            99999999875

>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=99.87  E-value=8.8e-22  Score=110.89  Aligned_cols=83  Identities=25%  Similarity=0.374  Sum_probs=77.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee---eeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC---RTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~---~~~~~   98 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|..|++.|+|..+   .++.+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            345678999999999999999999999999999999999988899999999999999999999999999998   89999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..+.
T Consensus        89 ~v~~a~   94 (106)
T 2dgp_A           89 QVKPAD   94 (106)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            998764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=3.6e-21  Score=109.66  Aligned_cols=82  Identities=23%  Similarity=0.401  Sum_probs=76.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+. ++.+++||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34567899999999999999999999999999999999987 68999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      ++.
T Consensus        90 ~a~   92 (114)
T 2do0_A           90 MDE   92 (114)
T ss_dssp             ECS
T ss_pred             Ecc
Confidence            764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.87  E-value=4.1e-22  Score=115.13  Aligned_cols=79  Identities=23%  Similarity=0.576  Sum_probs=74.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||.++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|+ .|+|..+.|+.++|..++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4579999999999999999999999999999999999889999999999999999999999 899999999999998764

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.87  E-value=5.2e-22  Score=109.80  Aligned_cols=80  Identities=15%  Similarity=0.106  Sum_probs=74.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|.+++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45799999999999999999999999999888888888889999999999999999999999999999999999999875

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.87  E-value=1.9e-22  Score=118.39  Aligned_cols=88  Identities=30%  Similarity=0.449  Sum_probs=80.2

Q ss_pred             cccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           17 TRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        17 ~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      ..+..+....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+
T Consensus        38 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~  117 (135)
T 2lea_A           38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR  117 (135)
T ss_dssp             CCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            33444555678999999999999999999999999999999998888899999999999999999999999999999999


Q ss_pred             eeeeccCC
Q 034039           97 KDTDMLST  104 (105)
Q Consensus        97 ~~~v~~~~  104 (105)
                      .++|.+++
T Consensus       118 ~l~V~~a~  125 (135)
T 2lea_A          118 ELRVQMAR  125 (135)
T ss_dssp             CCEEEECC
T ss_pred             EEEEEECC
Confidence            99998875

>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=99.87  E-value=3.4e-22  Score=114.01  Aligned_cols=79  Identities=23%  Similarity=0.292  Sum_probs=74.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|+ .|+|..+.|+.++|..+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            34579999999999999999999999999999999999888999999999999999999999 99999999999999865

>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=99.86  E-value=1.1e-21  Score=106.94  Aligned_cols=80  Identities=26%  Similarity=0.418  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCC-ccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ-SRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||+++++++|+++|.+||.|..+.+..+..++. ++|||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457899999999999999999999999999999988876665 8899999999999999999999999999999999865


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        83 ~   83 (88)
T 4a8x_A           83 L   83 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.86  E-value=5e-21  Score=107.37  Aligned_cols=80  Identities=19%  Similarity=0.351  Sum_probs=75.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..|| |..+.+..+..++.++|||||+|.+.++|+.|+ .|+|..+.|+.++|..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34578999999999999999999999996 999999999888999999999999999999999 9999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        90 a~   91 (103)
T 2dng_A           90 AE   91 (103)
T ss_dssp             CC
T ss_pred             ec
Confidence            64

>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=99.86  E-value=1.7e-21  Score=112.76  Aligned_cols=82  Identities=23%  Similarity=0.332  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            44578999999999999999999999999999999999988999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        99 a~  100 (126)
T 3ex7_B           99 CF  100 (126)
T ss_dssp             SE
T ss_pred             ec
Confidence            63

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=3.9e-21  Score=108.13  Aligned_cols=82  Identities=32%  Similarity=0.549  Sum_probs=76.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|+.|+.. ++..+.|+.++|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345678999999999999999999999999999999999988999999999999999999999988 9999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        91 ~a~   93 (105)
T 2dh8_A           91 PCT   93 (105)
T ss_dssp             CSC
T ss_pred             Ecc
Confidence            764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.86  E-value=4.9e-21  Score=105.29  Aligned_cols=80  Identities=25%  Similarity=0.462  Sum_probs=74.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+  ++.+++||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346789999999999999999999999999999998874  788999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        83 a~   84 (92)
T 2dgv_A           83 DR   84 (92)
T ss_dssp             CS
T ss_pred             cC
Confidence            65

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.86  E-value=5.6e-21  Score=114.31  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.++.+..++.+++||||+|.+.++|+.|+..|++..+.|+.|+|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999999999886


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       117 ~  117 (156)
T 1h2v_Z          117 A  117 (156)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.86  E-value=8e-21  Score=106.48  Aligned_cols=81  Identities=26%  Similarity=0.382  Sum_probs=74.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+.+++++|+++|..||.|..+.+..+..+  +++||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            4456789999999999999999999999999999999988533  68999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        89 ~a~   91 (103)
T 2cqi_A           89 WAT   91 (103)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            765

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.1e-21  Score=109.19  Aligned_cols=78  Identities=15%  Similarity=0.242  Sum_probs=72.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+.. |.++|||||+|.+.++|..|+. ++|..+.|+.+.|..
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999985 9999999999999999999998 999999999999875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.86  E-value=5.7e-21  Score=110.40  Aligned_cols=81  Identities=23%  Similarity=0.369  Sum_probs=76.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+. +|.++|||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456899999999999999999999999999999999998 899999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       111 a~  112 (124)
T 2kt5_A          111 VA  112 (124)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.2e-20  Score=105.70  Aligned_cols=81  Identities=27%  Similarity=0.512  Sum_probs=74.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+..  .+++||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999988763  388999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        89 ~a~   91 (103)
T 2cq3_A           89 NAT   91 (103)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            764

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.3e-21  Score=108.77  Aligned_cols=80  Identities=26%  Similarity=0.549  Sum_probs=75.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|++.|+|..+.|+.++|..+.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45789999999999999999999999999999999998889999999999999999999999999999999999998764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.86  E-value=8.6e-22  Score=114.94  Aligned_cols=81  Identities=16%  Similarity=0.287  Sum_probs=75.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE--EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc----eeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE--VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL----VCRTS   96 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~----~~~~~   96 (105)
                      ....++|||+|||+++++++|+++|..||.|..  +.++.++.+|.++|||||+|.+. +|..|+..|||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            456789999999999999999999999999966  99999998999999999999999 999999999999    99999


Q ss_pred             eeeeccCC
Q 034039           97 KDTDMLST  104 (105)
Q Consensus        97 ~~~v~~~~  104 (105)
                      .++|.+++
T Consensus        99 ~l~V~~a~  106 (131)
T 2m2b_A           99 TINVEFAK  106 (131)
T ss_dssp             CCCCEECC
T ss_pred             EEEEEECC
Confidence            99998764

>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=99.86  E-value=5.3e-21  Score=107.45  Aligned_cols=79  Identities=18%  Similarity=0.323  Sum_probs=74.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCC-CCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT-GQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+.+++++|+++|..|| |..+.+..+..+ +.++|||||+|.+.++|+.|+ .|++..+.|+.++|..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4568999999999999999999999999 999999998876 899999999999999999999 9999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        91 a~   92 (104)
T 1wi8_A           91 AD   92 (104)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.86  E-value=5.2e-21  Score=106.16  Aligned_cols=78  Identities=17%  Similarity=0.214  Sum_probs=72.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLK----DAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      ...++|||+|||+.+++++|+    ++|.+||.|..+.++.+..+   ++||||+|.+.++|+.|++.|||..+.|+.++
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            356789999999999999999    99999999999999988744   78999999999999999999999999999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |..++
T Consensus        84 V~~a~   88 (96)
T 2dgx_A           84 VSLAT   88 (96)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            98775

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.85  E-value=1.1e-21  Score=104.14  Aligned_cols=75  Identities=28%  Similarity=0.445  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|++|++ ++|..+.|+.++|..+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999988889999999999999999999997 9999999999998754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=8.2e-21  Score=104.27  Aligned_cols=79  Identities=14%  Similarity=0.271  Sum_probs=73.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|..| .+..+.++.+ .+|.++|||||+|.+.++|+.|+. |+|..+.|+.++|..
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4567899999999999999999999999 9999999998 589999999999999999999999 999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        84 a~   85 (91)
T 2dgw_A           84 EK   85 (91)
T ss_dssp             ES
T ss_pred             CC
Confidence            64

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.1e-21  Score=109.36  Aligned_cols=82  Identities=27%  Similarity=0.512  Sum_probs=75.0

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ......++|||+|||..+++++|+++|..||.|..+.+..+.  +.++|||||+|.+.++|+.|++.|+|..+.|+.++|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345577899999999999999999999999999999998875  348899999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus       102 ~~a~  105 (109)
T 2err_A          102 NNAT  105 (109)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=4.9e-21  Score=108.57  Aligned_cols=83  Identities=33%  Similarity=0.527  Sum_probs=72.5

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        21 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+....++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|+..+ +..+.|+.++|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            34456789999999999999999999999999999999999888999999999999999999999876 59999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..+.
T Consensus        99 ~~a~  102 (109)
T 2rs2_A           99 KVAF  102 (109)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            8764

>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=99.85  E-value=2.7e-20  Score=105.34  Aligned_cols=80  Identities=19%  Similarity=0.317  Sum_probs=72.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..   ++.+++||||+|.+.++|+.|++.||+..+.|+.|+|.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            445678999999999999999999999999999998854   44578999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        95 ~a~   97 (109)
T 1x4a_A           95 FPR   97 (109)
T ss_dssp             CCC
T ss_pred             Ecc
Confidence            875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.85  E-value=2.9e-21  Score=108.80  Aligned_cols=81  Identities=22%  Similarity=0.294  Sum_probs=73.4

Q ss_pred             CCCCCceEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           22 DANSRTKLFIGGLSYDT------NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      .....++|||+|||+.+      ++++|+.+|++||.|..+.++  +.+|.++|||||+|.+.++|..|+..|||..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      789999999999999999887  3578999999999999999999999999999999


Q ss_pred             e-eeeeccCC
Q 034039           96 S-KDTDMLST  104 (105)
Q Consensus        96 ~-~~~v~~~~  104 (105)
                      + .++|..+.
T Consensus        89 ~~~l~V~~a~   98 (105)
T 2nlw_A           89 QHTFRVNLFT   98 (105)
T ss_dssp             TCEEEEECSC
T ss_pred             CceEEEEEcc
Confidence            8 99998764

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.85  E-value=1.1e-21  Score=109.64  Aligned_cols=81  Identities=17%  Similarity=0.303  Sum_probs=72.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC-CCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-VTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .....++|||+|||+++++++|+++|..|| |..+.+..+. .+|.++|||||+|.+.++|..|+ .|+|..+.|+.++|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345678999999999999999999999999 9999998887 58999999999999999999999 99999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        93 ~~a~   96 (100)
T 2j76_E           93 DVAD   96 (100)
T ss_dssp             EECC
T ss_pred             Eecc
Confidence            8765

>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=99.85  E-value=1.1e-20  Score=114.11  Aligned_cols=82  Identities=22%  Similarity=0.305  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+.+|..||.|..+.+..+..+|.++|||||+|.+.++|..|+..|||..+.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       149 a~  150 (165)
T 1rk8_A          149 CF  150 (165)
T ss_dssp             SE
T ss_pred             ec
Confidence            63

>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=99.85  E-value=3.6e-20  Score=103.82  Aligned_cols=80  Identities=28%  Similarity=0.427  Sum_probs=73.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|+.  ++..+.|+.++|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            4566889999999999999999999999999999999998889999999999999999999998  47889999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        90 a~   91 (103)
T 2cqg_A           90 PN   91 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=99.85  E-value=8.4e-21  Score=113.61  Aligned_cols=81  Identities=30%  Similarity=0.470  Sum_probs=76.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       148 ~  148 (158)
T 2kn4_A          148 R  148 (158)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.7e-20  Score=106.05  Aligned_cols=81  Identities=25%  Similarity=0.454  Sum_probs=73.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-------
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-------   94 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-------   94 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|||..+.       
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34567899999999999999999999999999999999998 8999999999999999999999999999994       


Q ss_pred             -eeeeeeccC
Q 034039           95 -TSKDTDMLS  103 (105)
Q Consensus        95 -~~~~~v~~~  103 (105)
                       ++.+.|.++
T Consensus       100 ~~~~l~v~~a  109 (114)
T 1x5o_A          100 PTEPLLCKFS  109 (114)
T ss_dssp             CSSCBEEEEC
T ss_pred             CCCceeEEcc
Confidence             566777655

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.7e-20  Score=105.47  Aligned_cols=76  Identities=16%  Similarity=0.155  Sum_probs=69.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC--ceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG--LVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~~~~~~v  100 (105)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|+.|++.|++  ..+.|+.++|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999998864      58999999999999999998864  7899999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        87 ~~A~   90 (105)
T 1sjq_A           87 QFSN   90 (105)
T ss_dssp             CCCS
T ss_pred             EEcC
Confidence            8875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.84  E-value=3.1e-21  Score=103.94  Aligned_cols=73  Identities=22%  Similarity=0.328  Sum_probs=67.0

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeee-ee
Q 034039           26 RTKLFIGGLSYDT------NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTS-KD   98 (105)
Q Consensus        26 ~~~l~v~~l~~~~------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~-~~   98 (105)
                      +++|||+|||+.+      ++++|+++|++||.|..+.+.  +.+|.++|||||+|.+.++|+.|++.|||..+.|+ .+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      679999999999999999877  34788999999999999999999999999999999 88


Q ss_pred             ee
Q 034039           99 TD  100 (105)
Q Consensus        99 ~v  100 (105)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.84  E-value=1.3e-20  Score=102.29  Aligned_cols=74  Identities=15%  Similarity=0.244  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+..|||+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.+.++|++|++.||+..+.|+.|+|..++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            356899999999999999999999999999999865      56999999999999999999999999999999998764

>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=99.84  E-value=1e-20  Score=107.50  Aligned_cols=81  Identities=20%  Similarity=0.270  Sum_probs=73.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHH---HHHhccCCeEEEEEEecCCCC---CccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLK---DAFGQHGEIIEVKVICDRVTG---QSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~---~~f~~~g~v~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      ...++|||+|||+.+++++|+   ++|.+||.|..+.+..+..++   .++|||||+|.+.++|+.|++.|||..+.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            456789999999999999999   999999999999998887543   45699999999999999999999999999999


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      ++|.+++
T Consensus        93 l~V~~a~   99 (111)
T 2cpi_A           93 LKASLGT   99 (111)
T ss_dssp             EEEESCC
T ss_pred             EEEEecc
Confidence            9998865

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.9e-21  Score=103.69  Aligned_cols=76  Identities=34%  Similarity=0.591  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++|||+|||+++++++|+++|++||.+..+.+..++.++.++|||||+|.+.++|+.|++.++ ..+.|+.++|..+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            469999999999999999999999999999999998889999999999999999999999999 9999999998765

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.84  E-value=5.9e-21  Score=120.68  Aligned_cols=80  Identities=26%  Similarity=0.412  Sum_probs=75.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccC--CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHG--EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..++|||+|||+++++++|+++|..||  .|..+.++.++.+++++|||||+|.+.++|++||+.|||..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999988999999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.84  E-value=4.7e-21  Score=112.54  Aligned_cols=81  Identities=19%  Similarity=0.189  Sum_probs=74.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGE---IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      +....++|||+|||+++++++|+++|..||.   |..+.++.++. |+++|||||+|.+.++|++|++ +++..+.|+.+
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   88999999985 9999999999999999999998 99999999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..++
T Consensus       118 ~V~~a~  123 (136)
T 2hgl_A          118 EVFKSH  123 (136)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            998764

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.1e-20  Score=106.26  Aligned_cols=81  Identities=21%  Similarity=0.256  Sum_probs=73.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .....++|||+|||+.+++++|+++|..||.|.. +.++.+ .+|+++|||||+|.+.++|+.|+.. ++..+.|+.++|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999987 888888 5899999999999999999999987 999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T 1wg5_A           89 FKSS   92 (104)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            7653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.84  E-value=8.9e-21  Score=108.91  Aligned_cols=81  Identities=19%  Similarity=0.205  Sum_probs=74.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGE---IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      +....++|||+|||+++++++|+++|..||.   |..+.++.+. .|+++|||||+|.+.++|++|++ +++..+.|+.+
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~-~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS-SSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC-CCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999998   8999999988 49999999999999999999998 99999999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..+.
T Consensus        91 ~V~~a~   96 (118)
T 2db1_A           91 EVFKSH   96 (118)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            997653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6e-21  Score=109.12  Aligned_cols=79  Identities=32%  Similarity=0.494  Sum_probs=74.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++. ++..+.|+.++|..+.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            458999999999999999999999999999999999988899999999999999999999987 9999999999998764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.84  E-value=2.8e-20  Score=116.14  Aligned_cols=80  Identities=30%  Similarity=0.448  Sum_probs=74.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.|++.+++..+.|+.+++..+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45679999999999999999999999999999999999989999999999999999999999999999999999988754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.84  E-value=8.2e-21  Score=107.99  Aligned_cols=78  Identities=22%  Similarity=0.173  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....+|||+|||+++++++|+++|..|| .|..+.+..    ..++|||||+|.+.++|+.|++.|||..+.|+.|+|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567999999999999999999999999 898888743    2478999999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus       101 ~a~  103 (111)
T 2jvr_A          101 RDD  103 (111)
T ss_dssp             ESC
T ss_pred             ECC
Confidence            875

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.84  E-value=1.1e-21  Score=107.53  Aligned_cols=77  Identities=29%  Similarity=0.534  Sum_probs=72.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ++|||+|||+++++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.+ |..|+..|||..+.|+.++|..+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcC
Confidence            47999999999999999999999999999999999888999999999999999 999999999999999999998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.84  E-value=3.5e-20  Score=110.84  Aligned_cols=82  Identities=29%  Similarity=0.480  Sum_probs=77.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .....+|||+|||+.+++++|+++|+.||.|..+.+..+..+|.++|+|||+|.+.++|..|+..|||..+.|+.++|.+
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            44677999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            76

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=106.46  Aligned_cols=81  Identities=20%  Similarity=0.312  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEE-ecCCCCCccceEEEEeCCHHHHHHHHHHcC--Cceeeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGE-IIEVKVI-CDRVTGQSRGYGFVKFASEAAAGEAIKEMD--GLVCRTSKDT   99 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~-~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~--g~~~~~~~~~   99 (105)
                      ...++|||+|||+.+++++|+++|..||. |..+.+. .+..++.++|||||+|.+.++|..|++.|+  +..+.|+.++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999988 777788999999999999999999999996  5899999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |..++
T Consensus        86 V~~a~   90 (109)
T 2dis_A           86 VDWAE   90 (109)
T ss_dssp             EEESC
T ss_pred             EEEcC
Confidence            98764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.84  E-value=2.3e-20  Score=108.46  Aligned_cols=79  Identities=14%  Similarity=0.278  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLK----DAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..+.+..   ++.++|||||+|.+.++|..|++.|||..+.|+.+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4457899999999999999865    6899999998887642   67889999999999999999999999999999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..++
T Consensus       103 ~V~~a~  108 (127)
T 2a3j_A          103 VITFSE  108 (127)
T ss_dssp             EEEECC
T ss_pred             EEEEcc
Confidence            998875

