RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2134
(104 letters)
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 100 bits (251), Expect = 4e-28
Identities = 39/85 (45%), Positives = 51/85 (60%), Gaps = 15/85 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS +E A ALNG
Sbjct: 153 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIA---------------SETHKAIQALNG 197
Query: 80 RFFAGRMVRAELYDQSLFDHNDFSG 104
R+FAGR V AE+YDQ FD++D S
Sbjct: 198 RWFAGRKVVAEVYDQERFDNSDLSA 222
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 70.6 bits (173), Expect = 2e-17
Identities = 39/85 (45%), Positives = 50/85 (58%), Gaps = 15/85 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS E A ALN G
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN---------------G 93
Query: 80 RFFAGRMVRAELYDQSLFDHNDFSG 104
R+FAGR V AE+YDQ FD++D S
Sbjct: 94 RWFAGRKVVAEVYDQERFDNSDLSA 118
>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 = 58.3 bits (141), Expect = 9e-13
Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 17/94 (18%)
Query: 9 IYNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
I + + + YG V+ + I + D KIFV F+ +
Sbjct: 28 IVEDVRDECSKYGLVKSIEIP--RPVDGVEVPGCGKIFVEFTSV---------------F 70
Query: 69 EAEYARDALNGRFFAGRMVRAELYDQSLFDHNDF 102
+ + A L GR FA R+V + D + DF
Sbjct: 71 DCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 104
>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 = 52.0 bits (125), Expect = 2e-10
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 24/86 (27%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+GQ+ K+++++ VSF +EA+Y L+GR+F
Sbjct: 50 FGQIRKLLLFDR--------HPDGVASVSFRDPEEADYCIQTLDGRWF------------ 89
Query: 80 RFFAGRMVRAELYDQSL-FDHNDFSG 104
GR + A+ +D + + SG
Sbjct: 90 ---GGRQITAQAWDGTTDYQSGPSSG 112
>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 = 52.0 bits (125), Expect = 2e-10
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 23/79 (29%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V + + ++V + A A +AL+GR+F
Sbjct: 41 HGGVIHIYVDKNSAQ--------GNVYVKCPSIAAAIAAVNALHGRWF------------ 80
Query: 80 RFFAGRMVRAELYDQSLFD 98
AG+M+ A +
Sbjct: 81 ---AGKMITAAYVPLPTYH 96
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 50.6 bits (121), Expect = 8e-10
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 18/84 (21%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
YG+V K VI+ + D+ V+IF+ F +++ A A LNGR+F
Sbjct: 37 YGKVGKCVIFEIPGAPDD---EAVRIFLEFERVESAIKAVVDLNGRYFG----------- 82
Query: 80 RFFAGRMVRAELYDQSLFDHNDFS 103
GR+V+A Y+ F D +
Sbjct: 83 ----GRVVKACFYNLDKFRVLDLA 102
>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 = 49.5 bits (118), Expect = 3e-09
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 20/73 (27%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
YG+VE++ + D+ ++ ++V F + ++AE A LN R+F
Sbjct: 51 YGEVEEMNVC-----DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF------------ 93
Query: 80 RFFAGRMVRAELY 92
G+ + AEL
Sbjct: 94 ---NGQPIHAELS 103
>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 = 36.0 bits (82), Expect = 8e-04
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+GQ+ +++ + +A FV F ++ A A ++ G F
Sbjct: 35 SQFGQILDILVSRSLKMRGQA-------FVIFKEVSSATNALRSMQGFPF 77
Score = 27.1 bits (59), Expect = 0.96
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F +A ARDAL G
Sbjct: 248 FVEFDNEVQAGAARDALQGFKI 269
>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 = 33.0 bits (76), Expect = 0.004
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+GQ+ +++ + +A FV F ++ A A ++ G F
Sbjct: 34 SRFGQILDILVSRSLKMRGQA-------FVIFKEVSSATNALRSMQGFPF 76
>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 = 32.2 bits (73), Expect = 0.009
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 10/48 (20%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
E G V+ +++ K F + +E++ A LNG+
Sbjct: 49 EKCGLVDALLMPPNKPY----------SFARYRTTEESKRAYVTLNGK 86
>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 = 31.8 bits (72), Expect = 0.012
Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 16/72 (22%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G++ KVVI N +V++ + ++A A +N
Sbjct: 42 FGKIHKVVINNSTSYAGSQGPSAS-AYVTYIRSEDALRAIQCVNNVVVD----------- 89
Query: 80 RFFAGRMVRAEL 91
GR ++A L
Sbjct: 90 ----GRTLKASL 97
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 32.1 bits (72), Expect = 0.019
Identities = 9/48 (18%), Positives = 19/48 (39%), Gaps = 10/48 (20%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
G ++++ K FV F AE+A++A++ +
Sbjct: 165 SRLGDIDRIRYVESKN----------CGFVKFKYQANAEFAKEAMSNQ 202
>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 = 31.1 bits (71), Expect = 0.022
Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGRFFA--------EAEYARDALNGRFFAGRMVR 88
+I+++F + + + + + +A A A+NGR G+ V+
Sbjct: 30 VLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK 86
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 30.4 bits (69), Expect = 0.034
Identities = 9/68 (13%), Positives = 23/68 (33%), Gaps = 10/68 (14%)
Query: 34 SDDEASEVIVKIFVSFSKMQEAEYARDALNGRF--FA--------EAEYARDALNGRFFA 83
