RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14686
(306 letters)
>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 = 197 bits (504), Expect = 2e-63
Identities = 87/158 (55%), Positives = 110/158 (69%), Gaps = 13/158 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 99 DEAMSNRPHEIDGRVVETKRAVPREVKVR-----RVTKVQI------ALEQM--DYFGQY 145
D AM+ RPH++DGRVVE KRAV RE R V K+ + E DYF QY
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 146 GTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
G IE + ++T++ +G KRGFAF+ FDD+D VDKIV+ K
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Score = 114 bits (288), Expect = 3e-31
Identities = 24/91 (26%), Positives = 54/91 (59%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+ + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+ VD+ + + H ++G E ++A+ ++
Sbjct: 154 DDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>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 = 188 bits (481), Expect = 3e-60
Identities = 54/156 (34%), Positives = 97/156 (62%), Gaps = 10/156 (6%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+ K+FIGGL++ T +D+L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VDE
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 101 AMSNRPHEIDGRVVETKRAVPREVKVRRVTKV------QIALEQM--DYFGQYGTIESVN 152
+ + H +DG+V++ KRA+PR+ + + K+ + ++F Q+GTI
Sbjct: 61 VVKTQ-HILDGKVIDPKRAIPRD-EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 153 MVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLE 188
++ +K+TG RGF F+ +D D VD++ +K + +
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFK 154
Score = 113 bits (284), Expect = 6e-31
Identities = 33/84 (39%), Positives = 46/84 (54%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
E + K+F+GG+ + FF QWG I+D +M D T +SRGFGF+TY + V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 99 DEAMSNRPHEIDGRVVETKRAVPR 122
D N+ + R +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>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 = 157 bits (399), Expect = 8e-49
Identities = 37/86 (43%), Positives = 59/86 (68%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + + KLF+GGLD+ T ++L+++F Q+GE+VD V+MKD T +SRGFGF+ + +
Sbjct: 11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
V +++RPH +DGR ++ K PR
Sbjct: 71 VGTVLASRPHTLDGRNIDPKPCTPRG 96
Score = 53.8 bits (130), Expect = 1e-09
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
YF QYG + ++ +K T RGF F++F D + V VL ++G
Sbjct: 35 SYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT-------VLASRPHTLDG 84
>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 = 156 bits (397), Expect = 2e-48
Identities = 53/86 (61%), Positives = 66/86 (76%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E E RKLFIGGL + T ++SL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
VD AM+ RPH IDGRVVE KRAV RE
Sbjct: 82 VDAAMAARPHSIDGRVVEPKRAVARE 107
Score = 60.0 bits (146), Expect = 1e-11
Identities = 20/98 (20%), Positives = 37/98 (37%), Gaps = 18/98 (18%)
Query: 110 DGRVVETKRAVPREVKVR---RVTKV-------QIALEQM-DYFGQYGTIESVNMVTNKE 158
+ +T VP E K R + K+ + E + +Y+ Q+G + ++ +
Sbjct: 5 SSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64
Query: 159 TGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+ RGF F+ F VD + I+G
Sbjct: 65 SKRSRGFGFVTFSSMAEVDA-------AMAARPHSIDG 95
>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 = 155 bits (394), Expect = 5e-48
Identities = 36/90 (40%), Positives = 60/90 (66%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S K+FIGGL ++T + L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ +
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPREVKVR 127
VD+ ++ HE+D + ++ K A PR + +
Sbjct: 80 VDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 55.7 bits (135), Expect = 2e-10
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+YFGQ+G ++ ++ + T RGF F+ F D VDK VL + ++
Sbjct: 44 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK-------VLAQSRHELDS 93
>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 = 148 bits (377), Expect = 2e-45
Identities = 30/86 (34%), Positives = 47/86 (54%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + K+F+GGL Y T D SL+ +FE +G+I + VV+ D T +SRG+GF+T ++
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
+ A + IDGR A
Sbjct: 72 AERACKDPNPIIDGRKANVNLAYLGA 97
Score = 57.3 bits (139), Expect = 1e-10
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
YF +G IE ++T+++TG RG+ F+ D ++ + +I+G
Sbjct: 36 KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER-------ACKDPNPIIDG 85
>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 = 144 bits (365), Expect = 7e-44
Identities = 34/91 (37%), Positives = 58/91 (63%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
S S K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ +
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 95 SKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
+ VD+A++ H+I G+ VE KRA PR+ K
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSK 92
Score = 64.9 bits (159), Expect = 1e-13
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YF ++G + V M+ + E RGF FI F+D VD+ V
Sbjct: 29 EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
>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 = 142 bits (361), Expect = 2e-43