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.1e-20  Score=107.12  Aligned_cols=78  Identities=21%  Similarity=0.286  Sum_probs=71.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ....+|||+|||+++++++|+++|..| .|..+.++.+. +|+++|||||+|.+.++|++|+ .+|+..+.|+.+.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            345799999999999999999999999 89999999987 5999999999999999999999 79999999999999765


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        91 ~   91 (109)
T 2dnn_A           91 T   91 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.7e-21  Score=111.24  Aligned_cols=81  Identities=19%  Similarity=0.208  Sum_probs=72.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|+.|+. |||..+.|+.+.|..
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999875555565699999999999999999999998 999999999999986


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       101 a~  102 (124)
T 1wel_A          101 IT  102 (124)
T ss_dssp             EC
T ss_pred             CC
Confidence            53

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=1.2e-19  Score=102.66  Aligned_cols=74  Identities=22%  Similarity=0.319  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee-----eee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT-----SKD   98 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~-----~~~   98 (105)
                      ...++|||+|||+++++++|+++|..||.|..+.+..+       +||||+|.+.++|+.|++.|||..+.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45789999999999999999999999999999998765       799999999999999999999999999     999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..+.
T Consensus        86 ~V~~a~   91 (108)
T 1x4c_A           86 RVKVDG   91 (108)
T ss_dssp             EEEESS
T ss_pred             EEEeCC
Confidence            998764

>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=99.83  E-value=5.3e-20  Score=110.87  Aligned_cols=100  Identities=24%  Similarity=0.400  Sum_probs=85.2

Q ss_pred             CCCceecccccccccccc--CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            4 LNGSVRFSHSVRFTRLLS--DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~--~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      +++..+.++.+....+..  .....++|||+|||+.+++++|+++|.+||.|..+.+..+..+|.++|+|||+|.+.++|
T Consensus        70 ~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A  149 (172)
T 2g4b_A           70 FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT  149 (172)
T ss_dssp             GTTCEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHH
T ss_pred             hCCcEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHH
Confidence            456666555544333222  234468999999999999999999999999999999999988999999999999999999


Q ss_pred             HHHHHHcCCceeeeeeeeeccC
Q 034039           82 GEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        82 ~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .+|++.|||..+.|+.++|..+
T Consensus       150 ~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          150 DQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999999876

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.83  E-value=3.2e-20  Score=103.49  Aligned_cols=77  Identities=21%  Similarity=0.152  Sum_probs=69.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce--eeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV--CRTSKDT   99 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~--~~~~~~~   99 (105)
                      ...++.+|||+|||+.+++++|+++|.+||.|..+.+..      .+|+|||+|.+.++|.+|++.|++..  +.|+.+.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            345678999999999999999999999999999998874      35899999999999999999999876  7799999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.+++
T Consensus        91 V~~S~   95 (100)
T 3r27_A           91 VNYST   95 (100)
T ss_dssp             EEECS
T ss_pred             EEecc
Confidence            99875

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.2e-20  Score=105.87  Aligned_cols=79  Identities=19%  Similarity=0.248  Sum_probs=72.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|..||.+ .+.++.++ +++++|||||+|.+.++|++|+ .+|+..+.++.++|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            3456899999999999999999999999965 99999998 8999999999999999999999 5799999999999986


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        89 ~~   90 (102)
T 1wez_A           89 NS   90 (102)
T ss_dssp             EC
T ss_pred             CC
Confidence            54

>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=99.83  E-value=1.2e-20  Score=107.74  Aligned_cols=80  Identities=15%  Similarity=0.144  Sum_probs=73.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCe-EEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ....++|||+|||+.+++++|+++|..||.+ ..+.++.+. +|.++|||||+|.+.++|+.|++. ++..+.|+.+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456899999999999999999999999999 889999998 999999999999999999999977 9999999999997


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .+.
T Consensus        90 ~a~   92 (114)
T 2cpy_A           90 VVT   92 (114)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            653

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=6.2e-20  Score=99.46  Aligned_cols=76  Identities=28%  Similarity=0.414  Sum_probs=69.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc-CCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM-DGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~~~~~~v~  101 (105)
                      ....++|||+|||+.+++++|+++|.+||.|..+.+..+      +|||||+|.+.++|+.|++.| +|..+.|+.++|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            456789999999999999999999999999999998753      589999999999999999999 9999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            764

>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=99.83  E-value=9.3e-20  Score=101.33  Aligned_cols=75  Identities=21%  Similarity=0.404  Sum_probs=68.9

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           22 DANSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .....++|||+|||+ .+++++|+++|..||.|..+.+.        +|||||+|.+.++|..|++.|+|..+.|+.++|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445678999999998 99999999999999999999882        589999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        90 ~~a~   93 (97)
T 2xnq_A           90 EVSS   93 (97)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=5.1e-20  Score=102.83  Aligned_cols=79  Identities=28%  Similarity=0.359  Sum_probs=71.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|   .++.+ .++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            34567899999999999999999999999987   45555 488899999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        87 ~a~   89 (101)
T 2fc9_A           87 LQG   89 (101)
T ss_dssp             ECS
T ss_pred             EcC
Confidence            864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.83  E-value=7.4e-20  Score=103.58  Aligned_cols=75  Identities=31%  Similarity=0.528  Sum_probs=69.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|.+||.|..+.+.        +|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999886        5899999999999999999999999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        99 ~a~  101 (108)
T 2jvo_A           99 YSK  101 (108)
T ss_dssp             SCS
T ss_pred             Eec
Confidence            875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.3e-19  Score=99.25  Aligned_cols=74  Identities=28%  Similarity=0.495  Sum_probs=68.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|.+||.|..+.+.        ++||||+|.+.++|+.|++.|+|..+.|+.++|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3467899999999999999999999999999999886        47999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        77 a~   78 (90)
T 2dnq_A           77 SK   78 (90)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.2e-19  Score=101.44  Aligned_cols=80  Identities=35%  Similarity=0.501  Sum_probs=72.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..|+   .+.++.+..++.+++||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345678999999999999999999999874   56777787789999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        88 ~a~   90 (102)
T 2fc8_A           88 WAK   90 (102)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=7.7e-20  Score=101.51  Aligned_cols=78  Identities=23%  Similarity=0.355  Sum_probs=69.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|. +.+..+    .++|||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345578999999999999999999999999986 555543    477999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        90 ~a~   92 (97)
T 2e5j_A           90 LAR   92 (97)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            765

>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=99.82  E-value=6.2e-21  Score=101.24  Aligned_cols=75  Identities=29%  Similarity=0.487  Sum_probs=70.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|+++|++||.+..+.+..+..++.++|||||+|.+.++|+.|++. ++..+.|+.++|..+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999888899999999999999999999974 899999999998754

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.82  E-value=1.3e-19  Score=103.27  Aligned_cols=78  Identities=21%  Similarity=0.344  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+.+|..||.|..+.+..+   +.++|||||+|.+.++|..|+..|||..+.|+.++|..+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45679999999999999999999999999999998864   446899999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        83 ~   83 (115)
T 3lqv_A           83 N   83 (115)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.82  E-value=9.2e-21  Score=107.07  Aligned_cols=81  Identities=12%  Similarity=0.148  Sum_probs=74.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCC---eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGE---IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      +....++|||+|||+++++++|+++|..||.   |..+.++.+.. |.++|||||+|.+.++|+.|+. +++..+.|+.+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999999999999999999988   88999998885 9999999999999999999998 99999999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|..+.
T Consensus        85 ~V~~a~   90 (107)
T 2lmi_A           85 EVYEIN   90 (107)
T ss_dssp             CCEECC
T ss_pred             EEEECC
Confidence            987653

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.82  E-value=1.7e-19  Score=107.91  Aligned_cols=79  Identities=32%  Similarity=0.530  Sum_probs=75.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|++.|+|..+.|+.++|..+.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            5789999999999999999999999999999999998899999999999999999999999999999999999987653

>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=99.82  E-value=2.4e-20  Score=103.44  Aligned_cols=80  Identities=21%  Similarity=0.365  Sum_probs=71.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLK----DAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      +..+.++|||+|||+.+++++|+    ++|.+||.|..+.+..   +|.++|||||+|.+.++|..|++.|+|..+.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34567899999999999999999    9999999999998763   5667899999999999999999999999999999


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      ++|..++
T Consensus        81 l~v~~a~   87 (97)
T 1nu4_A           81 MRIQYAK   87 (97)
T ss_dssp             CEEEECS
T ss_pred             EEEEEcc
Confidence            9998764

>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=99.82  E-value=9.1e-21  Score=108.12  Aligned_cols=82  Identities=20%  Similarity=0.235  Sum_probs=69.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34678999999999999999999999999884332222222778899999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       102 a~  103 (115)
T 2cpx_A          102 GK  103 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.82  E-value=1.6e-19  Score=102.32  Aligned_cols=73  Identities=22%  Similarity=0.403  Sum_probs=67.8

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+. +++++|+++|.+||.|..+.+        +++||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34579999999999 999999999999999999988        458999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        97 a~   98 (110)
T 1wf1_A           97 AG   98 (110)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.82  E-value=1.1e-19  Score=112.88  Aligned_cols=81  Identities=17%  Similarity=0.358  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||..+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|.+|++.|||..+.|+.++|..+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus       203 ~  203 (216)
T 2qfj_A          203 V  203 (216)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.82  E-value=2e-19  Score=99.82  Aligned_cols=76  Identities=24%  Similarity=0.404  Sum_probs=69.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee--eeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR--TSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~--~~~~~v  100 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+      ++||||+|.+.++|+.|++.|||..+.  |+.++|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            445689999999999999999999999999999988643      579999999999999999999999999  999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        88 ~~a~   91 (97)
T 1why_A           88 DFAK   91 (97)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8765

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.6e-19  Score=102.16  Aligned_cols=77  Identities=21%  Similarity=0.506  Sum_probs=71.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+.+|..||.|..+.+..+      ++||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999998765      5899999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        95 ~a~   97 (109)
T 1x4g_A           95 WGK   97 (109)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.82  E-value=4.1e-20  Score=106.65  Aligned_cols=78  Identities=19%  Similarity=0.198  Sum_probs=70.9

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCC----HHH----HHHHHH--HcCCce
Q 034039           27 TKLFIGGL----SYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFAS----EAA----AGEAIK--EMDGLV   92 (105)
Q Consensus        27 ~~l~v~~l----~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~----~~~----a~~a~~--~l~g~~   92 (105)
                      ..|||+||    |+.+++.+|+.+|+.||+|..+.++.|+.||.++|||||+|.+    ..+    |..|+.  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999995    323    788888  789999


Q ss_pred             eeeeeeeeccCC
Q 034039           93 CRTSKDTDMLST  104 (105)
Q Consensus        93 ~~~~~~~v~~~~  104 (105)
                      ++|+.++|.+.+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999865

>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=99.82  E-value=3.1e-20  Score=104.13  Aligned_cols=75  Identities=15%  Similarity=0.100  Sum_probs=67.6

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc--eeeeeeeee
Q 034039           24 NSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL--VCRTSKDTD  100 (105)
Q Consensus        24 ~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~~~~~~v  100 (105)
                      .+.++|||+|||+ .+++++|+++|.+||.|..+.++.++      +||||+|++.++|..|++.|++.  .+.|+.+.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4678999999999 99999999999999999999987543      79999999999999999999864  599999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        87 ~~a~   90 (102)
T 1x4d_A           87 HLSQ   90 (102)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8765

>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=99.82  E-value=1.3e-19  Score=108.75  Aligned_cols=100  Identities=23%  Similarity=0.421  Sum_probs=83.9

Q ss_pred             CCCceeccccccccc--cccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            4 LNGSVRFSHSVRFTR--LLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         4 ~~~~~~~~~~~~~~~--~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      +++..+..+.+....  +........+|||+|||..+++++|+++|..||.|..+.+..+..++.++|+|||+|.+.++|
T Consensus        65 l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A  144 (168)
T 1b7f_A           65 LNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA  144 (168)
T ss_dssp             HTTCEETTEECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             cCCCEeCCcEEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHH
Confidence            455555555444322  223345678999999999999999999999999999999999988899999999999999999


Q ss_pred             HHHHHHcCCceeee--eeeeeccC
Q 034039           82 GEAIKEMDGLVCRT--SKDTDMLS  103 (105)
Q Consensus        82 ~~a~~~l~g~~~~~--~~~~v~~~  103 (105)
                      ..|++.|+|..+.|  +.++|.++
T Consensus       145 ~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          145 QEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999977  88888764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.5e-19  Score=100.97  Aligned_cols=76  Identities=18%  Similarity=0.247  Sum_probs=69.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||.++++++|+++|..||.|..+.+..      ++|||||+|.+.++|..|+..|+|..+.|+.++|..
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            34568999999999999999999999999999998872      468999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        98 a~   99 (101)
T 2la4_A           98 GK   99 (101)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=4.4e-21  Score=107.19  Aligned_cols=80  Identities=24%  Similarity=0.309  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|..||.+.. .++.+..++.++|||||+|.+.++|+.|++ |+|..+.|+.++|..
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345789999999999999999999999998866 455555578899999999999999999998 999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        92 a~   93 (101)
T 1fj7_A           92 PK   93 (101)
T ss_dssp             CS
T ss_pred             cC
Confidence            75

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=8.9e-20  Score=111.32  Aligned_cols=80  Identities=24%  Similarity=0.373  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+. ++.++|||||+|.+.++|+.|++.|+|..+.|+.++|.++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346799999999999999999999999999999999988 8999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus       165 ~  165 (177)
T 2f3j_A          165 A  165 (177)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.81  E-value=1.8e-19  Score=101.42  Aligned_cols=75  Identities=19%  Similarity=0.165  Sum_probs=67.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc--eeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL--VCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~~~~~~v~  101 (105)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.+..+      +|||||+|.+.++|..|++.|++.  .+.|+.+.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45689999999999999999999999999999988653      589999999999999999988764  5899999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        87 ~a~   89 (104)
T 1wex_A           87 YST   89 (104)
T ss_dssp             ECS
T ss_pred             Ecc
Confidence            765

>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=99.81  E-value=3.9e-19  Score=99.51  Aligned_cols=76  Identities=17%  Similarity=0.105  Sum_probs=68.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc--CCceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM--DGLVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~~~~~~v  100 (105)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.+..+      +|||||+|.+.++|..|++.|  ++..+.|+.+.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345689999999999999999999999999999988754      589999999999999999977  467899999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        86 ~~a~   89 (101)
T 2cq1_A           86 QYSN   89 (101)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            8765

>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=99.81  E-value=1.3e-19  Score=104.09  Aligned_cols=77  Identities=16%  Similarity=0.151  Sum_probs=69.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC--ceeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG--LVCRTSKDT   99 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~~~~~~   99 (105)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|++.++|.+|++.|++  ..+.|+.++
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3456789999999999999999999999999999998764      58999999999999999999884  689999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.+++
T Consensus       101 V~~a~  105 (119)
T 2ad9_A          101 IQFSN  105 (119)
T ss_dssp             EEECS
T ss_pred             EEEcc
Confidence            98765

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.81  E-value=1.9e-19  Score=107.95  Aligned_cols=80  Identities=31%  Similarity=0.443  Sum_probs=75.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      +.++|||+|||+++++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|++.|+|..+.|+.++|..+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46789999999999999999999999999999999988889999999999999999999999999999999999988653

>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=99.81  E-value=2.3e-19  Score=122.33  Aligned_cols=81  Identities=25%  Similarity=0.463  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|..+|..||.|..|.|+.+..++.++|||||+|.+.++|.+||..|||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34579999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus       180 ~  180 (437)
T 3pgw_S          180 R  180 (437)
T ss_pred             C
Confidence            5

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=1.5e-21  Score=111.67  Aligned_cols=82  Identities=26%  Similarity=0.338  Sum_probs=76.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEE--------EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIE--------VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ....++|||+|||+.+++++|+++|..||.|..        +.+..++.++.++|||||+|.+.++|+.|++.|||..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345779999999999999999999999999988        888888778999999999999999999999999999999


Q ss_pred             eeeeeeccCC
Q 034039           95 TSKDTDMLST  104 (105)
Q Consensus        95 ~~~~~v~~~~  104 (105)
                      |+.++|..++
T Consensus        84 g~~l~V~~a~   93 (116)
T 2lcw_A           84 GNPIKVSFAT   93 (116)
Confidence            9999998764

>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=99.81  E-value=1.6e-19  Score=100.53  Aligned_cols=76  Identities=26%  Similarity=0.439  Sum_probs=69.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+      ++||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345679999999999999999999999999999988754      58999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        86 a~   87 (99)
T 2cpj_A           86 AC   87 (99)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.81  E-value=3.2e-19  Score=109.51  Aligned_cols=81  Identities=27%  Similarity=0.460  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|++.|+|..+.|+.++|..+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus       192 ~  192 (198)
T 2yh0_A          192 S  192 (198)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=3.3e-19  Score=98.01  Aligned_cols=75  Identities=28%  Similarity=0.451  Sum_probs=68.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      .....++|||+|||+.+++++|+++|..||.|..+.+.        ++||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999885        2499999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        78 ~a~   80 (92)
T 2dgt_A           78 LST   80 (92)
T ss_dssp             ESS
T ss_pred             Ecc
Confidence            864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=6.7e-20  Score=105.93  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCe----EEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEI----IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v----~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      ....+|||+|||+++++++|+++|..||.|    ..+.++.+. +|+++|||||+|.+.++|++|++. ++..+.++.+.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            456899999999999999999999999875    688888885 899999999999999999999976 99999999998


Q ss_pred             eccC
Q 034039          100 DMLS  103 (105)
Q Consensus       100 v~~~  103 (105)
                      |..+
T Consensus        99 V~~a  102 (123)
T 2dha_A           99 LFRS  102 (123)
T ss_dssp             CEEE
T ss_pred             EEEC
Confidence            8764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.1e-18  Score=97.15  Aligned_cols=74  Identities=31%  Similarity=0.459  Sum_probs=67.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhcc--CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQH--GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      ....++|||+|||+.+++++|+++|..|  |.|..+.+.        ++||||+|.+.++|+.|+..|||..+.|+.++|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3467899999999999999999999999  889888763        479999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        84 ~~a~   87 (99)
T 2cpd_A           84 TLAK   87 (99)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            8875

>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=99.80  E-value=2.5e-19  Score=107.20  Aligned_cols=99  Identities=30%  Similarity=0.469  Sum_probs=81.3

Q ss_pred             CCCceeccccccccc--cccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHH
Q 034039            4 LNGSVRFSHSVRFTR--LLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA   81 (105)
Q Consensus         4 ~~~~~~~~~~~~~~~--~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a   81 (105)
                      +++..+..+.+....  +........+|||+|||+.+++++|+++|..||.+..+.+..+..+|.++|+|||+|.+.++|
T Consensus        64 l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A  143 (167)
T 1fxl_A           64 LNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA  143 (167)
T ss_dssp             HTTCEETTEECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             cCCCccCCceEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHH
Confidence            455555555444322  222334668999999999999999999999999999999999888899999999999999999