+D+ + + + +++E E + A A+ L+
Sbjct: 15 NDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM 74
Query: 84 GRMVRAEL 91
G ++ A+L
Sbjct: 75 GNIIHAQL 82
>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 = 30.3 bits (69), Expect = 0.062
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAE 69
FV+F+ A+ A A++ E
Sbjct: 140 FVTFTTRAMAQTAIKAMHQAQTME 163
Score = 28.3 bits (64), Expect = 0.35
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
E YG V ++ + ++ + S+ FV+F + A A++AL+
Sbjct: 25 EQYGAVYEINVLRDRSQNPPQSKGCC--FVTFYTRKAALEAQNALHNM 70
>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 = 30.4 bits (68), Expect = 0.065
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
YG V++V I K+ V + +A+ A LNG
Sbjct: 57 GVYGDVQRVKILFNKKE---------NALVQMADGNQAQLAMSHLNGHKL 97
Score = 25.3 bits (55), Expect = 4.0
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 46 FVSFSKMQEAEYARDALNG 64
+ ++EA A L+
Sbjct: 193 LIQMGSVEEAVQALIDLHN 211
>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*
Length = 345
Score = 30.5 bits (68), Expect = 0.072
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 10/56 (17%)
Query: 10 YNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
N+ E G V+ +++ K F + +E++ A LNG+
Sbjct: 34 RNQLLPVLEKCGLVDALLMPPNKP----------YSFARYRTTEESKRAYVTLNGK 79
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 29.9 bits (67), Expect = 0.074
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+ G + +V+ + +A ++ F+ + A+ +A G F
Sbjct: 55 SSQGDILDIVVDLSDDNSGKA-------YIVFATQESAQAFVEAFQGYPF 97
>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 = 29.2 bits (66), Expect = 0.098
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAE 69
FV FS EA+ A AL+G
Sbjct: 60 FVKFSSHTEAQAAIHALHGSQTMP 83
>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 = 29.7 bits (66), Expect = 0.12
Identities = 12/50 (24%), Positives = 14/50 (28%), Gaps = 9/50 (18%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
YG VEKV K V + + A LN F
Sbjct: 27 CLYGNVEKVKFMKSKPG---------AAMVEMADGYAVDRAITHLNNNFM 67
Score = 24.3 bits (52), Expect = 9.2
Identities = 3/19 (15%), Positives = 6/19 (31%)
Query: 46 FVSFSKMQEAEYARDALNG 64
+ + +A LN
Sbjct: 169 LLEWDSKSDALETLGFLNH 187
>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 = 28.7 bits (65), Expect = 0.13
Identities = 5/48 (10%), Positives = 14/48 (29%), Gaps = 10/48 (20%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G + + A ++ + + A+ A + G
Sbjct: 41 FGSIRTIDHVKGDSF---A-------YIQYESLDAAQAACAKMRGFPL 78
>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 = 28.8 bits (65), Expect = 0.13
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 18 EAYGQVEKV-VIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G++ V +I+NE+ S FV+F +A+ AR+ L+G
Sbjct: 37 GQFGKILDVEIIFNERGSKGFG-------FVTFENSADADRAREKLHGTVV 80
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 29.2 bits (65), Expect = 0.13
Identities = 7/50 (14%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G V K++ + + + + ++ A++A+ +L+G+
Sbjct: 50 SKFGTVLKIITFTKNNQ--------FQALLQYADPVSAQHAKLSLDGQNI 91
>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 = 28.8 bits (65), Expect = 0.14
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAEAEYAR 74
FV F+ + AE +NG+ A A+
Sbjct: 56 FVEFADLATAEKCLHKINGKPLPGATPAK 84
>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 = 28.7 bits (65), Expect = 0.15
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+SF + ++A A ++G +
Sbjct: 61 FISFHRREDAARAIAGVSGFGY 82
Score = 27.2 bits (61), Expect = 0.58
Identities = 4/23 (17%), Positives = 10/23 (43%)
Query: 68 AEAEYARDALNGRFFAGRMVRAE 90
+A A ++G + ++ E
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVE 90
>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 = 29.6 bits (67), Expect = 0.15
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F + K A A+ L G+
Sbjct: 141 FAEYMKKDSAARAKSDLLGKPL 162
Score = 28.0 bits (63), Expect = 0.49
Identities = 8/59 (13%), Positives = 17/59 (28%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
+ ++ F ++ G+ F A A+ L G+ R +
Sbjct: 110 QQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY 168
Score = 26.9 bits (60), Expect = 1.3
Identities = 7/50 (14%), Positives = 14/50 (28%), Gaps = 9/50 (18%)
Query: 18 EAYGQVEKVVIYNEK--QSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
A + + Q A + + + AE A+ +G
Sbjct: 207 SAVHSPTFCQLACGQDGQLKGFA-------VLEYETAEMAEEAQQQADGL 249
Score = 25.7 bits (57), Expect = 2.9
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV+ ++AE A +A +
Sbjct: 61 FVTLLNGEQAEAAINAFHQS 80
>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 = 29.1 bits (66), Expect = 0.19
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV F+ +++ A LNG
Sbjct: 49 FVDFTSEMDSQRAIKVLNGI 68
Score = 28.7 bits (65), Expect = 0.21
Identities = 9/60 (15%), Positives = 19/60 (31%), Gaps = 10/60 (16%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDALNGR--------FF--AEAEYARDALNGRFFAGRMVR 88
+ +F + + RD G F +++ A LNG + ++
Sbjct: 17 DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Score = 28.7 bits (65), Expect = 0.22