Identities = 33/82 (40%), Positives = 53/82 (64%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E K+F+GGL + T+ LK +F ++GE+VD + DP T RSRGFGFI + ++
Sbjct: 6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS 65
Query: 98 VDEAMSNRPHEIDGRVVETKRA 119
V++ + + H +DGRV++ K+A
Sbjct: 66 VEKVLDQKEHRLDGRVIDPKKA 87
Score = 54.1 bits (131), Expect = 6e-10
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
DYF ++G + + + TG RGF FI F D V+K VL+ + ++G
Sbjct: 30 DYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEK-------VLDQKEHRLDG 79
>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 = 141 bits (357), Expect = 1e-42
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ L + GL ++T + LK +F +GE++ V V KD T S+GFGF+ ++E +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
+ MS H IDGR + K ++
Sbjct: 70 QVKVMSQ-RHMIDGRWCDCKLPNSKQ 94
Score = 61.1 bits (149), Expect = 3e-12
Identities = 12/44 (27%), Positives = 25/44 (56%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YF +G + V + + +TG +GF F+ F +Y+ K++ +
Sbjct: 34 EYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 138 bits (351), Expect = 5e-42
Identities = 33/75 (44%), Positives = 55/75 (73%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL ++T + L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD+ ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 105 RPHEIDGRVVETKRA 119
HE+D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 53.3 bits (129), Expect = 9e-10
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+YFGQ+G ++ ++ + T RGF F+ F D VDK VL + ++
Sbjct: 19 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK-------VLAQSRHELDS 68
>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 = 137 bits (348), Expect = 3e-40
Identities = 26/150 (17%), Positives = 63/150 (42%), Gaps = 14/150 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV-----VMKDPVTKRSRGFGFITYSESKMV 98
R+L++G + + ++++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 99 DEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIA-LEQ-------MDYFGQYGTIES 150
+AM+ G+ ++ +R + K+ I L + +G +++
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPL-PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 123
Query: 151 VNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
N+V + TG +G+AF E+ D +V D+ +
Sbjct: 124 FNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Score = 89.6 bits (223), Expect = 5e-22
Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 25 AMIINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRS 84
++ I + + KLFIGGL NDD +K +G + ++KD T S
Sbjct: 79 SLKIRRPHDYQP---LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS 135
Query: 85 RGFGFITYSESKMVDEAMSN-RPHEIDGRVVETKRA 119
+G+ F Y + + D+A++ ++ + + +RA
Sbjct: 136 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 130 bits (330), Expect = 7e-39
Identities = 30/75 (40%), Positives = 49/75 (65%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T + +K +FEQ+G++ D ++M D T R RGFGF+T+ +V++
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 105 RPHEIDGRVVETKRA 119
HEI+ ++VE K+A
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 62.1 bits (152), Expect = 7e-13
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
YF Q+G ++ ++ +K T RGF F+ F+ D+V+K+
Sbjct: 18 HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
>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 = 119 bits (301), Expect = 1e-34
Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T ++ ++ +F +GE+ + + D T + RGF FIT+ E + V + M
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 105 RPHEIDGRVVETKRA 119
+ H + E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 66.8 bits (164), Expect = 1e-14
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YFG +G +ES+ + + +T +RGF FI F + + V KI+ K
Sbjct: 18 EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
>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 = 120 bits (302), Expect = 2e-34
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 6/86 (6%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
K+F+G + L+ FF Q+GE+VDV + K R F F+T+++ K+
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKV 60
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
I G V A P+
Sbjct: 61 AQSLCG-EDLIIKGISVHISNAEPKH 85
Score = 44.1 bits (105), Expect = 2e-06
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVV 186
+F QYG + V + R FAF+ F D V + + +++
Sbjct: 30 QFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGEDLII 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 = 121 bits (305), Expect = 2e-33
Identities = 28/161 (17%), Positives = 60/161 (37%), Gaps = 19/161 (11%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
+ ++++G + Y +D+++ F +G I + + D VT + +GF F+ Y +
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83
Query: 99 DEAMSNR-PHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM------------------ 139
A+ + GR ++ R + ++
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F +G I+S + + TG +G+ FIE++ V
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Score = 91.2 bits (227), Expect = 3e-22
Identities = 22/93 (23%), Positives = 50/93 (53%), Gaps = 1/93 (1%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+ D E + ++++ + +DD +K+ FE +G+I + +DP T + +G+GFI
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172