Q ss_pred             HHHHHHcCCceeeeee--eeecc
Q 034039           82 GEAIKEMDGLVCRTSK--DTDML  102 (105)
Q Consensus        82 ~~a~~~l~g~~~~~~~--~~v~~  102 (105)
                      ..|++.|||..+.|+.  ++|..
T Consensus       144 ~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A          144 EEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             HHHHHHhcCCccCCCccceEEEe
Confidence            9999999999999976  55543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.6e-19  Score=97.09  Aligned_cols=74  Identities=30%  Similarity=0.479  Sum_probs=68.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+.+|..||.|..+.+..        +||||+|.+.++|+.|++.|+|..+.|+.++|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999998862        4899999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        78 a~   79 (90)
T 2dnp_A           78 ST   79 (90)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=7.8e-20  Score=102.09  Aligned_cols=73  Identities=29%  Similarity=0.451  Sum_probs=68.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ++|||+|||+++++++|+++|++||.|..+.+..+     ++|||||+|.+.++|+.|++.|+|..+.|+.++|..++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEcc
Confidence            47999999999999999999999999999998865     56899999999999999999999999999999998764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.80  E-value=6.1e-20  Score=102.70  Aligned_cols=75  Identities=31%  Similarity=0.532  Sum_probs=67.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+. +|.++|||||+|.+.++|+.|++  ++..+.|+.+.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~   81 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLG   81 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEE
Confidence            346799999999999999999999999999999999998 99999999999999999999998  7777777776654

>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=99.80  E-value=3.2e-19  Score=106.02  Aligned_cols=77  Identities=30%  Similarity=0.469  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+.+..+     ++|||||+|.+.++|..|+..|||..+.|+.++|..
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999998765     468999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       145 a~  146 (150)
T 2i2y_A          145 SN  146 (150)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.80  E-value=1.2e-19  Score=103.09  Aligned_cols=74  Identities=15%  Similarity=0.104  Sum_probs=67.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|.+||.|..+.+..      .++||||+|.+.++|+.|++.|||..+.|+.+.|..++
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999998763      45799999999999999999999999999999998653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=1.1e-18  Score=96.38  Aligned_cols=75  Identities=13%  Similarity=0.226  Sum_probs=66.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+.+|..||.|..+  ..+..++.   ||||+|.+.++|++|+. |+|..+.|+.++|..+
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            356799999999999999999999999999987  55555554   99999999999999999 9999999999999865


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        80 ~   80 (94)
T 2e5g_A           80 E   80 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=8.6e-20  Score=101.02  Aligned_cols=77  Identities=26%  Similarity=0.369  Sum_probs=69.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.|..+     ..++.++|||||+|.+.++|..|+..|+|..+.|+.++|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3456899999999999999999999999988666     23788999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        88 a~   89 (96)
T 1fjc_A           88 TG   89 (96)
T ss_dssp             CS
T ss_pred             cC
Confidence            64

>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=99.80  E-value=6.4e-19  Score=98.73  Aligned_cols=73  Identities=26%  Similarity=0.448  Sum_probs=67.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+.        ++||||+|.+.++|+.|++.|+|..+.|+.++|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456799999999999999999999999999999875        359999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        81 ~   81 (103)
T 2dgu_A           81 K   81 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=2.5e-19  Score=99.27  Aligned_cols=74  Identities=22%  Similarity=0.384  Sum_probs=67.2

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           23 ANSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ..+.++|||+|||+ .+++++|+.+|.+||.|..+.+.        +|||||+|.+.++|+.|++.|+|..+.|+.++|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999998 99999999999999999999884        5899999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        79 ~a~   81 (96)
T 2kvi_A           79 VSS   81 (96)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            763

>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=99.79  E-value=1.4e-19  Score=102.97  Aligned_cols=77  Identities=10%  Similarity=0.081  Sum_probs=67.9

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC--ceeeeeee
Q 034039           22 DANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG--LVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g--~~~~~~~~   98 (105)
                      ...+.++|||+|||++ +++++|+++|.+||.|..+.+..      .+|||||+|.+.++|+.|++.|++  ..+.|+.+
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3456789999999998 99999999999999999998864      358999999999999999998864  56999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      .|.+++
T Consensus        95 ~V~~a~  100 (112)
T 1x4f_A           95 KVDLSE  100 (112)
T ss_dssp             EEEEEC
T ss_pred             EEEECc
Confidence            998764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=3.5e-19  Score=98.55  Aligned_cols=77  Identities=19%  Similarity=0.154  Sum_probs=69.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+++++++|+.+|..||.|..+ .+..++.++    .|||+|.+.++|+.|+..|||..+.|+.++|..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999999999999999 477766443    399999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        89 a~   90 (96)
T 2e44_A           89 IP   90 (96)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.79  E-value=4.1e-19  Score=110.87  Aligned_cols=78  Identities=33%  Similarity=0.576  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...+|||+|||+.+++++|+++|..||.|..+.++.+.  +.++|||||+|.+.++|+.|++.|||..+.|+.|+|..++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999885  3478999999999999999999999999999999998764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.79  E-value=9e-19  Score=107.37  Aligned_cols=81  Identities=30%  Similarity=0.486  Sum_probs=74.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|..|++. ++..+.|+.+.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            345678999999999999999999999999999999999988899999999999999999999966 8999999999887


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        88 ~~   89 (196)
T 1l3k_A           88 RA   89 (196)
T ss_dssp             EC
T ss_pred             cc
Confidence            65

>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=99.79  E-value=5.3e-20  Score=108.38  Aligned_cols=79  Identities=19%  Similarity=0.244  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|.+|| +..+.++.++ +++++|||||+|.+.++|++|+ .+|+..+.++.++|..
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34567999999999999999999999999 6699999887 5999999999999999999999 8999999999999986


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       120 a~  121 (139)
T 2hgn_A          120 NS  121 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.79  E-value=1.9e-19  Score=104.36  Aligned_cols=78  Identities=21%  Similarity=0.252  Sum_probs=70.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeE--EEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEII--EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .....+|||+|||+++++++|+++|..| .+.  .+.++.++. |+++|||||+|.+.++|++|++. ++..+.|+.+.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3456789999999999999999999999 566  899998884 99999999999999999999974 779999999998


Q ss_pred             ccC
Q 034039          101 MLS  103 (105)
Q Consensus       101 ~~~  103 (105)
                      ..+
T Consensus       116 ~~a  118 (126)
T 2hgm_A          116 FKS  118 (126)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            765

>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=99.79  E-value=7.1e-20  Score=108.09  Aligned_cols=81  Identities=21%  Similarity=0.321  Sum_probs=70.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEE------EEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV------KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~------~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      ....++|||+|||+.+++++|+.+|..||.|..+      .+... .+|.++|||||+|.+.++|..|+..|||..+.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~-~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM-KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE-EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec-cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            4567899999999999999999999999988653      11111 2688999999999999999999999999999999


Q ss_pred             eeeeccCC
Q 034039           97 KDTDMLST  104 (105)
Q Consensus        97 ~~~v~~~~  104 (105)
                      .++|.+++
T Consensus       121 ~l~V~~a~  128 (143)
T 3egn_A          121 PMVVQFAR  128 (143)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEECC
Confidence            99998874

>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=99.79  E-value=2.8e-19  Score=102.19  Aligned_cols=68  Identities=24%  Similarity=0.391  Sum_probs=61.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      ...++|||+|||+++++++|+++|.+||.|..+.+..+       +||||+|.+.++|+.|++.|||..+.|+.+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~   81 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   81 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEe
Confidence            45689999999999999999999999999999988654       799999999999999999999999999983

>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=99.79  E-value=5.2e-19  Score=96.58  Aligned_cols=73  Identities=16%  Similarity=0.187  Sum_probs=67.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|.+| .|..+.+.      .++|||||+|.+.++|+.|++.|||..+.|+.++|..++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 99888874      467999999999999999999999999999999998764

>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=99.78  E-value=1.2e-18  Score=104.98  Aligned_cols=78  Identities=32%  Similarity=0.439  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee---eeeeeec
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR---TSKDTDM  101 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~---~~~~~v~  101 (105)
                      ..++|||+|||+.+++++|+++|..||.|..+.+..+. +|.++|||||+|.+.++|..|++.|||..+.   ++.++|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            56799999999999999999999999999999999886 7899999999999999999999999998876   4889887


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      ++
T Consensus       173 ~a  174 (175)
T 3nmr_A          173 FA  174 (175)
T ss_dssp             EC
T ss_pred             ec
Confidence            65

>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=99.78  E-value=5.1e-19  Score=97.39  Aligned_cols=74  Identities=24%  Similarity=0.354  Sum_probs=65.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC-ceeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGE-IIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG-LVCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g-~~~~~~~~~v~  101 (105)
                      ...++|||+|||+++++++|+++|.+||. +..+.+.       +++||||+|.+.++|+.|++.||| ..+.|+.++|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45679999999999999999999999999 6555542       458999999999999999999999 99999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        79 ~a~   81 (93)
T 2cqh_A           79 YSV   81 (93)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            764

>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=99.78  E-value=2e-18  Score=103.75  Aligned_cols=77  Identities=16%  Similarity=0.251  Sum_probs=68.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee--eeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT--SKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~--~~~~v~  101 (105)
                      ....+|||+||++.+++++|+++|++||.|.++.+....    .++||||+|.+.++|+.|++.|||..+.+  +.|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            445679999999999999999999999999999986443    46899999999999999999999999965  899998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus       120 ~Ak  122 (164)
T 1sjr_A          120 FSK  122 (164)
T ss_dssp             ECS
T ss_pred             Eec
Confidence            765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.3e-18  Score=103.93  Aligned_cols=76  Identities=22%  Similarity=0.411  Sum_probs=71.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++|||+|||+++++++|+++|+.||.|..+.+..+. +++++|||||+|.+.++|..|++.|+|..+.|+.+++..+
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEc
Confidence            479999999999999999999999999999999887 6889999999999999999999999999999999998765

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.78  E-value=2.2e-18  Score=107.02  Aligned_cols=79  Identities=22%  Similarity=0.428  Sum_probs=71.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||+++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|..|++.|+|..+.|+.+.|..+
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            4679999999999999999999999999999999998888999999999999999999999999999999999998654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=99.54  Aligned_cols=68  Identities=26%  Similarity=0.506  Sum_probs=60.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCC---CCccceEEEEeCCHHHHHHHHHHc---CCce
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVT---GQSRGYGFVKFASEAAAGEAIKEM---DGLV   92 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a~~~l---~g~~   92 (105)
                      ...++|||+|||+.+++++|+++|.+||.|. +.++.+..+   |.++|||||+|.+.++|+.|++.|   +|..
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~   79 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKL   79 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcE
Confidence            4568899999999999999999999999999 777777656   789999999999999999999988   6653

>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=99.77  E-value=2.6e-18  Score=97.86  Aligned_cols=75  Identities=13%  Similarity=0.217  Sum_probs=65.6

Q ss_pred             CCCCceEEE--cCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee-----ee
Q 034039           23 ANSRTKLFI--GGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC-----RT   95 (105)
Q Consensus        23 ~~~~~~l~v--~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-----~~   95 (105)
                      ..+..+|||  +||++++++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|++.|||..+     .+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345678999  78999999999999999999999987753      258999999999999999999999998     67


Q ss_pred             eeeeeccC
Q 034039           96 SKDTDMLS  103 (105)
Q Consensus        96 ~~~~v~~~  103 (105)
                      +.+.|.++
T Consensus        96 ~~l~v~~a  103 (114)
T 2cq2_A           96 ITLYLNFV  103 (114)
T ss_dssp             EECEEEEE
T ss_pred             cEEEEEec
Confidence            77777654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.76  E-value=8.9e-18  Score=97.60  Aligned_cols=76  Identities=16%  Similarity=0.293  Sum_probs=67.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccce-EEEEeCCHHHHHHHHHHcCCceeee--eeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGY-GFVKFASEAAAGEAIKEMDGLVCRT--SKDTD  100 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~g~~~~~--~~~~v  100 (105)
                      ...-.|||+||++.+++++|+++|++||.|.++.+....     +++ |||+|.+.++|+.|++.|||..+.+  +.+++
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            345578899999999999999999999999999876542     467 9999999999999999999999988  88998


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus       101 ~~ak  104 (130)
T 3zzy_A          101 DFSK  104 (130)
T ss_dssp             EECS
T ss_pred             EecC
Confidence            8765

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.76  E-value=3.7e-18  Score=106.26  Aligned_cols=75  Identities=21%  Similarity=0.222  Sum_probs=69.1

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLS-YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~-~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+||| +.+++++|+++|..||.|.++.+..+     .+|||||+|.+.++|+.|++.|||..+.|+.|+|..+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46789999999 79999999999999999999998754     3689999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        78 ~   78 (205)
T 3tyt_A           78 K   78 (205)
T ss_dssp             S
T ss_pred             c
Confidence            4

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-17  Score=91.88  Aligned_cols=74  Identities=23%  Similarity=0.424  Sum_probs=66.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|+  .+++++|+++|.+||.|..+.+.      .++|||||+|.+.++|+.|+..|+|..+.|+.++|..
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  89999999999999999999884      3568999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        84 a~   85 (97)
T 1x5p_A           84 AR   85 (97)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.76  E-value=8.5e-18  Score=103.01  Aligned_cols=79  Identities=27%  Similarity=0.466  Sum_probs=73.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|.+|+.. +|..+.|+.+.|..+.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            457999999999999999999999999999999999988899999999999999999999976 7999999999998653

>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=99.76  E-value=4.3e-18  Score=92.45  Aligned_cols=71  Identities=21%  Similarity=0.507  Sum_probs=64.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQH----G-------EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      ...++|||+|||+++++++|+++|..|    |       .+..+.+..+      +|||||+|.+.++|+.|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            346789999999999999999999999    8       8999887644      589999999999999999 999999


Q ss_pred             eeeeeeeec
Q 034039           93 CRTSKDTDM  101 (105)
Q Consensus        93 ~~~~~~~v~  101 (105)
                      +.|+.++|.
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999999885

>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=99.76  E-value=7.3e-18  Score=108.81  Aligned_cols=98  Identities=15%  Similarity=0.207  Sum_probs=84.5

Q ss_pred             cCCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHH
Q 034039            3 WLNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG   82 (105)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   82 (105)
                      .+++..+.++.+....    ....++|||+|||+.+++++|+++|..||.|..+.+..+..+|.++|||||+|.+.++|.
T Consensus        76 ~l~~~~~~g~~i~v~~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~  151 (284)
T 3smz_A           76 AFHQSRLRERELSVQL----QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA  151 (284)
T ss_dssp             HHTTCEETTEECEEEE----CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             HcCCCeeCCeEEEEEe----cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHH
Confidence            3456666555554432    235679999999999999999999999999999999999889999999999999999999


Q ss_pred             HHHHHcCCceeeeeeeeeccCC
Q 034039           83 EAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        83 ~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .|+..|+|..+.|+.+.|..+.
T Consensus       152 ~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A          152 RAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             HHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHhCCCEeCCcEEEEEECC
Confidence            9999999999999999987653

>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=99.75  E-value=1.4e-18  Score=104.12  Aligned_cols=79  Identities=29%  Similarity=0.487  Sum_probs=74.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...+|||+|||+.+++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|.+|++ ++|..+.|+.+.|..+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            45789999999999999999999999999999999988789999999999999999999997 89999999999998764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-17  Score=91.56  Aligned_cols=69  Identities=17%  Similarity=0.274  Sum_probs=61.8

Q ss_pred             CceEEEcCCCCCCCHHH----HHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           26 RTKLFIGGLSYDTNETV----LKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~----l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+.|||+|||..+++++    |+++|..|| .|..+       ++   |+|||.|.+.++|.+|++.|+|..+.|+.++|
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            33499999999999987    568999995 99887       33   89999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        79 ~~A~   82 (96)
T 2diu_A           79 SFTP   82 (96)
T ss_dssp             ESSC
T ss_pred             EecC
Confidence            9875

>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=99.75  E-value=1.2e-17  Score=103.10  Aligned_cols=77  Identities=14%  Similarity=0.230  Sum_probs=70.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+.+++++|+++|.+||.|..+.++.+. ++.++|||||+|.+.++|+.|+..++ ..+.|+.+.|+.++
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKD  185 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhH
Confidence            4789999999999999999999999999999999887 68899999999999999999997665 58999999998654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.75  E-value=9.6e-18  Score=101.00  Aligned_cols=70  Identities=31%  Similarity=0.478  Sum_probs=65.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCC--CccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG--QSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ..++|||+|||+++++++|+++|.+||.|..+.+..+..++  .++|||||+|.+.++|+.|++.|+|..+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~   73 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL   73 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEc
Confidence            46789999999999999999999999999999999998665  79999999999999999999999998775

>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=99.74  E-value=1.5e-17  Score=107.38  Aligned_cols=80  Identities=19%  Similarity=0.237  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCC-CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSYDT-NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~-~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ...++|||+|||+.+ ++++|+++|..||.|..+.+..+. +|.++|+|||+|.+.++|..|+..|+|..+.|+.++|.+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            466899999999995 999999999999999999999887 899999999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus       261 a~  262 (284)
T 3smz_A          261 CA  262 (284)
T ss_dssp             CC
T ss_pred             ec
Confidence            64

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.74  E-value=8.1e-18  Score=101.64  Aligned_cols=76  Identities=26%  Similarity=0.374  Sum_probs=69.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+     ..++.++|||||+|.+.++|..|++.|+|..+.|+.++|.++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            356799999999999999999999999988766     347889999999999999999999999999999999999877


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       172 ~  172 (175)
T 1fje_B          172 G  172 (175)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=2.8e-17  Score=94.96  Aligned_cols=72  Identities=18%  Similarity=0.164  Sum_probs=64.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccce-EEEEeCCHHHHHHHHHHcCCceeee--eeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGY-GFVKFASEAAAGEAIKEMDGLVCRT--SKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a~~~l~g~~~~~--~~~~v~~~  103 (105)
                      -.|||+||++.+++++|+++|++||.|..+.+...      .|| |||+|.+.++|..|++.|||..+.|  +.++|..+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45789999999999999999999999999988642      176 9999999999999999999999987  57888876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus       100 k  100 (124)
T 2e5i_A          100 R  100 (124)
T ss_dssp             S
T ss_pred             c
Confidence            5

>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=99.74  E-value=8.6e-18  Score=100.69  Aligned_cols=77  Identities=32%  Similarity=0.622  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +.++|||+|||+++++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|+.|++.  +..+.|+.+.+..+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            357899999999999999999999999999999999988899999999999999999999985  45677777766543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.74  E-value=4.9e-17  Score=91.55  Aligned_cols=81  Identities=10%  Similarity=0.071  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCC-----CCCHHHHHHHHhccCCeEEEEEEecCCC-CCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           24 NSRTKLFIGGLSY-----DTNETVLKDAFGQHGEIIEVKVICDRVT-GQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        24 ~~~~~l~v~~l~~-----~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      .++++|+|.|+..     +-++++|++.|++||.|..+.++.++.+ +.++|++||+|.+.++|.+|++.|||..+.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567899999863     2368899999999999999999987643 578999999999999999999999999999999