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV ++K +EA+ A ALN
Sbjct: 135 FVRYNKREEAQEAISALNNVIP 156
>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 = 28.3 bits (64), Expect = 0.19
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
I F F ++ +A +D G+ F +AE A + G++ GR +R
Sbjct: 21 AAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 79
>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 = 28.3 bits (64), Expect = 0.19
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV FS +EA A +NGR
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIV 80
>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 = 29.1 bits (65), Expect = 0.22
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
YG V++V I K+ V + +A+ A LNG
Sbjct: 26 GVYGDVQRVKILFNKKE---------NALVQMADGNQAQLAMSHLNGHKL 66
Score = 24.5 bits (53), Expect = 6.8
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 46 FVSFSKMQEAEYARDALNG 64
+ ++EA A L+
Sbjct: 162 LIQMGSVEEAVQALIDLHN 180
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 28.4 bits (64), Expect = 0.22
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 18 EAYGQVEKV-VIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G++ V +I+NE+ S FV+F +A+ AR+ L+G
Sbjct: 51 GQFGKILDVEIIFNERGSKGFG-------FVTFENSADADRAREKLHGTVV 94
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.5 bits (63), Expect = 0.23
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 19 AYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
G+V+++VI+ ++ V F + A+ A+ ALNG
Sbjct: 48 PVGKVQRIVIFKRNG---------IQAMVEFESVLCAQKAKAALNGADI 87
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 28.5 bits (64), Expect = 0.24
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
E I F F ++ +A +D G+ F +AE A + G++ GR +R
Sbjct: 30 EDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 88
>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 = 28.9 bits (64), Expect = 0.24
Identities = 7/50 (14%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G V K++ + + + + ++ A++A+ +L+G+
Sbjct: 68 SKFGTVLKIITFTKNNQ--------FQALLQYADPVSAQHAKLSLDGQNI 109
>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 = 28.8 bits (65), Expect = 0.25
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
++ + ++A Y + LNG
Sbjct: 163 YIDVTSKEDARYCVEKLNGL 182
Score = 26.5 bits (59), Expect = 1.8
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 68 AEAEYARDALNGRFFAGRMVRAELYDQS 95
+A Y + LNG G + ++ +
Sbjct: 170 EDARYCVEKLNGLKIEGYTLVTKVSNPL 197
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 28.2 bits (63), Expect = 0.25
Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 7/47 (14%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
YG VE N V++S +A A D LNG
Sbjct: 37 VQYGVVESCEQVNTDSETAVV-------NVTYSSKDQARQALDKLNG 76
Score = 24.3 bits (53), Expect = 6.6
Identities = 10/59 (16%), Positives = 18/59 (30%), Gaps = 7/59 (11%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGRFF-------AEAEYARDALNGRFFAGRMVRAEL 91
EV+ + V + ++ E +A A D LNG ++
Sbjct: 30 EVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY 88
>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 = 28.0 bits (63), Expect = 0.25
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV++ KM+ A+ A LNG
Sbjct: 53 FVTYEKMESADQAVAELNGT 72
>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 = 28.4 bits (64), Expect = 0.26
Identities = 5/23 (21%), Positives = 8/23 (34%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
F ++ E NG+F
Sbjct: 70 FARMESTEKCEAVIGHFNGKFIK 92
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 28.0 bits (63), Expect = 0.28
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 10/50 (20%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+ +G + Y EK F+ + ++A AL F
Sbjct: 49 QNFGFILDFKHYPEKGCC----------FIKYDTHEQAAVCIVALANFPF 88
Score = 27.3 bits (61), Expect = 0.57
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A AL F GR +R
Sbjct: 74 EQAAVCIVALANFPFQGRNLR 94
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 28.8 bits (65), Expect = 0.28
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
+V+F + +AE A D +N
Sbjct: 61 YVNFQQPADAERALDTMNFD 80
Score = 27.6 bits (62), Expect = 0.52
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F + AE A + +NG
Sbjct: 147 FVHFETQEAAERAIEKMNGMLL 168
Score = 24.9 bits (55), Expect = 5.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+AE A D +N G+ VR
Sbjct: 68 ADAERALDTMNFDVIKGKPVR 88
Score = 24.5 bits (54), Expect = 7.9
Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 8/57 (14%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR---F-----FAEAEYARDALNGRFFAGRMVR 88
+ + F +F + + D + F AE A + +NG R V
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
>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 = 27.6 bits (62), Expect = 0.33
Identities = 8/20 (40%), Positives = 9/20 (45%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV F + YA LNG
Sbjct: 61 FVCFKHPESVSYAIALLNGI 80
Score = 25.7 bits (57), Expect = 1.7
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
YA LNG GR +
Sbjct: 68 ESVSYAIALLNGIRLYGRPIN 88