Query: 91 TYSESKMVDEAMSN-RPHEIDGRVVETKRAVPR 122
Y +++ +A+S+ ++ G+ + +AV
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
>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 = 115 bits (290), Expect = 1e-32
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
+F+G +D L+ FF Q+G+++DV + K R F F+T+++ ++
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQ 56
Query: 100 EAMSNRPHEIDGRVVETKRAVPRE 123
I G V A P+
Sbjct: 57 SLCG-EDLIIKGISVHISNAEPKH 79
Score = 47.2 bits (113), Expect = 2e-07
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
++F QYG + V + R FAF+ F D + + +
Sbjct: 24 EFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCGED 62
>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 = 111 bits (279), Expect = 8e-30
Identities = 23/167 (13%), Positives = 60/167 (35%), Gaps = 32/167 (19%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV-----VMKDPVTKRSRGFGFITYSESKMV 98
R+L++G + + ++++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 99 DEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQ-------------------- 138
+AM+ G+ ++ +R + + +
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 139 -------MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ +G +++ N+V + TG +G+AF E+ D +V D+
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Score = 85.9 bits (213), Expect = 3e-20
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
P+S KLFIGGL NDD +K +G + ++KD T S+G+ F Y + +
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPRE 123
D+A++ ++ + + +RA
Sbjct: 169 TDQAIAGLNGMQLGDKKLLVQRASVGA 195
>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 = 106 bits (266), Expect = 4e-29
Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 1/87 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
KLF+GGL + TN+ SL+ F ++G+I +VVV+KD T+RSRGFGF+T+
Sbjct: 7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 66
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPRE 123
+AM +DGR + +A
Sbjct: 67 AKDAMMAMNGKSVDGRQIRVDQAGKSS 93
Score = 53.0 bits (128), Expect = 2e-09
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F +YG I V +V ++ET RGF F+ F++ D
Sbjct: 31 QVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
>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 = 106 bits (267), Expect = 2e-28
Identities = 36/151 (23%), Positives = 68/151 (45%), Gaps = 16/151 (10%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
S L + L + ++ F GEI +++D +T +S G+GF+ Y + K ++A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 102 MS--NRPHEIDGRVVETKRAVPREVKVRRVTKVQI----------ALEQMDYFGQYGTIE 149
++ N + + ++ A P + R + + LEQ+ F QYG I
Sbjct: 61 INTLNG-LRLQTKTIKVSYARPSSASI-RDANLYVSGLPKTMTQKELEQL--FSQYGRII 116
Query: 150 SVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ ++ ++ TG RG FI FD ++ +
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Score = 73.0 bits (180), Expect = 6e-16
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 6/95 (6%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
++ A S L++ GL L+ F Q+G I+ ++ D VT SRG
Sbjct: 76 VSYA---RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132
Query: 88 GFITYSESKMVDEA---MSNRPHEIDGRVVETKRA 119
GFI + + +EA ++ + + K A
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 106 bits (266), Expect = 4e-28
Identities = 33/156 (21%), Positives = 65/156 (41%), Gaps = 19/156 (12%)
Query: 36 QCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES 95
+ SE + LFIG L+ + LK + D+ V+ D T +R FG++ + +
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64
Query: 96 KMVDEAMSNRPHEIDGRVVETKRAVPR-EVKVRRVTKVQI----------ALEQMDYFGQ 144
+ +++A+ ++ G ++ ++ R KVR + L+++ F
Sbjct: 65 EDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEV--FED 122
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
I V + G +G A+IEF +K +
Sbjct: 123 ALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNL 153
Score = 71.9 bits (177), Expect = 2e-15
Identities = 20/98 (20%), Positives = 35/98 (35%), Gaps = 7/98 (7%)
Query: 26 MIINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSR 85
+ + K + + R L L + +D LK FE EI +S+
Sbjct: 83 IKLEKPKGRDS-KKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSK 136
Query: 86 GFGFITYSESKMVDEAMSN-RPHEIDGRVVETKRAVPR 122
G +I + ++ + + EIDGR V +
Sbjct: 137 GIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 102 bits (255), Expect = 2e-27
Identities = 20/101 (19%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGF 89
+ S+ + +FI L + + +++L +Q+G++ V V+ P T+ S+G F
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 90 ITYSESKMVDEAMSNRPH-------EIDGRVVETKRAVPRE 123
+ + + ++ ++DGR ++ AV R+
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 102
Score = 53.9 bits (130), Expect = 1e-09
Identities = 12/57 (21%), Positives = 26/57 (45%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+ Q+G ++ V +V + +T +G AF +F + K + + E ++G
Sbjct: 34 EVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG 90
>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 = 101 bits (254), Expect = 3e-27
Identities = 18/79 (22%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+F+GG+D R ++ +++FF ++G + +V ++ D T S+G+GF+++ V + + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 105 RPHEIDGRVVETKRAVPRE 123
G+ ++ A+ ++
Sbjct: 70 -QINFHGKKLKLGPAIRKQ 87