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      +.|.++.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9998764

>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=99.74  E-value=2.1e-17  Score=90.47  Aligned_cols=72  Identities=24%  Similarity=0.293  Sum_probs=59.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee--eeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR--TSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~--~~~~~v  100 (105)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|+    .+++..+.  |+.+.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~----~~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQ----SLCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHH----HHTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHH----HHcCCCcccCCEEEEE
Confidence            356789999999999999999999999999999998764     6799999999999988    35666655  777777


Q ss_pred             ccC
Q 034039          101 MLS  103 (105)
Q Consensus       101 ~~~  103 (105)
                      ..+
T Consensus        79 ~~a   81 (89)
T 3d2w_A           79 SNA   81 (89)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            654

>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=99.74  E-value=2.4e-17  Score=106.30  Aligned_cols=80  Identities=23%  Similarity=0.370  Sum_probs=72.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLK----DAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      +....++|||+|||+.+++++|+    ++|..||.|..+.+..   +++++|||||+|.+.++|..|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            44568899999999999999966    8999999999998764   6778999999999999999999999999999999


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      ++|..++
T Consensus        82 l~v~~a~   88 (282)
T 3pgw_A           82 MRIQYAK   88 (282)
T ss_pred             EEEEEec
Confidence            9998653

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.73  E-value=8.4e-18  Score=108.88  Aligned_cols=80  Identities=18%  Similarity=0.308  Sum_probs=73.0

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCC-CCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRV-TGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ...++|||+|||+. +++++|+++|..||.|..+.+..+.. +|.++|||||+|.+.++|..|+ .|||..+.|+.+.|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            35689999999999 99999999999999999999988774 4889999999999999999999 999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus       287 ~a~  289 (292)
T 2ghp_A          287 LAD  289 (292)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            875

>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=99.72  E-value=3.7e-17  Score=102.95  Aligned_cols=78  Identities=19%  Similarity=0.268  Sum_probs=71.1

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           22 DANSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .....++|||+|||+ .+++++|+++|..||.|..+.+..+.     +|||||+|.+.++|+.|++.|+|..+.|+.+.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999998764     579999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus       105 ~~a~  108 (229)
T 2adc_A          105 TLSK  108 (229)
T ss_dssp             ECCS
T ss_pred             EEec
Confidence            8764

>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=99.71  E-value=1.4e-16  Score=102.76  Aligned_cols=77  Identities=26%  Similarity=0.368  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-eeeeeecc
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-TSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-~~~~~v~~  102 (105)
                      ...++|||+|||..+++++|+++|..||.|..+.+..++     +|||||+|.+.++|..|++.|||..+. |+.|+|.+
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            456889999999999999999999999999999988553     479999999999999999999999999 99999998


Q ss_pred             CCC
Q 034039          103 STG  105 (105)
Q Consensus       103 ~~~  105 (105)
                      ++.
T Consensus       280 akk  282 (282)
T 3pgw_A          280 AKK  282 (282)
T ss_pred             ecC
Confidence            763

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.70  E-value=7.4e-17  Score=103.37  Aligned_cols=95  Identities=25%  Similarity=0.339  Sum_probs=78.0

Q ss_pred             CCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHH
Q 034039            4 LNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE   83 (105)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   83 (105)
                      +++..+.++.+....    .....+|||+|||+.+++++|+++|..||.|..+.+..+. +|.++|||||+|.+.++|..
T Consensus        78 l~g~~i~g~~l~v~~----a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~  152 (261)
T 3sde_A           78 LDGTILKSRPLRIRF----ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARK  152 (261)
T ss_dssp             HTTCEETTEECEEEE----CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHH
T ss_pred             cCCcEECCceeEeee----cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHH
Confidence            456666555544433    2346799999999999999999999999999999999995 89999999999999999999


Q ss_pred             HHHHcCCc-eee---eeeeeeccC
Q 034039           84 AIKEMDGL-VCR---TSKDTDMLS  103 (105)
Q Consensus        84 a~~~l~g~-~~~---~~~~~v~~~  103 (105)
                      |+..|++. .+.   ++.+.|..+
T Consensus       153 A~~~l~~~~~~~~~~~r~i~v~~~  176 (261)
T 3sde_A          153 ALERCGDGAFLLTTTPRPVIVEPM  176 (261)
T ss_dssp             HHHHHHHSCEESSSSCCBCEEEEC
T ss_pred             HHHHhcCCeEEecCCCceEEEeec
Confidence            99999654 433   888887654

>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=99.68  E-value=3.1e-17  Score=89.39  Aligned_cols=71  Identities=23%  Similarity=0.319  Sum_probs=59.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCce--eeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLV--CRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~--~~~~~~~v~  101 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..+     ++|||||+|.+.++|+++    ++..  +.++.++|.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~   73 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL----CGEDLIIKGISVHIS   73 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEE
Confidence            34689999999999999999999999999999988654     578999999999999754    4444  467777776


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        74 ~a   75 (88)
T 1wf0_A           74 NA   75 (88)
T ss_dssp             CC
T ss_pred             ec
Confidence            54

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.68  E-value=1.2e-16  Score=101.39  Aligned_cols=76  Identities=22%  Similarity=0.321  Sum_probs=68.9

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           23 ANSRTKLFIGGLSYDT---------NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~---------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      ....++|||+||+..+         ++++|+.+|.+||.|..+.++.      .+|||||+|.+.++|+.|++.|+|..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3467899999999998         7999999999999999999875      358999999999999999999999999


Q ss_pred             ------------eeeeeeeccCC
Q 034039           94 ------------RTSKDTDMLST  104 (105)
Q Consensus        94 ------------~~~~~~v~~~~  104 (105)
                                  .|+.|.|..++
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~  227 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWAN  227 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC
T ss_pred             eccccccccccCCCCEEEEEEcc
Confidence                        89999998764

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.67  E-value=3.2e-16  Score=100.42  Aligned_cols=76  Identities=33%  Similarity=0.490  Sum_probs=68.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|..||.|..+.+..+      +|||||+|.+.++|..|+..|+|..+.|+.++|..
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345679999999999999999999999999999988543      58999999999999999999999999999999986


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      +.
T Consensus        93 a~   94 (261)
T 3sde_A           93 AT   94 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.67  E-value=1.4e-17  Score=100.62  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=68.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||.+..+ ++.+..++.++|||||+|.+.++|..|+ .|+|..+.|+.++|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEe
Confidence            45678899999999999999999999999866442 2233346778999999999999999999 599999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .+.
T Consensus        87 ~~~   89 (175)
T 1fje_B           87 KPK   89 (175)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.67  E-value=7.5e-17  Score=99.20  Aligned_cols=74  Identities=20%  Similarity=0.281  Sum_probs=68.1

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+ .+++++|+++|..||.|..+.+..+.     +|||||+|.+.++|..|++.|+|..+.|+.++|..+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            57899999999 99999999999999999999887654     5799999999999999999999999999999998653

>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=99.67  E-value=2.8e-16  Score=101.73  Aligned_cols=94  Identities=12%  Similarity=0.195  Sum_probs=75.1

Q ss_pred             CCCceeccccccccccccCCCCCceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHH
Q 034039            4 LNGSVRFSHSVRFTRLLSDANSRTKLFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAG   82 (105)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   82 (105)
                      +++..+..+.+....     ...++|||+|||+.+++++|+++|..|| .|..+.+..+. .|.++|||||+|.+.++|.
T Consensus       100 ~~~~~~~g~~i~v~~-----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~  173 (292)
T 2ghp_A          100 KTHKVVGQNEIIVSH-----LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDAR  173 (292)
T ss_dssp             TTTCEETTEECEEEE-----CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHH
T ss_pred             hCCcEeCCcEEEEEE-----CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHH
Confidence            455555555444322     3578999999999999999999999999 99999998877 4788999999999999999


Q ss_pred             HHHHHcCCceeeeeeeeeccC
Q 034039           83 EAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        83 ~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .|+..|+|..+.|+.+.|..+
T Consensus       174 ~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          174 YCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             HHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHhCCCEeCCcEEEEEEC
Confidence            999999999999999998865

>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=99.66  E-value=1.6e-16  Score=98.86  Aligned_cols=71  Identities=14%  Similarity=0.206  Sum_probs=63.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCe--EEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEI--IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK   97 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v--~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~   97 (105)
                      +.++|||+|||+.+++++|+++|++||.|  ..+.+..+.  +..+|+|||+|.+.++|..|+..|||..+.|+.
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            35689999999999999999999999998  788877654  455699999999999999999999999999885

>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=99.66  E-value=4.7e-16  Score=97.89  Aligned_cols=75  Identities=16%  Similarity=0.192  Sum_probs=68.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-eeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-TSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-~~~~~v~~  102 (105)
                      +.++|||+|||+.+++++|+++|..|| .|..+.+..+     .+|+|||+|.+.++|..|++.|+|..+. |+.++|.+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468899999999999999999999999 9999988542     3579999999999999999999999999 99999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       225 a~  226 (229)
T 2adc_A          225 SK  226 (229)
T ss_dssp             CS
T ss_pred             ec
Confidence            75

>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=5e-17  Score=91.34  Aligned_cols=72  Identities=21%  Similarity=0.285  Sum_probs=63.2

Q ss_pred             EcCCCCCCCHHHHHHHH------------hccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           31 IGGLSYDTNETVLKDAF------------GQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        31 v~~l~~~~~~~~l~~~f------------~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      +.||++.+++++|++.|            ++||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||..+.|+.+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45677777777777666            999999999998876 57899999999999999999999999999999999


Q ss_pred             eeccC
Q 034039           99 TDMLS  103 (105)
Q Consensus        99 ~v~~~  103 (105)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99876

>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=99.65  E-value=2.1e-15  Score=85.62  Aligned_cols=79  Identities=18%  Similarity=0.198  Sum_probs=66.6

Q ss_pred             CCCCCceEEEcCCCCCCC-----------HHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           22 DANSRTKLFIGGLSYDTN-----------ETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~-----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ......+|+|.||.....           +++|+++|.+||.|..+.+ .+.   .++|||||+|.+.++|+.|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345678999999954432           5789999999999999965 443   2789999999999999999999999


Q ss_pred             ceeeeeeeeeccCC
Q 034039           91 LVCRTSKDTDMLST  104 (105)
Q Consensus        91 ~~~~~~~~~v~~~~  104 (105)
                      ..+.|+.++|.++.
T Consensus        87 ~~~~gr~l~v~~a~  100 (112)
T 2dit_A           87 RWFGGRQITAQAWD  100 (112)
T ss_dssp             CEETTEECEEEECC
T ss_pred             CEECCcEEEEEEeC
Confidence            99999999998764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.63  E-value=1.2e-15  Score=93.78  Aligned_cols=75  Identities=16%  Similarity=0.192  Sum_probs=68.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccC-CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-eeeeeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHG-EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-TSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-~~~~~v~~  102 (105)
                      +.++|||+|||..+++++|+++|..|| .|..+.+..+     .+|+|||+|.+.++|..|+..|||..+. |+.++|.+
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            478999999999999999999999999 9999988543     2589999999999999999999999999 99999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       194 a~  195 (198)
T 1qm9_A          194 SK  195 (198)
T ss_dssp             EC
T ss_pred             ec
Confidence            64

>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=99.62  E-value=2.4e-15  Score=90.32  Aligned_cols=73  Identities=19%  Similarity=0.463  Sum_probs=64.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQH----G-------EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      ..++|||+|||+++++++|+++|+.|    |       .+..+.+..      ++|||||+|.+.++|+.|+ .++|..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            35789999999999999999999999    6       677776543      4689999999999999999 9999999


Q ss_pred             eeeeeeeccCC
Q 034039           94 RTSKDTDMLST  104 (105)
Q Consensus        94 ~~~~~~v~~~~  104 (105)
                      .|+.++|..+.
T Consensus        76 ~g~~i~v~~~~   86 (172)
T 2g4b_A           76 QGQSLKIRRPH   86 (172)
T ss_dssp             TTEECEEECCS
T ss_pred             cCceeeecCCc
Confidence            99999987653

>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=99.62  E-value=2.1e-15  Score=84.85  Aligned_cols=79  Identities=13%  Similarity=0.090  Sum_probs=66.4

Q ss_pred             CCceEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEEecCCC--CCccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           25 SRTKLFIGGL--SYDTN--------ETVLKDAFGQHGEIIEVKVICDRVT--GQSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        25 ~~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      +++.|.+.|+  |....        .++|++.|++||.|..+.++.+..+  +.++|++||+|.+.++|.+|++.|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4667888887  32332        3689999999999999999887643  3578999999999999999999999999


Q ss_pred             eeeeeeeeccC
Q 034039           93 CRTSKDTDMLS  103 (105)
Q Consensus        93 ~~~~~~~v~~~  103 (105)
                      +.|+.++|.++
T Consensus        84 f~GR~i~v~~~   94 (105)
T 3v4m_A           84 FANRVVVTKYC   94 (105)
T ss_dssp             ETTEECEEEEE
T ss_pred             eCCCEEEEEEe
Confidence            99999999764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.60  E-value=4e-15  Score=91.16  Aligned_cols=73  Identities=19%  Similarity=0.469  Sum_probs=63.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhcc----C-------CeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQH----G-------EIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      ..++|||+|||+++++++|+++|..|    |       .+..+.+.      .++|||||+|.+.++|+.|+ .|+|..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            36789999999999999999999999    5       56666543      35689999999999999999 9999999


Q ss_pred             eeeeeeeccCC
Q 034039           94 RTSKDTDMLST  104 (105)
Q Consensus        94 ~~~~~~v~~~~  104 (105)
                      .|+.++|..+.
T Consensus        76 ~g~~i~v~~~~   86 (198)
T 2yh0_A           76 QGQSLKIRRPH   86 (198)
T ss_dssp             TTEEEEEECCC
T ss_pred             cCceEEEeCCC
Confidence            99999998653

>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=99.59  E-value=8.4e-15  Score=83.93  Aligned_cols=79  Identities=16%  Similarity=0.208  Sum_probs=67.6

Q ss_pred             CCceEEEcCCCC--C---CCHHHHHHHHhccCCeEEEEEEecCC----CCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           25 SRTKLFIGGLSY--D---TNETVLKDAFGQHGEIIEVKVICDRV----TGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        25 ~~~~l~v~~l~~--~---~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ++++|++.|+-.  .   --+++|++.|.+||.|..+.++.+..    ++.++|++||+|.+.++|.+|++.|||..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            467899998832  1   23588999999999999999988753    35678999999999999999999999999999


Q ss_pred             eeeeeccC
Q 034039           96 SKDTDMLS  103 (105)
Q Consensus        96 ~~~~v~~~  103 (105)
                      +.++|.++
T Consensus        99 R~i~v~~~  106 (118)
T 3ue2_A           99 RKVVAEVY  106 (118)
T ss_dssp             EECEEEEE
T ss_pred             cEEEEEEc
Confidence            99999864

>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=99.52  E-value=3.7e-14  Score=94.07  Aligned_cols=66  Identities=12%  Similarity=0.231  Sum_probs=58.2

Q ss_pred             CCCCceEEEcC--CCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           23 ANSRTKLFIGG--LSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        23 ~~~~~~l~v~~--l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      +.+..+|||+|  |+..+++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|++.|||..+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            45677999998  578899999999999999998876642      4689999999999999999999999884

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=1.4e-13  Score=76.68  Aligned_cols=62  Identities=19%  Similarity=0.178  Sum_probs=53.9

Q ss_pred             CCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           36 YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        36 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..+++++|+++|.+||.|..+.++     +.++|||||+|.+.++|+.|++.+++  +.++.++|..++
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~   88 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLE   88 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEcc
Confidence            468999999999999999999987     35789999999999999999998665  568888888764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=4.7e-13  Score=76.69  Aligned_cols=77  Identities=22%  Similarity=0.176  Sum_probs=66.4

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCC-HHHHHHHHHHcC--Cceeeeee
Q 034039           22 DANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFAS-EAAAGEAIKEMD--GLVCRTSK   97 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~-~~~a~~a~~~l~--g~~~~~~~   97 (105)
                      .......|||+||++. ++.++|+++|..||+|..+.+..+..      .|||.|.+ ..+|..|++.++  +..|.+..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3457889999999999 99999999999999999999977652      59999999 899999999995  67788887


Q ss_pred             eeeccCC
Q 034039           98 DTDMLST  104 (105)
Q Consensus        98 ~~v~~~~  104 (105)
                      +++.+..
T Consensus        88 ~~~evL~   94 (121)
T 1owx_A           88 VTWEVLE   94 (121)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            7776543

>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=99.43  E-value=2.2e-13  Score=77.57  Aligned_cols=75  Identities=19%  Similarity=0.176  Sum_probs=61.0

Q ss_pred             CCceEEEcCCCCCC----------CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           25 SRTKLFIGGLSYDT----------NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        25 ~~~~l~v~~l~~~~----------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      +++.|.+.|+=..-          .+++|++.|++||.|..+.+..+.    .+|++||+|.+.++|.+|++.|||..+.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45567777763221          224789999999999999886543    5799999999999999999999999999


Q ss_pred             eeeeeeccC
Q 034039           95 TSKDTDMLS  103 (105)
Q Consensus        95 ~~~~~v~~~  103 (105)
                      |+.++|.++
T Consensus        82 GR~i~v~~~   90 (114)
T 3s6e_A           82 GKMITAAYV   90 (114)
T ss_dssp             TEECEEEEE
T ss_pred             CEEEEEEEE
Confidence            999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=2.4e-12  Score=69.89  Aligned_cols=72  Identities=19%  Similarity=0.256  Sum_probs=59.7

Q ss_pred             CCCceEEEcCCCC----CCCH----HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           24 NSRTKLFIGGLSY----DTNE----TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        24 ~~~~~l~v~~l~~----~~~~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ++..+|+|.-.+.    +...    .+|.+.|.+||.+..++++.++        +||+|.+.++|.+|+. |||..+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            4466787875552    2333    5688999999999999998764        8999999999999997 99999999


Q ss_pred             eeeeeccCC
Q 034039           96 SKDTDMLST  104 (105)
Q Consensus        96 ~~~~v~~~~  104 (105)
                      +.++|.+++
T Consensus        76 r~LkV~lkt   84 (91)
T 2dnr_A           76 RTITIALKS   84 (91)
T ss_dssp             EEEEEEECC
T ss_pred             eEEEEEeCC
Confidence            999999875

>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=99.18  E-value=8.6e-11  Score=73.48  Aligned_cols=66  Identities=17%  Similarity=0.198  Sum_probs=58.3

Q ss_pred             CCHHHHHHHHhccCCeEEEEEEecC----CCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           38 TNETVLKDAFGQHGEIIEVKVICDR----VTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        38 ~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      -.+++|.+.|.+||.|..+.+..+.    .++.++|++||+|.+.++|.+|++.|||..+.|+.+.+.+.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~  210 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVY  210 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEc
Confidence            3457899999999999999988554    34578999999999999999999999999999999998865

>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=99.16  E-value=7.2e-11  Score=64.43  Aligned_cols=72  Identities=19%  Similarity=0.194  Sum_probs=60.1