>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 = 28.2 bits (63), Expect = 0.36
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F + +A+ A++ NG
Sbjct: 92 FVYFENVDDAKEAKERANGMEL 113
Score = 27.8 bits (62), Expect = 0.42
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A++ NG GR +R
Sbjct: 99 DDAKEAKERANGMELDGRRIR 119
>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 = 28.3 bits (64), Expect = 0.36
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+ F K EAE A LNG+
Sbjct: 134 FIRFDKRIEAEEAIKGLNGQKP 155
Score = 27.9 bits (63), Expect = 0.39
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV++ ++AE A + LNG
Sbjct: 48 FVNYIDPKDAEKAINTLNGL 67
Score = 27.5 bits (62), Expect = 0.62
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDALNGRFF----------AEAEYARDALNGRFFAGRMVR 88
E +F S +++ + RD + G+ +AE A + LNG + ++
Sbjct: 16 QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
>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 = 27.9 bits (63), Expect = 0.39
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV + + +A A LNG+
Sbjct: 45 FVEYHQSHDANIALQTLNGK 64
Score = 27.9 bits (63), Expect = 0.45
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 10/60 (16%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
E + F F D G F +A+ A D++ G+ GR +R
Sbjct: 101 DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 25.2 bits (56), Expect = 4.1
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A A LNG+ +V+
Sbjct: 52 HDANIALQTLNGKQIENNIVK 72
>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 = 27.2 bits (61), Expect = 0.39
Identities = 11/71 (15%), Positives = 21/71 (29%), Gaps = 24/71 (33%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDAL 77
+G++ + + +Q F+ F+ Q AE A +
Sbjct: 34 YQFGEIRTITVVQRQQCA----------FIQFATRQAAEVAAEKS--------------F 69
Query: 78 NGRFFAGRMVR 88
N GR +
Sbjct: 70 NKLIVNGRRLN 80
>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 = 27.7 bits (62), Expect = 0.43
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A +A ++NG G +V+
Sbjct: 72 ESAAHAIVSVNGTTIEGHVVK 92
Score = 26.9 bits (60), Expect = 0.74
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
+GQ+ ++ ++ EK FV FS + A +A ++NG
Sbjct: 47 SPFGQIMEIRVFPEKGYS----------FVRFSTHESAAHAIVSVNGTTIE 87
>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 = 27.2 bits (61), Expect = 0.46
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A A ++G+ F GRM+
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLH 81
>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 = 27.7 bits (62), Expect = 0.47
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FVS+ A+ A ++NG
Sbjct: 71 FVSYDNPVSAQAAIQSMNGFQI 92
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 27.6 bits (62), Expect = 0.48
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F + AE A + +NG
Sbjct: 49 FVHFETQEAAERAIEKMNGMLL 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 = 27.8 bits (62), Expect = 0.49
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F ++AE A DA++G
Sbjct: 93 FVRFHDKRDAEDAMDAMDGAVL 114
Score = 27.8 bits (62), Expect = 0.52
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+AE A DA++G GR +R
Sbjct: 100 RDAEDAMDAMDGAVLDGRELR 120
>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 = 27.3 bits (61), Expect = 0.49
Identities = 17/74 (22%), Positives = 24/74 (32%), Gaps = 22/74 (29%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDAL 77
YG + + + N + A FV F E RDA E A
Sbjct: 44 YKYGAIRDIDLKNRRGGPPFA-------FVEF------EDPRDA---------EDAVYGR 81
Query: 78 NGRFFAGRMVRAEL 91
+G + G +R E
Sbjct: 82 DGYDYDGYRLRVEF 95
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 27.2 bits (61), Expect = 0.52
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A A++G GR +R
Sbjct: 66 RDAQDAEAAMDGAELDGRELR 86
Score = 26.4 bits (59), Expect = 1.2
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F ++A+ A A++G
Sbjct: 59 FVRFHDRRDAQDAEAAMDGAEL 80
>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 = 27.5 bits (61), Expect = 0.53
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 10/50 (20%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G + +V++ + V F + EA A L F
Sbjct: 32 SRFGSLGRVLLPEGGIT----------AIVEFLEPLEARKAFRHLAYSKF 71
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 27.7 bits (62), Expect = 0.54
Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDALNGRF--FA--------EAEYARDALNGRFFAGRMVR 88
+ I + F F ++ + + D++ + FA A+ A + +N GR ++
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
Score = 27.3 bits (61), Expect = 0.80
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
F+ + K Q ++ A ++N
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLG 193
>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 = 27.2 bits (61), Expect = 0.58
Identities = 6/22 (27%), Positives = 15/22 (68%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F++F+ ++ A +A+NG++
Sbjct: 52 FINFASFDASDAAIEAMNGQYL 73
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 27.3 bits (61), Expect = 0.65
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FVSF A+ A A+NG
Sbjct: 86 FVSFDNPDSAQVAIKAMNGF 105
>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 = 26.7 bits (60), Expect = 0.66
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FVSF+ +A+ A D++ G+
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDL 68
Score = 24.4 bits (54), Expect = 4.4
Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
E + F F D G F +A+ A D++ G+ GR +R
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 27.4 bits (61), Expect = 0.66
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV F ++A A D +N
Sbjct: 109 FVEFELAEDAAAAIDNMNE 127
Score = 26.3 bits (58), Expect = 1.8
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A A D +N GR +R
Sbjct: 116 EDAAAAIDNMNESELFGRTIR 136
>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 = 26.8 bits (60), Expect = 0.75
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
AE A+ L+ G+ +R
Sbjct: 62 TLAEIAKVELDNMPLRGKQLR 82
>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 = 27.3 bits (61), Expect = 0.75
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
F+ AE A+ L+G
Sbjct: 62 FIRLESRTLAEIAKAELDGT 81
Score = 26.2 bits (58), Expect = 2.1
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDA----LNGRFFAEAEYARDALNGRFFAGRMVR 88
E ++F + + E RD + AE A+ L+G R +R
Sbjct: 36 EEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLR 89
Score = 25.8 bits (57), Expect = 3.2
Identities = 6/22 (27%), Positives = 8/22 (36%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F+ A A + F
Sbjct: 141 FVEFAAKPPARKALERCGDGAF 162
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 27.0 bits (60), Expect = 0.80
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV++ KM+ A+ A LNG
Sbjct: 77 FVTYEKMESADQAVAELNGT 96
>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 = 26.8 bits (60), Expect = 0.80
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A++ NG GR +R
Sbjct: 68 DDAKEAKERANGMELDGRRIR 88
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 26.8 bits (60), Expect = 0.85
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV F ++A+YA ++
Sbjct: 61 FVEFLSEEDADYAIKIMDM 79
Score = 26.5 bits (59), Expect = 1.0
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+YA ++ G+ +R
Sbjct: 68 EDADYAIKIMDMIKLYGKPIR 88
>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 = 26.5 bits (59), Expect = 0.97
Identities = 7/43 (16%), Positives = 12/43 (27%), Gaps = 9/43 (20%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAEAEYARDALNGRFFAGRMVR 88
F F + A+ A + G GR ++
Sbjct: 61 FAQFMTQEAAQKCLAAAS---------LEAEGGGLKLDGRQLK 94
>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 = 26.4 bits (59), Expect = 1.0
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
+A A L+ F G+ + +L
Sbjct: 55 EDAVEAIRGLDNTEFQGKRMHVQL 78
Score = 25.3 bits (56), Expect = 2.2
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV + ++A A L+ F
Sbjct: 48 FVHMERAEDAVEAIRGLDNTEF 69
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 26.5 bits (59), Expect = 1.1
Identities = 7/39 (17%), Positives = 11/39 (28%), Gaps = 8/39 (20%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAEA--------EYARDA 76
FV S +A L ++A+ A
Sbjct: 57 FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
>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 = 26.9 bits (60), Expect = 1.1
Identities = 9/59 (15%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----FF-----AEAEYARDALNGRFFAGRMVR 88
+ + ++ SF ++ +D+ G F + A LNG + +
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 187
>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 = 26.7 bits (59), Expect = 1.2
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+AE A DA++G GR +R
Sbjct: 123 RDAEDAMDAMDGAVLDGRELR 143
Score = 26.0 bits (57), Expect = 2.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F ++AE A DA++G
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVL 137
>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 = 26.5 bits (59), Expect = 1.2
Identities = 5/20 (25%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
F+++ + + A A+ AL+ +
Sbjct: 59 FLTYCERESALKAQSALHEQ 78
>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 = 26.0 bits (58), Expect = 1.3
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV K +A+ A LNG+
Sbjct: 47 FVHMEKEADAKAAIAQLNGKEV 68
Score = 25.2 bits (56), Expect = 2.2
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
A+A+ A LNG+ G+ + EL
Sbjct: 54 ADAKAAIAQLNGKEVKGKRINVEL 77
>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 = 26.1 bits (58), Expect = 1.3
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F++F + A A +NG
Sbjct: 71 FITFPNKEIAWQALHLVNGYKL 92
Score = 25.3 bits (56), Expect = 3.1
Identities = 11/59 (18%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGRF--FA--------EAEYARDALNGRFFAGRMVR 88
+V +F F + + + GR A A A +NG G+++
Sbjct: 40 RDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98
>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 = 26.1 bits (58), Expect = 1.4
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+ F + A A + +NG+
Sbjct: 49 FIHFDERDGAVKAMEEMNGKDL 70
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 102
Score = 26.1 bits (58), Expect = 1.4