Q ss_pred             CCCCceEEEcCCCCC------CCH---HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           23 ANSRTKLFIGGLSYD------TNE---TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~------~~~---~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      .++..+|+|.-+++.      ..+   .+|.+.|..||.+..++++.++        +||+|.+.++|.+|+. |+|..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            345778999877642      232   4588899999999999998764        9999999999999997 999999


Q ss_pred             eeeeeeeccC
Q 034039           94 RTSKDTDMLS  103 (105)
Q Consensus        94 ~~~~~~v~~~  103 (105)
                      .|+.++|.+.
T Consensus        83 ~Gr~L~V~~k   92 (95)
T 1ufw_A           83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             CCeEEEEecc
Confidence            9999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.78  E-value=7.1e-08  Score=53.87  Aligned_cols=71  Identities=11%  Similarity=0.107  Sum_probs=63.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhcc-----CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQH-----GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~-----g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      ..++|-+-+||..++...++.+...+     |.+..+.+..+.      +-|+|+|.+...|-+|.=.|+|..+.|+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            45678888999999999999999999     999999887665      4599999999999999889999999999998


Q ss_pred             ec
Q 034039          100 DM  101 (105)
Q Consensus       100 v~  101 (105)
                      +-
T Consensus        94 ~g   95 (117)
T 2l9w_A           94 SG   95 (117)
T ss_dssp             EE
T ss_pred             ec
Confidence            74

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=98.29  E-value=8.4e-06  Score=44.58  Aligned_cols=58  Identities=17%  Similarity=0.257  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD   89 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   89 (105)
                      ....+.+++ ++|+.+...+|.++|+.||.+ .+.++-|.       .|||.|.+++.|..|+..+.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            345667777 999999999999999999943 45555553       69999999999999998763

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=98.24  E-value=1.5e-05  Score=43.31  Aligned_cols=70  Identities=13%  Similarity=0.121  Sum_probs=56.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCC--ccceEEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ--SRGYGFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      ++|.|++||+..+++++.+.+.....+....++....+.+  ...-|||.|.+.+++....+.++|..+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            4688999999999999999999888777666655443322  224589999999999999999999987544

>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=98.12  E-value=1.1e-05  Score=44.71  Aligned_cols=73  Identities=8%  Similarity=-0.020  Sum_probs=59.1

Q ss_pred             CCceEEEcCCCCCCCH-----HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNE-----TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~-----~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      -.++|+|.||+.++-.     +.++.+|..|+++.......+-      .-..|.|.+.++|.+|-..|++..+.|+.++
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            3568999999886522     4678899999988776665443      2367999999999999999999999999999


Q ss_pred             eccC
Q 034039          100 DMLS  103 (105)
Q Consensus       100 v~~~  103 (105)
                      +..+
T Consensus        78 ~YFg   81 (104)
T 1wey_A           78 LYFA   81 (104)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            8764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.88  E-value=2.8e-05  Score=42.61  Aligned_cols=55  Identities=18%  Similarity=0.243  Sum_probs=45.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD   89 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   89 (105)
                      .+.+++ ++|+.+...+|..+|+.|| -..+.++-|.       .|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            455666 9999999999999999998 4556666553       69999999999999998764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.73  E-value=0.00054  Score=37.82  Aligned_cols=56  Identities=16%  Similarity=0.255  Sum_probs=45.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhc---c--CCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHH
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQ---H--GEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE   87 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~---~--g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~   87 (105)
                      ....+|.|.|||+.+.++.|.-+|+.   -  |.+..++...        +-|+|+|.+...|+..++.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC
Confidence            34578999999999999999999976   2  4677766532        3589999999999999955

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.70  E-value=7.5e-05  Score=40.87  Aligned_cols=71  Identities=10%  Similarity=0.058  Sum_probs=50.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCC--ccceEEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQ--SRGYGFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      +-+|.|+.||+..|++++.+.+...-......+.....+.+  ...-|||.|.+.++.....+.++|..+.+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            44789999999999999888777655543333322211111  123589999999999999999999987544

>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=97.55  E-value=0.00044  Score=39.21  Aligned_cols=63  Identities=17%  Similarity=0.283  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT   95 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~   95 (105)
                      ..+-|.|-++|+.. ...+...|.+||.|.+....    +  ...+-.|.|.++.+|++|+ ..||..+.+
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL-~kNG~ii~g   85 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKAL-SKDGRIFGE   85 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHH-TTTTCEETT
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHH-HhCCeEecC
Confidence            45678888999885 45677889999999877652    1  1247889999999999999 558888864

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.00  E-value=0.00048  Score=47.52  Aligned_cols=54  Identities=19%  Similarity=0.218  Sum_probs=41.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHH
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI   85 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~   85 (105)
                      .++|+|. .|...++.+|.+.|++||+|..+.+..+.  |   .|+.|+|.+.+++..++
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHH
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHH
Confidence            4789997 79999999999999999999998876543  2   69999999999988765

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.47  E-value=0.0033  Score=36.71  Aligned_cols=33  Identities=18%  Similarity=0.193  Sum_probs=26.4

Q ss_pred             EEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           56 VKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        56 ~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      +.+..+.  ..++||+||+|.+.++|+.|++.+++
T Consensus         3 ~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            3 YKLILNG--KTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEecC--ccccchhHHHHHHHHhHHHHHHhhcc
Confidence            3455553  35889999999999999999988764

>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=96.35  E-value=0.0012  Score=38.42  Aligned_cols=40  Identities=15%  Similarity=-0.022  Sum_probs=34.4

Q ss_pred             CCCccceEEEEeCCHHHHHHHHHHc-CCceeeeeeeeeccCC
Q 034039           64 TGQSRGYGFVKFASEAAAGEAIKEM-DGLVCRTSKDTDMLST  104 (105)
Q Consensus        64 ~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~~~~~~v~~~~  104 (105)
                      ....+|+++++|.+.++|++|++.+ ||..++| .+.+..+.
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~   49 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDAT   49 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceeccccc
Confidence            3457799999999999999999999 9999999 88777653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.69  E-value=0.015  Score=33.46  Aligned_cols=75  Identities=15%  Similarity=0.198  Sum_probs=47.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEE-EEEEec--------CCCCC-----ccceEEEEeCCHHHHHHHHHHcCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIE-VKVICD--------RVTGQ-----SRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~--------~~~~~-----~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ....|.|-+.|++.... +...|++||.|.. ......        +...+     ...+-.|+|.++.+|.+|+ ..||
T Consensus         6 ~e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENG   83 (132)
T ss_dssp             --CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTT
T ss_pred             CceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCC
Confidence            34567777998766544 5678999998744 211100        00000     2346789999999999999 6688


Q ss_pred             ceeeeeeeeec
Q 034039           91 LVCRTSKDTDM  101 (105)
Q Consensus        91 ~~~~~~~~~v~  101 (105)
                      ..+.|.-+-|.
T Consensus        84 ~ii~G~mIGV~   94 (132)
T 3p3d_A           84 AVFNGVLLGVI   94 (132)
T ss_dssp             CEETTEECEEE
T ss_pred             eEeCcEEEEEE
Confidence            88877644443

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=94.67  E-value=0.19  Score=35.13  Aligned_cols=57  Identities=18%  Similarity=0.227  Sum_probs=44.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG   90 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g   90 (105)
                      ....++++ +|+.+...+|.+.|+.||.+ .+.++-+       ..+||.|.+.+.|..+++.++.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            34566665 88899999999999999954 4444322       3599999999999999998863

---

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	105
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-17
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-16
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-16
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-15
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	4e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.003

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.0 bits (166), Expect = 4e-17
 Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-VTGQSRGYGFVKFASE 78
          +    + +K+ +  + +  N+  +++ F   GE+  V++      TG  RG+GFV F ++
Sbjct: 2  VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 79 AAAGEAIKEMD 89
            A +A   + 
Sbjct: 62 QDAKKAFNALC 72

>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 = 67.3 bits (164), Expect = 6e-17
 Identities = 21/65 (32%), Positives = 35/65 (53%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + L + GL + T E  LK+ F   GE++ V+V  D  TG S+G+GFV+F       + + 
Sbjct: 9  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 87 EMDGL 91
          +   +
Sbjct: 69 QRHMI 73

>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 = 66.9 bits (163), Expect = 8e-17
 Identities = 19/69 (27%), Positives = 37/69 (53%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          ++   T L++  L     +  L   FG++G I++  ++ D++TG+ RG  FV++     A
Sbjct: 2  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 82 GEAIKEMDG 90
           EAI  ++ 
Sbjct: 62 QEAISALNN 70

>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 = 66.5 bits (162), Expect = 1e-16
 Identities = 21/63 (33%), Positives = 33/63 (52%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
           L++G L  D  E +L + F   G I+ ++V  D +T +S GY +V F   A A  A+  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 88 MDG 90
          M+ 
Sbjct: 62 MNF 64

>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 = 64.6 bits (157), Expect = 5e-16
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
          K+FIGGLS+ T +  L++ FGQ GE+ E  V+ D +T +SRG+GFV F  +A   + +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 87 ---EMDGLVCRTSK 97
             E+D        
Sbjct: 62 SRHELDSKTIDPKV 75

>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 = 63.1 bits (153), Expect = 2e-15
 Identities = 25/64 (39%), Positives = 38/64 (59%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++ GL     +  L+  F Q+G II  +++ D+VTG SRG GF++F     A EAIK
Sbjct: 7  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 87 EMDG 90
           ++G
Sbjct: 67 GLNG 70

>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 = 63.1 bits (153), Expect = 2e-15
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
          K+F+GGLS DT E  +++ FG  GE+  +++  D  T + RG+ F+ F  E    + ++ 
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 87 ---EMDGLVCRTSK 97
              +    C    
Sbjct: 61 KYHNVGLSKCEIKV 74

>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 = 62.7 bits (152), Expect = 4e-15
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T L +  L  D  +  L   F   G I   +++ D  TG S GY FV F SE  +  A
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 85 IKEMDG 90
          IK ++G
Sbjct: 61 IKVLNG 66

>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 = 62.4 bits (151), Expect = 5e-15
 Identities = 30/71 (42%), Positives = 43/71 (60%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          +S+ N    +++GGL    +E +L + F Q G ++   +  DRVTGQ +GYGFV+F SE 
Sbjct: 3  ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 80 AAGEAIKEMDG 90
           A  AIK MD 
Sbjct: 63 DADYAIKIMDM 73

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-14
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 4/71 (5%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK- 86
          K+FIGGLS+DT +  LKD F + GE+++  +  D +TG+SRG+GFV F    +  + +  
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 87 ---EMDGLVCR 94
             +++G V  
Sbjct: 61 KEHKLNGKVID 71

>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 = 61.6 bits (149), Expect = 1e-14
 Identities = 20/63 (31%), Positives = 32/63 (50%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLFIGGL    N+  +K+     G +    ++ D  TG S+GY F ++       +AI  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 88 MDG 90
          ++G
Sbjct: 63 LNG 65

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 1e-14
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 4/80 (5%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +     KLFIGGLS++T E  L++ + Q G++ +  V+ D  + +SRG+GFV F+S A  
Sbjct: 16 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 75

Query: 82 GEAIK----EMDGLVCRTSK 97
            A+      +DG V    +
Sbjct: 76 DAAMAARPHSIDGRVVEPKR 95

>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 = 60.9 bits (147), Expect = 2e-14
 Identities = 24/66 (36%), Positives = 37/66 (56%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S+T L +  L  +  +   +  FG  GEI   K++ D++TGQS GYGFV +     A +A
Sbjct: 1  SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 85 IKEMDG 90
          I  ++G
Sbjct: 61 INTLNG 66

>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 = 61.1 bits (148), Expect = 2e-14
 Identities = 18/64 (28%), Positives = 38/64 (59%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++G LS+ T E  + + F + G+I ++ +  D++   + G+ FV++ S A A  A++
Sbjct: 8  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 87 EMDG 90
           ++G
Sbjct: 68 YING 71

>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 = 60.4 bits (146), Expect = 2e-14
 Identities = 25/66 (37%), Positives = 37/66 (56%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLFIGGLS++T +  L+  F Q G + +  V+ D  T +SRG+GFV +A+      A+  
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 88 MDGLVC 93
              V 
Sbjct: 68 RPHKVD 73

>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 = 60.4 bits (146), Expect = 5e-14
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           +R  L+I  L Y      + D FG++G I +   I    T ++RG  +V +     A  
Sbjct: 6  VNRI-LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 84 AIKEMDG 90
          A   + G
Sbjct: 62 ACDHLSG 68

>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 = 59.7 bits (144), Expect = 7e-14
 Identities = 22/68 (32%), Positives = 39/68 (57%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A ++  L++GGL+ + ++ VL  AF   G+I ++++  D  T + RG+ FV+F     A 
Sbjct: 2  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 83 EAIKEMDG 90
           AI  M+ 
Sbjct: 62 AAIDNMNE 69

>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 = 59.3 bits (143), Expect = 8e-14
 Identities = 22/70 (31%), Positives = 40/70 (57%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          ++ +    L + GLS  T E  L++ F ++G I +V ++ D+ + +SRG+ FV F +   
Sbjct: 4  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 81 AGEAIKEMDG 90
          A EA +  +G
Sbjct: 64 AKEAKERANG 73

>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 = 57.7 bits (139), Expect = 5e-13
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +      +F   L+       L+D F   G++ +V++I DR + +S+G  +V+F    + 
Sbjct: 14 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 73

Query: 82 GEAIKEMDG 90
                + G
Sbjct: 74 -PLAIGLTG 81

>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 = 57.3 bits (138), Expect = 5e-13
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR---VTGQSRGYGFVKFASEAAAGEAI 85
          LFI  L++ T E  LK  F + G I    +   +       S G+GFV++     A +A+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 86 KEMDG 90
          K++ G
Sbjct: 61 KQLQG 65

>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 = 57.4 bits (138), Expect = 6e-13
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIE--VKVICDRVTGQSRGYGFVKFASEAAAGEA 84
           +LFIGG+        + +   +  E +   +         ++RG+ FV++ S  AA  A
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 85 IKEMDG 90
           +++  
Sbjct: 62 RRKLMP 67

>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 = 56.6 bits (136), Expect = 8e-13
 Identities = 11/66 (16%), Positives = 23/66 (34%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
            T + +  + +  +   + D F  +  I     +     G   G   V F S   A  A
Sbjct: 8  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 85 IKEMDG 90
          + +++ 
Sbjct: 68 VIDLND 73

>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 = 56.5 bits (136), Expect = 1e-12
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KL +  L +  ++  +++ F + G + +  V  DR +G+S G   V F  +A A +A+K+
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 88 MDG 90
           +G
Sbjct: 61 YNG 63

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 1e-12
 Identities = 11/71 (15%), Positives = 29/71 (40%), Gaps = 4/71 (5%)

Query: 20 LSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
          ++  +   ++ +  L Y     VL   F + G ++++          ++    +++A   
Sbjct: 1  MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 56

Query: 80 AAGEAIKEMDG 90
          +A  A   +DG
Sbjct: 57 SAQHAKLSLDG 67

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 1e-12
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 28  KLFIGGLSYDTNETVLKDAFGQHGEIIEVKV-----ICDRVTGQSRGYGFVKFASEAAAG 82
           +L++G + +   E  + D F     +  +       +      Q + + F++F S     
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 83  EAI----KEMDGLVCRTSKDTD 100
           +A+        G   +  +  D
Sbjct: 63  QAMAFDGIIFQGQSLKIRRPHD 84

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 1e-12
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 9/70 (12%)

Query: 22 DANSRTKLFIGGLS-YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            +  +++FIG L+     ++ ++  F ++G+I+   V          G+ FV++ +E  
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERN 62

Query: 81 AGEAIKEMDG 90
          A  A+   DG
Sbjct: 63 ARAAVAGEDG 72

>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 = 56.5 bits (136), Expect = 1e-12
 Identities = 17/78 (21%), Positives = 44/78 (56%), Gaps = 7/78 (8%)

Query: 14 VRFTRLLSDANSR-TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGF 72
          +RF  +++ ++ +   ++ GG++    + +++  F   G+I+E++V  ++       Y F
Sbjct: 5  LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSF 58

Query: 73 VKFASEAAAGEAIKEMDG 90
          V+F++  +A  AI  ++G
Sbjct: 59 VRFSTHESAAHAIVSVNG 76

>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 = 58.5 bits (140), Expect = 1e-12
 Identities = 25/72 (34%), Positives = 38/72 (52%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          +     KLFIGGLS++T +  L+  F Q G + +  V+ D  T +SRG+GFV +A+    
Sbjct: 2  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 82 GEAIKEMDGLVC 93
            A+      V 
Sbjct: 62 DAAMNARPHKVD 73

>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 = 49.2 bits (116), Expect = 4e-09
 Identities = 21/65 (32%), Positives = 39/65 (60%)

Query: 25  SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
           +  K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F    +  + 
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 85  IKEMD 89
           + +  
Sbjct: 156 VIQKY 160

>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 = 55.4 bits (133), Expect = 3e-12
 Identities = 23/68 (33%), Positives = 35/68 (51%)

Query: 23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAG 82
          A+    + +  LS DT ET L++ F   G I  + +  D+ TGQS+G+ F+ F     A 
Sbjct: 5  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 83 EAIKEMDG 90
           AI  + G
Sbjct: 65 RAIAGVSG 72

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 4e-12
 Identities = 32/69 (46%), Positives = 43/69 (62%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          + TK+F+GGL Y T +  L+  F   G+I E  VI DR TG+SRGYGFV  A  AAA  A
Sbjct: 9  TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 85 IKEMDGLVC 93
           K+ + ++ 
Sbjct: 69 CKDPNPIID 77

>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 = 55.1 bits (132), Expect = 6e-12
 Identities = 20/70 (28%), Positives = 33/70 (47%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           +      LFI  L  +  +  L   F   G ++  KV  D+ T  S+ +GFV + +  +
Sbjct: 13 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 81 AGEAIKEMDG 90
          A  AI+ M+G
Sbjct: 73 AQAAIQSMNG 82

>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 = 54.7 bits (131), Expect = 7e-12
 Identities = 22/70 (31%), Positives = 38/70 (54%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S ++   +LF+  LSY ++E  L+  F  +G + E+    D +T + +G+ FV F     
Sbjct: 3  SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 81 AGEAIKEMDG 90
          A +A  E+DG
Sbjct: 63 AVKAYAEVDG 72

>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 = 54.3 bits (130), Expect = 8e-12
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 19 LLSDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE 78
          ++ D      L++G LS D  E ++   F Q G     K+I +     +  Y FV+F   
Sbjct: 1  MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEH 58

Query: 79 AAAGEAIKEMDG 90
            A  A+  M+G
Sbjct: 59 RDAAAALAAMNG 70

>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 = 54.3 bits (130), Expect = 1e-11
 Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          +    +FI  L    +   L D F   G I+  KV+CD     S+GYGFV F ++ AA  
Sbjct: 6  SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 63

Query: 84 AIKEMDG 90
          AI++M+G
Sbjct: 64 AIEKMNG 70

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.0 bits (129), Expect = 1e-11
 Identities = 21/80 (26%), Positives = 35/80 (43%)