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A++A+ G V
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVT 85
Score = 25.7 bits (57), Expect = 1.8
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F+ ++A+ A++A+
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEI 79
>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 = 25.6 bits (57), Expect = 1.6
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV F ++A A D +N
Sbjct: 53 FVEFELAEDAAAAIDNMNE 71
Score = 24.8 bits (55), Expect = 3.3
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A A D +N GR +R
Sbjct: 60 EDAAAAIDNMNESELFGRTIR 80
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 26.1 bits (58), Expect = 1.6
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 67 FAEAEYARDALNGRFFAGRMVR 88
+ EA+ A + LNG+ G+ +
Sbjct: 75 YKEAQAAMEGLNGQDLMGQPIS 96
Score = 24.9 bits (55), Expect = 4.2
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
V + +EA+ A + LNG+
Sbjct: 69 LVEYETYKEAQAAMEGLNGQDLM 91
>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 = 26.2 bits (58), Expect = 1.6
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
A A NGR AG+ + +
Sbjct: 73 RHARAAVLGENGRVLAGQTLDINM 96
Score = 25.4 bits (56), Expect = 2.7
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV +S + A A NGR
Sbjct: 66 FVQYSNERHARAAVLGENGRVL 87
>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 = 25.6 bits (57), Expect = 1.7
Identities = 7/20 (35%), Positives = 8/20 (40%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV F A+ A AL
Sbjct: 51 FVDFDSPSAAQKAVTALKAS 70
Score = 25.6 bits (57), Expect = 1.7
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+ A+ A AL +M +
Sbjct: 58 SAAQKAVTALKASGVQAQMAK 78
>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 = 26.4 bits (59), Expect = 1.7
Identities = 9/60 (15%), Positives = 20/60 (33%), Gaps = 10/60 (16%)
Query: 39 SEVIVKIFVSFSKMQEAEYARDALNGR-----F-----FAEAEYARDALNGRFFAGRMVR 88
+ + ++ SF ++ +D+ G F + A LNG + +
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
>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 = 26.1 bits (58), Expect = 1.7
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V+F + EA A NG+
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLL 81
>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 = 25.7 bits (57), Expect = 1.8
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 46 FVSFSKMQEAEYARDALNGRF 66
FV + A A + L+G+
Sbjct: 48 FVDYPDQNWAIRAIETLSGKV 68
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 25.8 bits (57), Expect = 1.8
Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGR-----FF-----AEAEYARDALNGRFFAGR 85
+ + +F K+ E+ D G+ F +A+ + +G+ +
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>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 = 25.7 bits (57), Expect = 1.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV FS ++A A ALNG+
Sbjct: 55 FVHFSNREDAVEAMKALNGKVL 76
Score = 24.9 bits (55), Expect = 3.2
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 69 EAEYARDALNGRFFAGRMVRAEL 91
+A A ALNG+ G + L
Sbjct: 63 DAVEAMKALNGKVLDGSPIEVTL 85
>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 = 25.7 bits (57), Expect = 2.2
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A ++ N R GR +R
Sbjct: 64 EDAKEALNSCNKREIEGRAIR 84
Score = 24.9 bits (55), Expect = 4.2
Identities = 6/20 (30%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
F+ F+ ++A+ A ++ N R
Sbjct: 57 FIEFASFEDAKEALNSCNKR 76
>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 = 25.7 bits (57), Expect = 2.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A+ A A+NG+ GR +R
Sbjct: 65 DDAKDAMMAMNGKSVDGRQIR 85
Score = 25.3 bits (56), Expect = 2.8
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV+F + +A+ A A+NG+
Sbjct: 58 FVTFENIDDAKDAMMAMNGKSV 79
>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 = 25.3 bits (56), Expect = 2.4
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A A D +N GR +R
Sbjct: 65 EDAAAAIDNMNESELFGRTIR 85
Score = 25.3 bits (56), Expect = 2.4
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV F ++A A D +N
Sbjct: 58 FVEFELAEDAAAAIDNMNES 77
>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 = 25.8 bits (56), Expect = 2.5
Identities = 4/22 (18%), Positives = 6/22 (27%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V ++ D L R
Sbjct: 116 LVGVGSEASSKKLMDLLPKREL 137
Score = 25.1 bits (54), Expect = 4.6
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 10/49 (20%)
Query: 50 SKMQEAEYARDALNGR---F-------FAEAEYARDALNGRFFAGRMVR 88
+ + E ++ + NG+ F A ++ D L R G+
Sbjct: 95 NDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPV 143
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 25.3 bits (56), Expect = 2.6
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
+AE A L+G+ G VR EL
Sbjct: 48 RDAEDAVRGLDGKVICGSRVRVEL 71
Score = 24.2 bits (53), Expect = 7.2
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F ++AE A L+G+
Sbjct: 41 FVEFEDPRDAEDAVRGLDGKVI 62
>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 = 25.2 bits (56), Expect = 2.7
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A A + LNG AGR +R
Sbjct: 58 ECARRALEQLNGFELAGRPMR 78
Score = 24.1 bits (53), Expect = 6.4
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
F++FS + A A + LNG A
Sbjct: 51 FITFSDSECARRALEQLNGFELA 73
>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 = 25.3 bits (56), Expect = 2.7
Identities = 6/20 (30%), Positives = 8/20 (40%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
V F + +A A NG
Sbjct: 74 DVHFERKADALKAMKQYNGV 93
>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 = 25.4 bits (56), Expect = 2.7
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 67 FAEAEYARDALNGRFFAGRMVR 88
+ EA+ A + LNG+ G+ +
Sbjct: 74 YKEAQAAMEGLNGQDLMGQPIS 95
Score = 24.3 bits (53), Expect = 6.5
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V + +EA+ A + LNG+
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDL 89
>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 = 25.5 bits (56), Expect = 2.8
Identities = 10/51 (19%), Positives = 16/51 (31%), Gaps = 4/51 (7%)
Query: 18 EAYG-QVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
V V++Y S + + FV + + A AR L
Sbjct: 30 AKVTEGVLDVIVYA---SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI 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 = 25.7 bits (56), Expect = 2.9
Identities = 3/22 (13%), Positives = 6/22 (27%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V + + L G+
Sbjct: 103 EVVVASENSVHKLLELLPGKVL 124
Score = 24.9 bits (54), Expect = 4.8
Identities = 4/21 (19%), Positives = 6/21 (28%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+ L G+ G V
Sbjct: 110 NSVHKLLELLPGKVLNGEKVD 130
>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 = 25.4 bits (56), Expect = 3.0
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 69 EAEYARDALNGRFFAGRMVRAELYDQ 94
+A+ A D L+G + R + Y+
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYYNA 84
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 25.2 bits (55), Expect = 3.0
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
A A+ A L G +R L
Sbjct: 67 AAAQQAVSCLQGLRLGTDTLRVAL 90
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 24.9 bits (55), Expect = 3.0
Identities = 6/24 (25%), Positives = 8/24 (33%)
Query: 68 AEAEYARDALNGRFFAGRMVRAEL 91
AE A L+ G + E
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEA 76
Score = 24.5 bits (54), Expect = 5.4
Identities = 6/20 (30%), Positives = 7/20 (35%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV AE A L+
Sbjct: 46 FVHIEDKTAAEDAIRNLHHY 65
>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 = 24.9 bits (55), Expect = 3.0
Identities = 5/21 (23%), Positives = 8/21 (38%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+ A LNG R ++
Sbjct: 55 ESSASAVRNLNGYQLGSRFLK 75
>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 = 25.0 bits (55), Expect = 3.1
Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 10/57 (17%)
Query: 42 IVKIFVSFSKMQEAEYARDALNGRF--FA--------EAEYARDALNGRFFAGRMVR 88
I+ F + + + + G A EA A LN R R V+
Sbjct: 32 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK 88
>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 = 24.9 bits (55), Expect = 3.2
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+AE + G GR V
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVS 84
>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 = 24.9 bits (55), Expect = 3.3
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+ A+N + GR+++
Sbjct: 69 DSAQNCTRAINNKQLFGRVIK 89
Score = 24.5 bits (54), Expect = 5.2
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
F+ F A+ A+N +
Sbjct: 62 FILFLDKDSAQNCTRAINNK 81
>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 = 25.5 bits (56), Expect = 3.4
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV F A+ A LNG
Sbjct: 88 FVKFQSGSSAQQAIAGLNG 106
>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 = 25.0 bits (55), Expect = 3.4
Identities = 6/28 (21%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 67 FAEAEYARDA---LNGRFFAGRMVRAEL 91
F + RDA + G+ + E+
Sbjct: 64 FDNPQSVRDAIEXESQEMNFGKKLILEV 91
Score = 24.2 bits (53), Expect = 6.3
Identities = 4/22 (18%), Positives = 7/22 (31%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+ F Q A + +
Sbjct: 61 FIQFDNPQSVRDAIEXESQEMN 82
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 24.9 bits (55), Expect = 3.6
Identities = 6/22 (27%), Positives = 8/22 (36%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV F+ E + A G
Sbjct: 55 FVKFTDELEQKRALTECQGAVG 76
>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 = 25.0 bits (55), Expect = 3.7
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 14/43 (32%)
Query: 46 FVSFSKMQEAEYARDALNGRFFAEAEYARDALNGRFFAGRMVR 88
FV F Q+A+ A +AL + GR +
Sbjct: 62 FVDFITKQDAKKAFNALC--------------HSTHLYGRRLV 90
>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 = 25.0 bits (55), Expect = 3.9
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F++F +A+ A +NG+
Sbjct: 52 FITFENPADAKNAAKDMNGKSL 73
Score = 24.2 bits (53), Expect = 7.9
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+A+ A +NG+ G+ ++
Sbjct: 59 ADAKNAAKDMNGKSLHGKAIK 79