Query: 21  SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
           SD      +FI  LS+D+ E  L +   Q G++  V+V+    T  S+G  F +F ++ A
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 81  AGEAIKEMDGLVCRTSKDTD 100
           A + +              D
Sbjct: 63  AQKCLAAASLEAEGGGLKLD 82

>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 = 53.2 bits (127), Expect = 1e-11
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GGLS +T    +K  F Q G++ +  ++ D+ T + RG+GFV F SE    E + E
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV-EKVCE 59

Query: 88 MDG 90
          +  
Sbjct: 60 IHF 62

>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 = 52.4 bits (125), Expect = 4e-11
 Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          +FIG L  + +E +L D F   G I    K++ D  TG S+GY F+ FAS  A+  AI+ 
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 88 MDG 90
          M+G
Sbjct: 61 MNG 63

>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 = 52.4 bits (125), Expect = 5e-11
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KLF+GGLS+DTNE  L+  F ++G+I EV V+ DR T +SRG+GFV F +   A +A+  
Sbjct: 7  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 88 MDG 90
          M+G
Sbjct: 67 MNG 69

>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 = 52.0 bits (124), Expect = 5e-11
 Identities = 18/64 (28%), Positives = 34/64 (53%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            LF+  +  +  E  +++ F  +GEI  + +  DR TG S+GY  V++ +   A  A +
Sbjct: 8  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 87 EMDG 90
           ++G
Sbjct: 68 ALNG 71

>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 = 51.6 bits (123), Expect = 1e-10
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           +L +  + +   +  L+  FGQ G+I++V++I +     S+G+GFV F + A A  A +
Sbjct: 12 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRARE 69

Query: 87 EMDG 90
          ++ G
Sbjct: 70 KLHG 73

>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 = 51.5 bits (123), Expect = 1e-10
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
            R++LF+G L  D  E  ++  F ++G+  EV +  D+       +GF++  +   A  
Sbjct: 6  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEI 59

Query: 84 AIKEMDG 90
          A  E+D 
Sbjct: 60 AKVELDN 66

>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 = 50.8 bits (121), Expect = 2e-10
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          N+  ++++G L  D     ++D F ++G    ++ I  +       + FV+F     A +
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVFYKYG---AIRDIDLKNRRGGPPFAFVEFEDPRDAED 68

Query: 84 AIKEMDG 90
          A+   DG
Sbjct: 69 AVYGRDG 75

>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 = 50.9 bits (121), Expect = 2e-10
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVIC--------DRVTGQSRGYGF 72
           + +  + +++ GL+       L D F Q G +   K           D+ TG+ +G   
Sbjct: 3  DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 73 VKFASEAAAGEAIKEMDG 90
          V +     A  A++  DG
Sbjct: 63 VSYEDPPTAKAAVEWFDG 80

>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 = 50.8 bits (121), Expect = 2e-10
 Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
          ++ + + +     +  E V  +   ++GE+ E+  +CD +     G  +VKF  E  A +
Sbjct: 25 SAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 84 AIKEMDG 90
          A+ +++ 
Sbjct: 84 AVIDLNN 90

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 3e-10
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          K+F+GG+  DT E  L+D F Q+G+I  ++++ DR +G+ RG+ FV F     + + I  
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 88 MDG 90
             
Sbjct: 63 QKY 65

>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 = 50.4 bits (120), Expect = 3e-10
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           +RT L    LS++  E  LK+ F    EI           G+S+G  +++F SEA A +
Sbjct: 15 AART-LLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 84 AIKEMDG 90
           ++E  G
Sbjct: 69 NLEEKQG 75

>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 = 49.3 bits (117), Expect = 6e-10
 Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          KL+IG LS       L+  FG     +              GY FV +  +  A  AI+ 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 88 MDG 90
          + G
Sbjct: 57 LSG 59

>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 = 48.6 bits (115), Expect = 1e-09
 Identities = 7/64 (10%), Positives = 23/64 (35%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++        +  ++D       +     +       SR + ++   S+  A   ++
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 87 EMDG 90
          +++G
Sbjct: 62 KLNG 65

>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 = 49.0 bits (116), Expect = 1e-09
 Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 1/69 (1%)

Query: 22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
          D + R+ +F+G + Y+  E  LKD F + G ++  +++ DR TG+ +GYGF ++  +  A
Sbjct: 5  DRSLRS-VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 82 GEAIKEMDG 90
            A++ ++G
Sbjct: 64 LSAMRNLNG 72

>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 = 47.5 bits (112), Expect = 2e-09
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          L+I GL   T +  L      +G+I+  K I D+ T + +GYGFV F S +AA +A+  +
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 89 DG 90
            
Sbjct: 61 KA 62

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 3e-09
 Identities = 13/85 (15%), Positives = 27/85 (31%), Gaps = 5/85 (5%)

Query: 21  SDANS-RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
            D NS +    I  + +   +  +               +     GQ  G   V+F +E 
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 80  AAGEAIK----EMDGLVCRTSKDTD 100
            A ++ +    +++G        T 
Sbjct: 62  DARKSERLHRKKLNGREAFVHVVTL 86

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 49.1 bits (116), Expect = 3e-09
 Identities = 27/69 (39%), Positives = 42/69 (60%)

Query: 22  DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAA 81
           + +    L +  +    +E  L+  F ++G I  VK++CDR T QSRGYGFVKF S ++A
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 82  GEAIKEMDG 90
            +AI  ++G
Sbjct: 98  QQAIAGLNG 106

>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 = 47.9 bits (113), Expect = 3e-09
 Identities = 16/64 (25%), Positives = 29/64 (45%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++  LS    E  L   F +  E     +    +TG+ RG  F+ F ++  A +A+ 
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 87 EMDG 90
           ++G
Sbjct: 79 LVNG 82

>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 = 47.4 bits (112), Expect = 4e-09
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 25 SRTKLFIGGLSYDTNETVLK----DAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          + T ++I  L+    +  LK      F + G+I+++ V       + RG  FV F   ++
Sbjct: 3  NHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSS 58

Query: 81 AGEAIKEMDG 90
          A  A++ M G
Sbjct: 59 ATNALRSMQG 68

>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 = 47.4 bits (112), Expect = 5e-09
 Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 6/70 (8%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S A     +  GGL    +   L     + G +  + +  ++       Y F ++ +   
Sbjct: 15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEE 68

Query: 81 AGEAIKEMDG 90
          +  A   ++G
Sbjct: 69 SKRAYVTLNG 78

>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 = 46.9 bits (111), Expect = 5e-09
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 5/62 (8%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          + +F+G  + D  E  L++ F Q+G++++V +         R + FV FA +  A     
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 87 EM 88
          E 
Sbjct: 61 ED 62

>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 = 46.6 bits (110), Expect = 7e-09
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 21 SDANSRTK-LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
           D  S  K L++  L   T+E +++  F         +V       + R Y FV F++  
Sbjct: 2  EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNRE 55

Query: 80 AAGEAIKEMDG 90
           A EA+K ++G
Sbjct: 56 DAVEAMKALNG 66

>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 = 46.7 bits (110), Expect = 8e-09
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 26 RTKLFIGGLSYDTNETVL---KDAFGQHGEIIEVKVICDRVTGQS---RGYGFVKFASEA 79
          +  +F+ GLS    +  +    + FG+ G+I +V +        S       +V +    
Sbjct: 8  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 80 AAGEAIKEMDG 90
           A  AI+ ++ 
Sbjct: 68 DALRAIQCVNN 78

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 6e-08
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
            F+G L YD  E  +K+ F                  + +G+G+ +F    +   +   
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSALS 75

Query: 88 MDG 90
          ++ 
Sbjct: 76 LNE 78

>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 = 44.0 bits (103), Expect = 1e-07
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T L+I  L    +E  L++   +    +    I    +G SRG GF +  S       I 
Sbjct: 19 TNLYISNLPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 87 EMDG 90
            +G
Sbjct: 78 HFNG 81

>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 = 42.9 bits (100), Expect = 3e-07
 Identities = 7/70 (10%), Positives = 20/70 (28%), Gaps = 11/70 (15%)

Query: 25 SRTKLFIGGLSYD-----TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEA 79
            + L     + D           +  F  + +    +        +S     + F++  
Sbjct: 4  GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPL 57

Query: 80 AAGEAIKEMD 89
          +A +A   + 
Sbjct: 58 SAADARLRLH 67

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 4e-07
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          S T L +  +    +E  LK  F  +G +    V   +   + R    ++  S   A +A
Sbjct: 10 SAT-LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQA 64

Query: 85 IKEMDG 90
          + ++  
Sbjct: 65 LIDLHN 70

>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 = 42.2 bits (98), Expect = 4e-07
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S++ +   LFIG L+ + +   LK A  +     ++ V+  R TG +R +G+V F S   
Sbjct: 8  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAED 66

Query: 81 AGEAI----KEMDGLVCRTSK 97
            +A+     ++ G   +  K
Sbjct: 67 LEKALELTGLKVFGNEIKLEK 87

>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 = 42.2 bits (99), Expect = 4e-07
 Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

Query: 36 YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
           +     L+    + G+I ++ +          G   V F     A   I+ +DG
Sbjct: 29 LNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDG 79

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 4e-07
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 8/64 (12%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            L++ G   D   T+L+ AF   G II++ +   R         FV +    +A +A+ 
Sbjct: 6  NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVA 57

Query: 87 EMDG 90
          E++G
Sbjct: 58 ELNG 61

>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 = 41.7 bits (97), Expect = 5e-07
 Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 26 RTKLFIGGLSYD-TNETVLKDAFGQHGEI-IEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
            ++ I  LS +  +E +L+++F   G I         +    +    F+ F ++ +A  
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 84 AIKEMDG 90
          A+ +M+ 
Sbjct: 64 AL-QMNR 69

>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 = 42.0 bits (98), Expect = 6e-07
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
          T+L++GGL  +T+   L   F + G I  +  +          + ++++ S  AA  A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACA 71

Query: 87 EMDG 90
          +M G
Sbjct: 72 KMRG 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 = 2e-06
 Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 14/86 (16%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
           + + +  L  D+N   + D    +        +      +++   FV   +   A  AI+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 87  EMDG-------LVCRTSKDTDMLSTG 105
                      L+ +      +L +G
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLCSG 84

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 2e-06
 Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          +D  +R+ ++I G   D     +K+     G+++    +   +    +G  FV F S  +
Sbjct: 2  NDVKNRS-VYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIES 59

Query: 81 AGEAIKEMD 89
          A + ++   
Sbjct: 60 AKKFVETPG 68

>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 = 40.7 bits (95), Expect = 2e-06
 Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 34 LSYDTNETVLKDAFGQHGEIIEVKVI--CDRVTGQSRGYGFVKFASEAAAGEAIKEMDG 90
            Y+     ++D   ++G +  +++    D V     G  FV+F S     +A++ + G
Sbjct: 22 EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 3e-06
 Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 7/65 (10%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE-AAAGEAI 85
             F G L   T    L   F  HGEI  +  +           G + F  +   A    
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKA 65

Query: 86 KEMDG 90
          K+ + 
Sbjct: 66 KDANN 70

>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 = 39.5 bits (91), Expect = 5e-06
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 6/77 (7%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S   S+T +    L   T    +++ F + G +  V +              V+F     
Sbjct: 5  SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLE 58

Query: 81 AGEAIKEMDGLVCRTSK 97
          A +A + +         
Sbjct: 59 ARKAFRHLAYSKFHHVP 75

>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 = 39.4 bits (91), Expect = 5e-06
 Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 7/67 (10%)

Query: 24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGE 83
           S  ++ + GL    +   LKD   +                Q  G G V++  +     
Sbjct: 13 RSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLRKEDMEY 65

Query: 84 AIKEMDG 90
          A++++D 
Sbjct: 66 ALRKLDD 72

>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 = 39.0 bits (90), Expect = 1e-05
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 6/64 (9%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK 86
            + + GL     E  L +A  + G I  V ++  +          V+F +  +A E + 
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVT 69

Query: 87 EMDG 90
              
Sbjct: 70 FAAD 73

>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 = 37.2 bits (86), Expect = 3e-05
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 14/83 (16%)

Query: 27  TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI- 85
           T + + G    +   +L   F Q+G I++  +           +  +++ S+  A +A+ 
Sbjct: 5   TWVTVFGFPQASASYILL-QFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALS 57

Query: 86  ---KEMDG---LVCRTSKDTDML 102
              +       +  +   D +++
Sbjct: 58  KDGRIFGESIMIGVKPCIDKNVM 80

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.8 bits (84), Expect = 3e-05
 Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI- 85
          T + +  L    N+  +   F   G II V V       ++  +  ++FA    A  AI 
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAIT 58

Query: 86 ---KEMDGLVCRTSKDT 99
             K +       S  T
Sbjct: 59 KTHKVVGQNEIIVSHLT 75

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 27 TKLFIGGLS-YDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAI 85
          + L +  L+        L   FG +G++  VK++ ++          V+ A    A  A+
Sbjct: 3  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 57

Query: 86 KEMDG 90
            ++G
Sbjct: 58 SHLNG 62

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.1 bits (77), Expect = 8e-04
 Identities = 15/66 (22%), Positives = 30/66 (45%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
          S   +   +++ GL ++     + D F +   + +   I     G++ G GFV+F +EA 
Sbjct: 13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 72

Query: 81 AGEAIK 86
             A+ 
Sbjct: 73 YKAALC 78

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 32.9 bits (74), Expect = 0.001
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEA 84
          ++  LF+  L  +TNE +L   F Q            R+        FV+F +E  +  A
Sbjct: 8  NQI-LFLTNLPEETNEMMLSMLFNQFPGF-----KEVRLVPNRHDIAFVEFTTELQSNAA 61

Query: 85 IKEMDG 90
           + + G
Sbjct: 62 KEALQG 67

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.6 bits (73), Expect = 0.002
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKE 87
          ++ + GL    +   LKD   + G++    V  D         G V+F  +     A+++
Sbjct: 2  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 88 MDG 90
          +D 
Sbjct: 55 LDN 57

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.4 bits (73), Expect = 0.002
 Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 3/70 (4%)

Query: 21 SDANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAA 80
            + +   + + GL Y   E  + + F     +     I     G+  G   V+FA+   
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHED 67

Query: 81 AGEAIKEMDG 90
          A  A+   D 
Sbjct: 68 AVAAM-AKDK 76

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 31.8 bits (71), Expect = 0.003
 Identities = 12/66 (18%), Positives = 19/66 (28%), Gaps = 7/66 (10%)

Query: 29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM 88
          + I GL  D     + D    +        +      + +G  FV   +   A  AI   
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 89 DGLVCR 94
               R
Sbjct: 54 HQSRLR 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	105
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.92
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.92
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.92
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.92
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.92
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.92
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.92
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.92
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.91
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.91
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.9
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.9
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.9
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.89
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.88
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.87
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.87
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.86
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.86
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.86
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.85
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.84
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.84
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.82
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.82
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.82
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.8
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.77
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
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	99.72
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.7
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.67
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.58
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.56
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.44
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.44
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.29
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.71
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.84

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.92  E-value=2.9e-25  Score=119.02  Aligned_cols=79  Identities=30%  Similarity=0.439  Sum_probs=75.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|+.|++.|||..+.|+.++|..++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5689999999999999999999999999999999988899999999999999999999999999999999999999875

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=5.4e-25  Score=120.51  Aligned_cols=83  Identities=35%  Similarity=0.501  Sum_probs=78.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +.+..++|||+|||..+++++|+++|++||+|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..+.|+.++|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44556799999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .++
T Consensus        85 ~A~   87 (93)
T d1x5ua1          85 KAS   87 (93)
T ss_dssp             ETT
T ss_pred             EcC
Confidence            765

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.1e-24  Score=119.22  Aligned_cols=82  Identities=23%  Similarity=0.408  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..+++|||+|||+++++++|+++|++||+|..+.++.+..++.++|||||+|.+.++|..|++.|||..+.|+.++|..+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999999989999999999999999999999999999999999999887


Q ss_pred             CC
Q 034039          104 TG  105 (105)
Q Consensus       104 ~~  105 (105)
                      .+
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=7.6e-25  Score=116.87  Aligned_cols=77  Identities=31%  Similarity=0.475  Sum_probs=74.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      +|||+|||+.+++++|+++|+.||+|..++++.++.+|+++|||||+|.+.++|..|++.|+|..+.|+.++|..++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999899999999999999999999999999999999999999875

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.6e-24  Score=116.01  Aligned_cols=79  Identities=32%  Similarity=0.530  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|++||.|..+++..+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|..++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4579999999999999999999999999999999998899999999999999999999999999999999999998764

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=8.4e-25  Score=119.09  Aligned_cols=82  Identities=28%  Similarity=0.403  Sum_probs=77.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .....+|||+|||.++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|++|++.|+|..+.|+.++|..
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44567899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        85 ak   86 (90)
T d2cq0a1          85 AK   86 (90)
T ss_dssp             SS
T ss_pred             ee
Confidence            75

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.92  E-value=1.5e-24  Score=117.65  Aligned_cols=81  Identities=22%  Similarity=0.318  Sum_probs=76.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|.++|+.||.|..++++.++.+|.++|||||+|.+.++|+.|+..|||..+.|+.++|..
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999986


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus        84 a   84 (88)
T d1rk8a_          84 C   84 (88)
T ss_dssp             S
T ss_pred             e
Confidence            5

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.8e-24  Score=120.26  Aligned_cols=82  Identities=26%  Similarity=0.396  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..+.++|||+|||+++++++|+++|..||.+..+.+..+..+|.++|||||+|.+.++|+.|++.|||..+.|+.|+|.+
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        95 a~   96 (102)
T d2cpza1          95 KR   96 (102)
T ss_dssp             CC
T ss_pred             eC
Confidence            75

>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=99.92  E-value=1.8e-24  Score=116.16  Aligned_cols=77  Identities=29%  Similarity=0.413  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|+.|++.|||..+.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34678999999999999999999999999999999999888999999999999999999999999999999999986

>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=99.91  E-value=3.5e-24  Score=115.44  Aligned_cols=81  Identities=25%  Similarity=0.480  Sum_probs=74.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeee--eeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRT--SKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~--~~~~v  100 (105)
                      ....++|||+|||+++++++|+++|++||+|..++++.++.+|.++|||||+|.+.++|..|++.|||..+.|  +.++|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3456789999999999999999999999999999999998899999999999999999999999999999976  77888


Q ss_pred             ccC
Q 034039          101 MLS  103 (105)
Q Consensus       101 ~~~  103 (105)
                      .+|
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            764

>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=99.91  E-value=1.7e-24  Score=116.68  Aligned_cols=78  Identities=27%  Similarity=0.461  Sum_probs=74.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ++|||+|||+++++++|+++|++||+|..+++..++.+|.++|||||+|.+.++|+.|++.|||..+.|+.+.|..+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            479999999999999999999999999999999998899999999999999999999999999999999999998765

>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=99.91  E-value=3.4e-24  Score=113.82  Aligned_cols=76  Identities=26%  Similarity=0.412  Sum_probs=73.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      +|||+|||+++++++|+++|++||+|..+++..+. +|.++|||||+|.+.++|+.|++.|||..+.|+.++|.+++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999886 89999999999999999999999999999999999999875