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 24.9 bits (55), Expect = 4.0
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
FV F + + A A + ++G+ FA
Sbjct: 69 FVEFEEAESAAKAIEEVHGKSFA 91
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 25.2 bits (55), Expect = 4.1
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 18 EAYGQVEKV-VIYNEK-QSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
+G ++K V Y+ +S A V F + +A A G
Sbjct: 110 AEFGTLKKAAVDYDRSGRSLGTA-------DVHFERRADALKAMKQYKGV 152
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 24.5 bits (54), Expect = 4.3
Identities = 3/23 (13%), Positives = 8/23 (34%)
Query: 69 EAEYARDALNGRFFAGRMVRAEL 91
A + + G+ + E+
Sbjct: 57 SVRDAIECESQEMNFGKKLILEV 79
Score = 23.7 bits (52), Expect = 8.3
Identities = 4/22 (18%), Positives = 7/22 (31%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+ F Q A + +
Sbjct: 49 FIQFDNPQSVRDAIECESQEMN 70
>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 = 25.0 bits (55), Expect = 4.5
Identities = 5/23 (21%), Positives = 7/23 (30%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
V F + +A A G
Sbjct: 80 DVHFERRADALKAMKQYKGVPLD 102
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 24.5 bits (54), Expect = 4.6
Identities = 3/21 (14%), Positives = 10/21 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
++A A ++G +++
Sbjct: 69 SQASQAVMKMDGMTIKENIIK 89
>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 = 24.5 bits (54), Expect = 4.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV + K ++A+ A L G
Sbjct: 54 FVEYKKPEQAQKALKQLQGH 73
>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 = 24.4 bits (54), Expect = 4.8
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 68 AEAEYARDALNGRFFAGRMVRAE 90
EAE A ++G G+ + A
Sbjct: 58 DEAEKALKHMDGGQIDGQEITAT 80
>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 = 24.8 bits (54), Expect = 5.1
Identities = 5/22 (22%), Positives = 7/22 (31%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
F+ + A A NG
Sbjct: 96 FIGLPNEKAAAKALKEANGYVL 117
>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 = 24.6 bits (54), Expect = 5.3
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V+F EA A LN R
Sbjct: 61 MVAFESRDEATAAVIDLNDRPI 82
>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 = 24.5 bits (54), Expect = 5.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A A LNGR F+GR +R
Sbjct: 61 ETALSAMRNLNGREFSGRALR 81
>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 = 24.4 bits (53), Expect = 5.9
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
V F + ++ YA L+ F
Sbjct: 54 VVEFVRKEDMTYAVRKLDNTKF 75
Score = 24.0 bits (52), Expect = 9.3
Identities = 4/21 (19%), Positives = 6/21 (28%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+ YA L+ F
Sbjct: 61 EDMTYAVRKLDNTKFRSHEGE 81
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 24.5 bits (54), Expect = 6.3
Identities = 4/23 (17%), Positives = 8/23 (34%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
++ F +AE + G
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEID 162
>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 = 24.8 bits (54), Expect = 6.5
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV + +AE A +NG
Sbjct: 85 FVEYYSRADAENAMRYING 103
Score = 24.0 bits (52), Expect = 9.2
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+AE A +NG R++R
Sbjct: 92 ADAENAMRYINGTRLDDRIIR 112
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 24.4 bits (53), Expect = 6.6
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 69 EAEYARDALNGRFFAGRMVRAELYDQ 94
A + LN F G ++ E D
Sbjct: 79 ILVEALERLNNIEFRGSVITVERDDN 104
>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 = 24.2 bits (53), Expect = 7.2
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
+A A++ALNG G+ ++
Sbjct: 79 KQALAAKEALNGAEIMGQTIQ 99
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 24.1 bits (53), Expect = 7.5
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 46 FVSFSKMQEAEYARDALNG 64
V F + AE A +NG
Sbjct: 52 VVKFESPEVAERACRMMNG 70
>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 = 24.2 bits (53), Expect = 8.0
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 68 AEAEYARDALNGRFFAGRMVR 88
A+ A + LNG AGR ++
Sbjct: 79 ECAKKALEQLNGFELAGRPMK 99
>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 = 24.1 bits (52), Expect = 8.5
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 11/56 (19%)
Query: 44 KIFVSFSKMQEAEYARDALNGRFFA--------EAEYARDALNGRFFAGRMVRAEL 91
+ F + ++ AR+ FA +A A L+GR G VR EL
Sbjct: 92 RAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL 144
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.133 0.364
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,641,900
Number of extensions: 90156
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 405
Number of HSP's successfully gapped: 246
Length of query: 104
Length of database: 6,701,793
Length adjustment: 69
Effective length of query: 35
Effective length of database: 4,775,244
Effective search space: 167133540
Effective search space used: 167133540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.4 bits)