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=4.6e-24  Score=117.98  Aligned_cols=81  Identities=30%  Similarity=0.429  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34668999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        86 ~   86 (99)
T d1whwa_          86 T   86 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.91  E-value=1.5e-24  Score=117.86  Aligned_cols=81  Identities=27%  Similarity=0.451  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+++|+.||+|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34678999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        83 ~   83 (89)
T d2cqba1          83 K   83 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.91  E-value=8.7e-24  Score=123.20  Aligned_cols=82  Identities=34%  Similarity=0.553  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|..|++.|||..+.|+.|+|..
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus       119 a~  120 (139)
T d1u6fa1         119 AA  120 (139)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>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=99.91  E-value=1.2e-23  Score=113.08  Aligned_cols=80  Identities=30%  Similarity=0.476  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..+.|+.++|..|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            345789999999999999999999999999999999999899999999999999999999996 6999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=9.3e-24  Score=113.77  Aligned_cols=79  Identities=33%  Similarity=0.547  Sum_probs=72.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee--eeecc
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK--DTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~--~~v~~  102 (105)
                      ..++|||+|||+.+++++|+++|++||+|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..+.|+.  ++|..
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            3567999999999999999999999999999999999888999999999999999999999999999998754  66654


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=1.4e-23  Score=115.04  Aligned_cols=81  Identities=20%  Similarity=0.400  Sum_probs=74.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC-CCCCccceEEEEeCCHHHHHHHHHHc-CCceeeeeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-VTGQSRGYGFVKFASEAAAGEAIKEM-DGLVCRTSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l-~g~~~~~~~~~v~  101 (105)
                      ...++|||+|||+.+++++|+.+|..||.|..+.++.+. .+|.++|||||+|.+.++|..|++.| ||..+.|+.++|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            456789999999999999999999999999999988774 37889999999999999999999998 8999999999999


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      .+.
T Consensus        86 ~A~   88 (94)
T d2cpha1          86 WAD   88 (94)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            875

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.90  E-value=5.4e-24  Score=113.73  Aligned_cols=78  Identities=12%  Similarity=0.175  Sum_probs=67.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ++|||+|||+++++++|+++|+.||.+..+.+..+..+|.++|||||+|.+.++|+.|++.|||..+.|+.++|.+++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            689999999999999999999999999888877777789999999999999999999999999999999999998874

>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=99.90  E-value=1.6e-23  Score=110.41  Aligned_cols=75  Identities=33%  Similarity=0.580  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|.++|++||+|..+.++.++.+++++|||||+|.+.++|++|++ +++..+.|+.+.|..+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999899999999999999999999996 7999999999998653

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=8.8e-24  Score=114.95  Aligned_cols=80  Identities=40%  Similarity=0.610  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ....+|||+|||+++++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|+.|++.|+|..+.|+.++|..+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35678999999999999999999999999999998888888999999999999999999999999999999999999865

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=4.2e-23  Score=114.78  Aligned_cols=80  Identities=43%  Similarity=0.642  Sum_probs=73.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|+.|++.+++ .+.|+.++|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3456799999999999999999999999999999999988999999999999999999999998876 799999999865


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        87 ~   87 (103)
T d2cqda1          87 Y   87 (103)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=4.6e-24  Score=113.03  Aligned_cols=76  Identities=34%  Similarity=0.584  Sum_probs=72.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++ +++..++|+.+.|..|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            479999999999999999999999999999999999899999999999999999999996 7999999999998765

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=5.7e-23  Score=110.61  Aligned_cols=76  Identities=29%  Similarity=0.467  Sum_probs=70.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCC---CccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTG---QSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      |||+|||+++++++|+++|++||.|..+.++.+..++   .++|||||+|.+.++|+.|++.|||..+.|+.++|.++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            7999999999999999999999999999998876554   368999999999999999999999999999999999864

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.2e-23  Score=116.08  Aligned_cols=79  Identities=25%  Similarity=0.547  Sum_probs=75.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|+.|++.|+|..+.|+.++|..+.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4579999999999999999999999999999999998899999999999999999999999999999999999998764

>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=99.89  E-value=8.3e-24  Score=117.28  Aligned_cols=78  Identities=23%  Similarity=0.294  Sum_probs=73.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||+++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|.+|+ .|||..+.|+.++|..+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEEC
Confidence            3468999999999999999999999999999999999889999999999999999999999 59999999999999764

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.4e-22  Score=110.11  Aligned_cols=79  Identities=28%  Similarity=0.435  Sum_probs=72.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.  ...++|+.+.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3457899999999999999999999999999999999998999999999999999999999974  45789999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        84 ~   84 (90)
T d2cqga1          84 N   84 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.89  E-value=1.1e-22  Score=110.64  Aligned_cols=80  Identities=25%  Similarity=0.365  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|+.||+|..+.+..+..++  ++||||+|.+.++|+.|+..|+|..+.|+.++|..
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4456799999999999999999999999999999998886443  78999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        83 a~   84 (90)
T d2cqia1          83 AT   84 (90)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=99.89  E-value=1.3e-22  Score=107.77  Aligned_cols=77  Identities=27%  Similarity=0.462  Sum_probs=72.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .++|||+|||+++++++|+++|++||.+..+.+..++.++.++|||||+|.+.+++++|+ .++|..+.|+.++|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            468999999999999999999999999999999999989999999999999999999999 58999999999999765

>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=99.89  E-value=9.2e-23  Score=113.04  Aligned_cols=80  Identities=24%  Similarity=0.477  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|..|++.|||..+.|+.+.|..
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456789999999999999999999999999999988875 888999999999999999999999999999999988865


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus        94 ~   94 (101)
T d1x5oa1          94 T   94 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.88  E-value=2.9e-23  Score=109.32  Aligned_cols=75  Identities=29%  Similarity=0.476  Sum_probs=70.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|+++|++||+|..+.++.++.++.++|||||+|.+.++|++|++ .++..+.|+.+.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58999999999999999999999999999999999899999999999999999999995 4777899999988764

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=4.2e-22  Score=108.84  Aligned_cols=80  Identities=28%  Similarity=0.520  Sum_probs=73.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|+.||+|..+.+..+.  +.++|||||+|.+.++|..|++.|||..+.|+.++|..
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4456789999999999999999999999999999998876  33689999999999999999999999999999999987


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        86 A~   87 (93)
T d2cq3a1          86 AT   87 (93)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.88  E-value=5.6e-23  Score=110.19  Aligned_cols=76  Identities=36%  Similarity=0.552  Sum_probs=70.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEE-EEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      |||+|||+++++++|+++|++||.+..+ .+..+..+|+++|||||+|.+.++|+.|++.|+|..+.|+.++|..+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEec
Confidence            7999999999999999999999998654 678888889999999999999999999999999999999999998764

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.6e-22  Score=111.89  Aligned_cols=83  Identities=23%  Similarity=0.342  Sum_probs=74.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeE--------EEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEII--------EVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC   93 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~   93 (105)
                      +....++|||+|||..+++++|+++|+.||++.        .+.+..+..+|.++|||||+|.+.++|..|++.|||..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345677999999999999999999999999873        456667777899999999999999999999999999999


Q ss_pred             eeeeeeeccCC
Q 034039           94 RTSKDTDMLST  104 (105)
Q Consensus        94 ~~~~~~v~~~~  104 (105)
                      .|+.|+|.+++
T Consensus        84 ~gr~i~V~~a~   94 (101)
T d2cpea1          84 QGSKLKVSLAR   94 (101)
T ss_dssp             TTEECEEECSS
T ss_pred             CCEEEEEEEcC
Confidence            99999999875

>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=99.88  E-value=3.9e-22  Score=109.77  Aligned_cols=82  Identities=26%  Similarity=0.413  Sum_probs=75.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC------Cceeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD------GLVCRTS   96 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~------g~~~~~~   96 (105)
                      ....++|||+|||+++++++|+++|.+||++..+.+..+..++.++|||||+|.+.++|..|++.|+      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456789999999999999999999999999999999888889999999999999999999999886      6789999


Q ss_pred             eeeeccCC
Q 034039           97 KDTDMLST  104 (105)
Q Consensus        97 ~~~v~~~~  104 (105)
                      .++|..+.
T Consensus        85 ~l~v~~a~   92 (98)
T d1x4ha1          85 QLKVDLAV   92 (98)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEECC
Confidence            99998764

>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=99.88  E-value=9.2e-23  Score=113.36  Aligned_cols=78  Identities=32%  Similarity=0.498  Sum_probs=73.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|++|+ .++|..+.|+.+.|..+.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECc
Confidence            478999999999999999999999999999999999888999999999999999999999 579999999999998754

>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=99.87  E-value=6.9e-23  Score=111.18  Aligned_cols=78  Identities=33%  Similarity=0.576  Sum_probs=71.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ...+|||+|||+++++++|+++|..||.|..+.+..+.  +.++|||||+|.+.++|+.|++.|||..+.|+.+.|..++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34579999999999999999999999999999998876  3367999999999999999999999999999999998764

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=1.1e-22  Score=107.00  Aligned_cols=75  Identities=28%  Similarity=0.445  Sum_probs=70.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           28 KLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        28 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +|||+|||+++++++|+++|+.||.+..+.+..+..++.+++||||+|.+.++|+.|++ +||..+.|+.++|..|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            58999999999999999999999999999998888889999999999999999999995 9999999999999754

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=7.8e-22  Score=111.33  Aligned_cols=77  Identities=22%  Similarity=0.329  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .+++|||+|||..+++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|..|++.|||..+.|+.|+|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999998875   45678999999999999999999999999999999998653

>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=99.87  E-value=9e-23  Score=106.67  Aligned_cols=71  Identities=31%  Similarity=0.502  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      |||+|||+++++++|+++|.+||.+..+.+..++.++.++|+|||+|.+.++|+.|++.|||..+.|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999988999999999999999999999999999999999875

>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=99.87  E-value=9.6e-22  Score=107.76  Aligned_cols=79  Identities=19%  Similarity=0.322  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|+++|..||.|..+.+..   ++.+++||||+|.+.++|+.|++.|||..+.|+.|+|.+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567899999999999999999999999998887654   345679999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        88 a~   89 (95)
T d1x4aa1          88 PR   89 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            76

>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=99.86  E-value=7.4e-23  Score=113.53  Aligned_cols=81  Identities=20%  Similarity=0.236  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .++++|||+|||.++++++|+++|..||.+..+.+..+..+|+++|||||+|.+.++|+.|++.|||..+.|+.|+|..+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999988888777778999999999999999999999999999999999999887


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        96 k   96 (102)
T d2cpxa1          96 K   96 (102)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.86  E-value=3.3e-22  Score=107.80  Aligned_cols=79  Identities=18%  Similarity=0.306  Sum_probs=68.4

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHHhccCCeEEEEEEec-CCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           25 SRTKLFIGGLSYDTN-ETVLKDAFGQHGEIIEVKVICD-RVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~-~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ..++|||+|||++++ +++|+++|++||.|..+.+..+ ..++.++|||||+|.+.++|++|++ |||..+.|+.++|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            467899999999976 5669999999999999998664 4578899999999999999999995 999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        82 a~   83 (86)
T d2ghpa3          82 AD   83 (86)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.86  E-value=2e-21  Score=104.52  Aligned_cols=76  Identities=17%  Similarity=0.277  Sum_probs=71.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      .++|||+|||.++++++|+++|+.||++..+.+..+. ++.++|||||+|.+.++|++|+ .++|..+.|+.+.|+..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFK   81 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEc
Confidence            5689999999999999999999999999999998876 8999999999999999999999 57999999999999864

>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=99.86  E-value=4.1e-23  Score=112.49  Aligned_cols=81  Identities=25%  Similarity=0.324  Sum_probs=72.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      +...++|||+|||+++++++|+++|..||.+..+.+..+ .+|+++|||||+|.+.++|+.|++ |||..+.|+.++|..
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            445678999999999999999999999999887777655 488999999999999999999995 999999999999998


Q ss_pred             CCC
Q 034039          103 STG  105 (105)
Q Consensus       103 ~~~  105 (105)
                      +++
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.86  E-value=6.1e-22  Score=106.72  Aligned_cols=78  Identities=17%  Similarity=0.161  Sum_probs=69.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEE-EEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEV-KVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ..++|||+|||+++++++|+++|..||.+... .+..+ .++.++|+|||+|.+.++|+.|++.||+..+.|+.++|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45679999999999999999999999988653 44444 48999999999999999999999999999999999999874

>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=99.85  E-value=6.9e-22  Score=107.17  Aligned_cols=76  Identities=20%  Similarity=0.288  Sum_probs=68.4

Q ss_pred             CCceEEEcCCCCCCCHHHH---HHHHhccCCeEEEEEEecCCCCCc---cceEEEEeCCHHHHHHHHHHcCCceeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVL---KDAFGQHGEIIEVKVICDRVTGQS---RGYGFVKFASEAAAGEAIKEMDGLVCRTSKD   98 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l---~~~f~~~g~v~~~~~~~~~~~~~~---~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~   98 (105)
                      ..+.|||+|||+.+++++|   .++|++||.|..+.+..++.++.+   .|||||+|.+.++|..|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3567999999999999999   668999999999999988755543   4899999999999999999999999999999


Q ss_pred             ee
Q 034039           99 TD  100 (105)
Q Consensus        99 ~v  100 (105)
                      +|
T Consensus        87 kv   88 (89)
T d2cpia1          87 KA   88 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            87

>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=99.85  E-value=4.4e-21  Score=105.26  Aligned_cols=74  Identities=22%  Similarity=0.523  Sum_probs=69.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||..+++++|+++|++||.|..+.+..+      +|||||+|.+.++|+.|+..|+|..+.|+.++|..++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4568999999999999999999999999999998865      4899999999999999999999999999999998765

>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=99.85  E-value=5.6e-21  Score=102.26  Aligned_cols=78  Identities=23%  Similarity=0.336  Sum_probs=69.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee-eeeeeec
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR-TSKDTDM  101 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~-~~~~~v~  101 (105)
                      .+++++|||+|||+++++++|..+|+.||.+..+++..+     .+|||||+|.+.++|..|++.|+|..+. |+.++|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            345679999999999999999999999999999988654     3579999999999999999999999985 6889998


Q ss_pred             cCCC
Q 034039          102 LSTG  105 (105)
Q Consensus       102 ~~~~  105 (105)
                      .++.
T Consensus        80 ~akk   83 (83)
T d2b0ga1          80 FAKK   83 (83)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            8863

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.1e-20  Score=102.17  Aligned_cols=76  Identities=14%  Similarity=0.196  Sum_probs=67.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCcee-eeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVC-RTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~-~~~~~~v~~~  103 (105)
                      ++++|||+|||+++++++|+++|+.||.+..+.+...    +.+++|||+|.+.++|..|+..|+|..+ +|+.++|.++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            4678999999999999999999999999988766543    3568999999999999999999999988 5899999987


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        85 k   85 (88)
T d2adca2          85 K   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            6

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=3.7e-21  Score=103.63  Aligned_cols=73  Identities=27%  Similarity=0.464  Sum_probs=67.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+++++++|+++|++||.|..+.+..+      ++||||+|.+.++|+.|++.|||..+.|+.++|..+.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            457999999999999999999999999999998754      4799999999999999999999999999999998764

>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=99.84  E-value=2.5e-21  Score=104.49  Aligned_cols=70  Identities=21%  Similarity=0.354  Sum_probs=64.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++|||+|||+.+++++|+++|++||.|.++.+..+       |||||+|.+.++|+.|++.|||..+.|+.++|..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~   70 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   70 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEE
Confidence            46999999999999999999999999999987532       79999999999999999999999999999988764

>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=99.84  E-value=1.6e-20  Score=98.73  Aligned_cols=74  Identities=20%  Similarity=0.148  Sum_probs=67.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ++|||+|||+++++++|+++|+.||+|..+.+..++. + .+++|||+|.+.++|++|+ .+++..++|+.+.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-~-~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-K-NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-S-SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-c-cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999988863 3 4579999999999999999 68999999999998754

>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=99.83  E-value=1.4e-20  Score=105.26  Aligned_cols=74  Identities=20%  Similarity=0.281  Sum_probs=67.8

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           26 RTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        26 ~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      .++|||+|||+ .+++++|+++|+.||.|..+.+..++     +|||||+|.+.++|.+|++.|+|..+.|+.|+|.+++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999966 58999999999999999999998764     5799999999999999999999999999999999874

>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=99.83  E-value=3.9e-21  Score=107.87  Aligned_cols=74  Identities=15%  Similarity=0.105  Sum_probs=67.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..      .++||||+|.+.++|..|++.|||..+.|+.|.|..+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3457899999999999999999999999999987742      4589999999999999999999999999999998754

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.5e-20  Score=104.45  Aligned_cols=81  Identities=17%  Similarity=0.161  Sum_probs=71.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ......|||+|||+++++++|+++|..+|.+....+.....++.++|+|||+|.+.++|++|+ .+++..+.|+.+.|..
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEEE
Confidence            345668999999999999999999999998877666666668999999999999999999999 5999999999999986


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        91 ~~   92 (104)
T d1wg5a_          91 SS   92 (104)
T ss_dssp             EC
T ss_pred             CC
Confidence            53

>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=99.83  E-value=5.9e-21  Score=104.74  Aligned_cols=76  Identities=26%  Similarity=0.375  Sum_probs=68.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+++++++|+++|..||.+..+..     ++.+++||||+|.+.++|+.|++.|||..+.|+.|+|.++
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45679999999999999999999999998766542     6778999999999999999999999999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        89 ~   89 (96)
T d1fjca_          89 G   89 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.82  E-value=2.1e-20  Score=102.89  Aligned_cols=73  Identities=23%  Similarity=0.421  Sum_probs=65.8

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           24 NSRTKLFIGGLSY-DTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        24 ~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....+|||+|||+ .+++++|+++|.+||.|.++.+        +++||||+|.+.++|+.|++.|||..+.|+.|+|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456799999975 6788899999999999999988        358999999999999999999999999999999998


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        85 a~   86 (98)
T d1wf2a_          85 AA   86 (98)
T ss_dssp             TT
T ss_pred             CC
Confidence            75

>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=99.82  E-value=6.6e-20  Score=98.61  Aligned_cols=74  Identities=27%  Similarity=0.334  Sum_probs=67.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+++++++|+++|+.||.+..+.+..      ++|||||+|.+.++|..|+..|||..+.|+.++|.+++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            346899999999999999999999999987777644      45899999999999999999999999999999999864

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.9e-20  Score=101.24  Aligned_cols=73  Identities=16%  Similarity=0.193  Sum_probs=63.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|||+|||+.+++++|+++|.+|| +..+.+      +..++||||+|.+.++|++|++.|||..+.|+.|+|.+++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            356899999999999999999999999 222332      3357899999999999999999999999999999999875

>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=99.82  E-value=1.1e-20  Score=104.66  Aligned_cols=80  Identities=19%  Similarity=0.247  Sum_probs=70.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      +....++|||+|||+++++++|+++|..||. ..+.+..+. ++..+|||||+|.+.++|++|++ +|+..+.|+.++|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3456679999999999999999999999985 467777776 78899999999999999999985 89999999999998


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        88 ~s~   90 (102)
T d1weza_          88 LNS   90 (102)
T ss_dssp             EEC
T ss_pred             EcC
Confidence            754

>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=99.82  E-value=1.4e-20  Score=102.27  Aligned_cols=77  Identities=22%  Similarity=0.367  Sum_probs=68.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----HHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeee
Q 034039           25 SRTKLFIGGLSYDTNETVLKD----AFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTD  100 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v  100 (105)
                      +.++|||+|||+++++++|++    +|++||+|..+.+..   ++.++|||||+|.+.++|..|++.|||..+.|+.++|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            357899999999999998864    589999999987643   5667899999999999999999999999999999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      ..++
T Consensus        79 ~~ak   82 (91)
T d1nu4a_          79 QYAK   82 (91)
T ss_dssp             EECS
T ss_pred             EEeC
Confidence            8875

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=7.9e-20  Score=100.52  Aligned_cols=73  Identities=19%  Similarity=0.311  Sum_probs=66.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..       +|||||+|.+.++|+.|++.|||..+.|+.++|...
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            4567899999999999999999999999999998753       379999999999999999999999999999988753

>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=99.82  E-value=6.8e-20  Score=96.24  Aligned_cols=69  Identities=20%  Similarity=0.242  Sum_probs=61.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           29 LFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        29 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      |||+|||+++++++|+++|++|| +..+.+      ++.+|||||+|.+.++|++|++.|||..+.|+.++|.+++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            79999999999999999999998 444443      3366899999999999999999999999999999999875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.4e-20  Score=102.98  Aligned_cols=78  Identities=18%  Similarity=0.317  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecC-CCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDR-VTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      +.++|||+|||+++++++|+++|..|| +..+.++.+. .++.++|||||+|.+.++|++|+ .||+..+.|+.++|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457999999999999999999999998 6666665543 46789999999999999998777 69999999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      .
T Consensus        92 ~   92 (104)
T d1wi8a_          92 D   92 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=1.4e-20  Score=100.01  Aligned_cols=72  Identities=26%  Similarity=0.349  Sum_probs=64.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc-eeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL-VCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~-~~~~~~~~v~~~~  104 (105)
                      ++|||+|||+++++++|+++|.+||.+....+..      .+|||||+|.+.++|+.|++.|||. .+.|+.++|..+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            4699999999999999999999999886665554      3589999999999999999999996 6999999998764

>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=99.81  E-value=1.4e-20  Score=104.46  Aligned_cols=78  Identities=10%  Similarity=0.066  Sum_probs=68.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...+|||+|||+++++++|+++|..||.+..+.+.....+|.++|+|||+|.+.++|+.|++ +|+..+.|+.+.|..+
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            45679999999999999999999999988764444444589999999999999999999995 9999999999999764

>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=99.81  E-value=4.6e-20  Score=97.82  Aligned_cols=73  Identities=22%  Similarity=0.391  Sum_probs=66.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|++  +++++|+++|++||.|.++.+..+      ++||||+|.+.++|..|++.|||..+.|+.++|..+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346789999986  899999999999999999988644      479999999999999999999999999999999887


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        75 ~   75 (79)
T d2bz2a1          75 R   75 (79)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.81  E-value=1.3e-19  Score=99.42  Aligned_cols=75  Identities=23%  Similarity=0.396  Sum_probs=66.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeee--eeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTS--KDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~--~~~v~  101 (105)
                      .+.++|||+|||+++++++|+++|++||+|..+.+..+      ++||||+|.+.++|+.|++.||+..+.|.  +++|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            45679999999999999999999999999999988654      47999999999999999999999999864  68887


Q ss_pred             cCC
Q 034039          102 LST  104 (105)
Q Consensus       102 ~~~  104 (105)
                      +++
T Consensus        89 ~ak   91 (97)
T d1whya_          89 FAK   91 (97)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            765

>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=99.80  E-value=6.3e-20  Score=102.55  Aligned_cols=76  Identities=16%  Similarity=0.249  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee--eeeeeec
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR--TSKDTDM  101 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~--~~~~~v~  101 (105)
                      .+..+|||+|||+.+++++|+++|++||.|..+.+..+.    .+|+|||+|.+.++|+.|+..|||..+.  +..+++.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            455689999999999999999999999999999988764    5789999999999999999999999984  6667766


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      .+
T Consensus        81 ~s   82 (108)
T d2adba1          81 FS   82 (108)
T ss_dssp             EC
T ss_pred             ec
Confidence            54

>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=99.80  E-value=1.9e-20  Score=105.28  Aligned_cols=80  Identities=18%  Similarity=0.199  Sum_probs=70.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+++++++|.++|..||.+..+.++....+|.++|+|||+|.+.++|++|+ .+||..|.|+.+.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEEE
Confidence            345678999999999999999999999998866555555558999999999999999999999 5999999999999875


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus        94 ~   94 (112)
T d1wela1          94 I   94 (112)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=99.80  E-value=9.1e-20  Score=99.91  Aligned_cols=78  Identities=21%  Similarity=0.289  Sum_probs=68.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCC-eEEEEEEecC-CCCCccceEEEEeCCHHHHHHHHHHcCCc--eeeeeeeeecc
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGE-IIEVKVICDR-VTGQSRGYGFVKFASEAAAGEAIKEMDGL--VCRTSKDTDML  102 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a~~~l~g~--~~~~~~~~v~~  102 (105)
                      ++|||+|||..+++++|+++|+.||+ +..+.+..+. .++.++|||||+|.+.++|..|++.|++.  .+.|+.++|..
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 8888888764 35789999999999999999999999754  55789999886


Q ss_pred             CC
Q 034039          103 ST  104 (105)
Q Consensus       103 ~~  104 (105)
                      ++
T Consensus        82 A~   83 (96)
T d2disa1          82 AE   83 (96)
T ss_dssp             SC
T ss_pred             cC
Confidence            54

>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=99.80  E-value=3.9e-19  Score=95.93  Aligned_cols=77  Identities=18%  Similarity=0.124  Sum_probs=68.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc--CCceeeeeeee
Q 034039           22 DANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM--DGLVCRTSKDT   99 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~~~~~~   99 (105)
                      +..++++|||+|||+.+++++|+++|++||.|..+.+..+      +++|||+|.+.++|+.|++.+  ++..+.|+.++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3457889999999999999999999999999999988754      379999999999999999865  57789999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      +.+++
T Consensus        78 v~~sk   82 (88)
T d2cq1a1          78 IQYSN   82 (88)
T ss_dssp             EEECS
T ss_pred             EEECC
Confidence            98875

>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=99.79  E-value=6.5e-20  Score=99.06  Aligned_cols=74  Identities=22%  Similarity=0.361  Sum_probs=65.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccC
Q 034039           24 NSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLS  103 (105)
Q Consensus        24 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~  103 (105)
                      ...++|||+|||+.+++++|+++|.+||.+..+.+.     ..+++||||+|.+.++|+.|+.  ++..+.|+.++|..+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            346799999999999999999999999999988764     3356899999999999999985  788999999999876


Q ss_pred             C
Q 034039          104 T  104 (105)
Q Consensus       104 ~  104 (105)
                      +
T Consensus        76 ~   76 (88)
T d1wf0a_          76 E   76 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=4.8e-19  Score=97.49  Aligned_cols=77  Identities=10%  Similarity=0.084  Sum_probs=67.8

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHH--HcCCceeeeeee
Q 034039           22 DANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIK--EMDGLVCRTSKD   98 (105)
Q Consensus        22 ~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~--~l~g~~~~~~~~   98 (105)
                      ....+++|||+|||.+ +++++|.++|+.||.|.++.+..+      +++|||+|.+.++|..|++  .+++..+.|+.+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456679999999985 899999999999999999988754      4799999999999999997  578889999999


Q ss_pred             eeccCC
Q 034039           99 TDMLST  104 (105)
Q Consensus        99 ~v~~~~  104 (105)
                      +|.+++
T Consensus        88 ~V~~s~   93 (99)
T d1x4fa1          88 KVDLSE   93 (99)
T ss_dssp             EEEEEC
T ss_pred             EEEEcC
Confidence            999875

>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=99.77  E-value=2.4e-18  Score=95.40  Aligned_cols=76  Identities=18%  Similarity=0.145  Sum_probs=66.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc--CCceeeeeeeee
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM--DGLVCRTSKDTD  100 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~~~~~~v  100 (105)
                      ..++.+|||+|||+.+++++|.++|..||.|..+.+..+      +++|||+|.+.++|+.|+..+  ++..+.|+.++|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345779999999999999999999999999999988643      479999999999999999987  556788999999


Q ss_pred             ccCC
Q 034039          101 MLST  104 (105)
Q Consensus       101 ~~~~  104 (105)
                      .+++
T Consensus        86 ~~s~   89 (104)
T d1wexa_          86 NYST   89 (104)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            8764

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6.2e-18  Score=101.67  Aligned_cols=80  Identities=26%  Similarity=0.438  Sum_probs=74.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeecc
Q 034039           23 ANSRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      ....++|||+|||+.+++++|+++|..||.+..+.+..+..++.++|||||+|.+.++|.+|++ +++..+.|+.++|..
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            4566899999999999999999999999999999999998889999999999999999999995 799999999999986


Q ss_pred             C
Q 034039          103 S  103 (105)
Q Consensus       103 ~  103 (105)
                      +
T Consensus       173 A  173 (183)
T d1u1qa_         173 A  173 (183)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.75  E-value=3.2e-18  Score=92.49  Aligned_cols=76  Identities=14%  Similarity=0.096  Sum_probs=67.1

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHc--CCceeeeeeee
Q 034039           23 ANSRTKLFIGGLSYD-TNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEM--DGLVCRTSKDT   99 (105)
Q Consensus        23 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l--~g~~~~~~~~~   99 (105)
                      ...+++|||+|||.. +++++|.++|++||.|..+.+..++      ++|||+|++.++|..|++.|  ++..+.|+.++
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456788999999986 7899999999999999999987554      58999999999999999966  67789999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.+++
T Consensus        79 V~~s~   83 (89)
T d1x4da1          79 VHLSQ   83 (89)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            98875

>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=99.72  E-value=4.7e-20  Score=99.97  Aligned_cols=76  Identities=16%  Similarity=0.353  Sum_probs=64.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEE-----EecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeec
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKV-----ICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDM  101 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~-----~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~  101 (105)
                      ++|||+|||.++++++|+++|+.||.+..+.+     ..+..++.++|||||+|.+.++|+.|+ .|||..+.|+.++|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            57999999999999999999999997654433     233446778999999999999999998 599999999999986


Q ss_pred             cC
Q 034039          102 LS  103 (105)
Q Consensus       102 ~~  103 (105)
                      -.
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.72  E-value=3.4e-19  Score=98.90  Aligned_cols=77  Identities=19%  Similarity=0.172  Sum_probs=70.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCC
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLST  104 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~  104 (105)
                      ..++|.+++..+++++|+++|++||+|.++.+..+. ++.++|+|||+|.+.++|.+|++.|||..++|+.|+|.++.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            357777888888999999999999999999998775 89999999999999999999999999999999999998763

>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=99.70  E-value=8.8e-18  Score=93.09  Aligned_cols=74  Identities=11%  Similarity=0.021  Sum_probs=64.9

Q ss_pred             CCceEEEcCCCCCC-CH----HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           25 SRTKLFIGGLSYDT-NE----TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        25 ~~~~l~v~~l~~~~-~~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      ...+|||+||+..+ ++    ++|+++|+.||.|..+.+..      ++++|||+|.+.++|..|++.|||..+.|+.++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45689999999885 32    56899999999999998864      357999999999999999999999999999999


Q ss_pred             eccCC
Q 034039          100 DMLST  104 (105)
Q Consensus       100 v~~~~  104 (105)
                      |.+++
T Consensus        78 v~~a~   82 (104)
T d1weya_          78 LYFAQ   82 (104)
T ss_dssp             EECCC
T ss_pred             Eeecc
Confidence            98764

>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=99.67  E-value=1e-16  Score=88.32  Aligned_cols=66  Identities=15%  Similarity=0.300  Sum_probs=57.8

Q ss_pred             CCCCceEEE--cCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           23 ANSRTKLFI--GGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        23 ~~~~~~l~v--~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ..+..+++|  +|||+++++++|+++|++||.+..+.+..+      ++||||+|.+.++|..|++.|||..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345678888  559999999999999999999999887654      479999999999999999999999874

>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=99.65  E-value=4.9e-16  Score=93.19  Aligned_cols=73  Identities=33%  Similarity=0.535  Sum_probs=64.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeee
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDT   99 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~   99 (105)
                      .++|||+|||+.+++++|+++|++||.|..+.+..+..++.++|+|||+|.+.++|.+|+.. ++..+.++.+.
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~   78 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   78 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchh
Confidence            46899999999999999999999999999999999988999999999999999999999965 44445544443

>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=99.63  E-value=2.6e-16  Score=88.27  Aligned_cols=71  Identities=20%  Similarity=0.169  Sum_probs=61.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCH-HHHHHHHHHcCCceeeeeeeeecc
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASE-AAAGEAIKEMDGLVCRTSKDTDML  102 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~-~~a~~a~~~l~g~~~~~~~~~v~~  102 (105)
                      .-.+||+|||+.+|+++|+++|.+||+|..+.++.+      ++||||.|.+. ++|..|+..+++..+.++.+.|..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            345699999999999999999999999999998744      48999999985 789999999999988877776654

>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=99.58  E-value=3.6e-15  Score=81.72  Aligned_cols=79  Identities=18%  Similarity=0.195  Sum_probs=65.7

Q ss_pred             CCCCceEEEcCC--CCCC---------CHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCc
Q 034039           23 ANSRTKLFIGGL--SYDT---------NETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGL   91 (105)
Q Consensus        23 ~~~~~~l~v~~l--~~~~---------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~   91 (105)
                      ...+++|+|.|+  |.+.         ..++|+..|++||.|..+.+..+.    .+|++||.|.+.++|..|+..|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCCc
Confidence            456789999998  4432         125788899999999999876543    5689999999999999999999999


Q ss_pred             eeeeeeeeeccCCC
Q 034039           92 VCRTSKDTDMLSTG  105 (105)
Q Consensus        92 ~~~~~~~~v~~~~~  105 (105)
                      .++|+.++|.+..|
T Consensus        81 ~~~gr~i~v~~~~g   94 (99)
T d2dita1          81 WFGGRQITAQAWDG   94 (99)
T ss_dssp             EETTEECEEEECCS
T ss_pred             EECCEEEEEEEeCC
Confidence            99999999987643

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.5e-15  Score=78.50  Aligned_cols=69  Identities=19%  Similarity=0.210  Sum_probs=57.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeee-eeecc
Q 034039           26 RTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSK-DTDML  102 (105)
Q Consensus        26 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~-~~v~~  102 (105)
                      .+.|+|+|+|++.+++.| ..|.+||.|.++.+..      .++|+||.|.+.++|++|+ .+||..++|+. +.|..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~   73 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKP   73 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEe
Confidence            457999999999886655 5799999999987643      4589999999999999999 59999999875 44654

>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=99.44  E-value=7.9e-14  Score=76.87  Aligned_cols=79  Identities=13%  Similarity=0.090  Sum_probs=64.5

Q ss_pred             CCceEEEcCC--CCCCC--------HHHHHHHHhccCCeEEEEEEecCCCC--CccceEEEEeCCHHHHHHHHHHcCCce
Q 034039           25 SRTKLFIGGL--SYDTN--------ETVLKDAFGQHGEIIEVKVICDRVTG--QSRGYGFVKFASEAAAGEAIKEMDGLV   92 (105)
Q Consensus        25 ~~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a~~~l~g~~   92 (105)
                      +++.|.+.|+  |....        .++|++.|.+||.|..+.++.+..+.  ...|++||.|.+.++|..|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4677889998  44432        24688899999999999988765332  245899999999999999999999999


Q ss_pred             eeeeeeeeccC
Q 034039           93 CRTSKDTDMLS  103 (105)
Q Consensus        93 ~~~~~~~v~~~  103 (105)
                      ++|+.+.+.+.
T Consensus        83 f~gR~v~v~f~   93 (104)
T d1o0pa_          83 FANRVVVTKYC   93 (104)
T ss_dssp             SSSSCCEEEEE
T ss_pred             ECCeEEEEEEc
Confidence            99999998754

>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=98.44  E-value=9.5e-07  Score=44.10  Aligned_cols=62  Identities=21%  Similarity=0.246  Sum_probs=52.2

Q ss_pred             HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceeeeeeeeeccCCC
Q 034039           41 TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCRTSKDTDMLSTG  105 (105)
Q Consensus        41 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~~~~~~v~~~~~  105 (105)
                      +.|...|..++.|..+.+.... .|  .-.|-|...+..+|..|+..|+...++++++.|.+++|
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4466779999999998875443 22  34689999999999999999999999999999999876

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.29  E-value=4.4e-06  Score=43.99  Aligned_cols=70  Identities=13%  Similarity=0.129  Sum_probs=57.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCc--cceEEEEeCCHHHHHHHHHHcCCceeeee
Q 034039           27 TKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQS--RGYGFVKFASEAAAGEAIKEMDGLVCRTS   96 (105)
Q Consensus        27 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~--~g~~fv~f~~~~~a~~a~~~l~g~~~~~~   96 (105)
                      ++|.|+.||+..|++++.+.+...|.+....+.....+.+.  ..-|||.|.+.++.....+.++|..+.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~   73 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcC
Confidence            46889999999999999999999888887776655433332  24589999999999999999999987544

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.71  E-value=2.4e-05  Score=40.81  Aligned_cols=70  Identities=20%  Similarity=0.206  Sum_probs=53.6

Q ss_pred             CCCceEEEcCCCCC------CCH---HHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcCCceee
Q 034039           24 NSRTKLFIGGLSYD------TNE---TVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMDGLVCR   94 (105)
Q Consensus        24 ~~~~~l~v~~l~~~------~~~---~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~g~~~~   94 (105)
                      ++..+|.|.=..+.      .++   .+|.+.|..||++.-++++.+.        -.|+|.+-.+|.+|+ .++|.++.
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al-~l~g~~v~   83 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVL-DVDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHH-HGGGSEET
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHh-ccCCeEEc
Confidence            44566777433322      222   3577789999999888887653        789999999999999 89999999


Q ss_pred             eeeeeecc
Q 034039           95 TSKDTDML  102 (105)
Q Consensus        95 ~~~~~v~~  102 (105)
                      |+.+++..
T Consensus        84 G~~l~It~   91 (95)
T d1ufwa_          84 GRAVKISG   91 (95)
T ss_dssp             TEEEEEEC
T ss_pred             ceEEEEec
Confidence            99998864

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.84  E-value=0.0033  Score=33.03  Aligned_cols=57  Identities=16%  Similarity=0.179  Sum_probs=44.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHcC
Q 034039           25 SRTKLFIGGLSYDTNETVLKDAFGQHGEIIEVKVICDRVTGQSRGYGFVKFASEAAAGEAIKEMD   89 (105)
Q Consensus        25 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a~~~l~   89 (105)
                      ....+|.-.+|......+|.++|+.||.|.--.+ -+.       -|||...+.++++.++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            3456777789999999999999999998744433 232       48999999999998875543