Score = 58.0 bits (141), Expect = 3e-11
Identities = 14/41 (34%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+F +YG+++ V ++T++ TG +G+ F+ F + V KIV
Sbjct: 28 SFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
>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 = 102 bits (256), Expect = 7e-27
Identities = 33/149 (22%), Positives = 62/149 (41%), Gaps = 16/149 (10%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L + L D L A F G I +M+D T S G+ F+ ++ A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 104 --NRPHEIDGRVVETKRAVPREVKVRRVTKVQI----------ALEQMDYFGQYGTIESV 151
N + + ++ A P + + T + + L+ + FG+YG+I
Sbjct: 64 VLNG-ITVRNKRLKVSYARPGG-ESIKDTNLYVTNLPRTITDDQLDTI--FGKYGSIVQK 119
Query: 152 NMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
N++ +K TG RG AF+ ++ + + +
Sbjct: 120 NILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 69.9 bits (172), Expect = 8e-15
Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 7/88 (7%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
++ A E L++ L DD L F ++G IV +++D +T R RG
Sbjct: 77 VSYA---RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 133
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVVE 115
F+ Y++ + EA+S ++ + E
Sbjct: 134 AFVRYNKREEAQEAIS----ALNNVIPE 157
>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 = 104 bits (261), Expect = 1e-26
Identities = 36/163 (22%), Positives = 65/163 (39%), Gaps = 26/163 (15%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
I ++ + +LF+G L ++ K FE++GE +V + +D RGF
Sbjct: 8 IKSFLKPGE-KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGF 60
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQI----------ALE 137
GFI + + A E+DG +++++ R + + LE
Sbjct: 61 GFIRLESRTLAEIAK----AELDGTILKSRPLRIR--FATHGAALTVKNLSPVVSNELLE 114
Query: 138 QMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F Q+G +E +V + + G G F+EF K +
Sbjct: 115 --QAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154
Score = 76.3 bits (188), Expect = 3e-16
Identities = 26/151 (17%), Positives = 53/151 (35%), Gaps = 19/151 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA--- 101
L + L +++ L+ F Q+G + VV+ D R+ G GF+ ++ +A
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALER 156
Query: 102 MSNRPHE--IDGRVVETKRAVPREVK-------VRRVTKVQIALEQMDYFGQYGTIESVN 152
+ R V + + + +++ + EQ F Q GT E
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEY 216
Query: 153 MVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+ +E + VD+ + +
Sbjct: 217 A------SRWKALDEMEKQQREQVDRNIREA 241
>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 = 101 bits (255), Expect = 1e-26
Identities = 31/155 (20%), Positives = 59/155 (38%), Gaps = 23/155 (14%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK--RSRGFGFITYSESKMVDEA 101
K+F+G + ++ L+ FEQ+G + ++ V++D +S+G F+T+ K EA
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 102 MSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQ----------------MDYFGQY 145
+ + V P ++K K ++ F +
Sbjct: 64 Q----NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 146 GTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
G IE ++ G RG AF+ F + +
Sbjct: 120 GQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 153
Score = 75.0 bits (185), Expect = 2e-16
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 5/92 (5%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
DS+ + RKLFIG + + ++ ++ F +G+I + +++ P SRG F+T++
Sbjct: 86 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFT 144
Query: 94 ESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
M A+ + + P VK
Sbjct: 145 TRAMAQTAIK----AMHQAQTMEGCSSPMVVK 172
>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 = 99.7 bits (249), Expect = 2e-26
Identities = 31/109 (28%), Positives = 51/109 (46%), Gaps = 2/109 (1%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
E + KLFIGGL+ TN+ LKA F + G I +V+++KD T +SRGF FIT+
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 99 DEAMSN-RPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDYFGQYG 146
A + + G+ ++ ++A + + + G
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110
Score = 44.6 bits (106), Expect = 3e-06
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
FG++G I V ++ ++ T RGFAFI F++
Sbjct: 26 AVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63
>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 = 97.8 bits (244), Expect = 1e-25
Identities = 19/86 (22%), Positives = 38/86 (44%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E R +F L R L+ FF G++ DV ++ D ++RS+G ++ + E +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
V A+ + G + + + +
Sbjct: 80 VPLAIGLTGQRLLGVPIIVQASQAEK 105
Score = 54.6 bits (132), Expect = 7e-10
Identities = 9/41 (21%), Positives = 22/41 (53%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
D+F G + V +++++ + +G A++EF + V +
Sbjct: 44 DFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
>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 = 99.7 bits (249), Expect = 1e-24
Identities = 18/154 (11%), Positives = 46/154 (29%), Gaps = 21/154 (13%)
Query: 37 CSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
+ L + L + +G + ++ T +S+G+GF Y +
Sbjct: 89 VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Query: 97 MVDEA---MSNRPHEIDGRVVETKRAVPREV--KVRRVTKVQI-----------ALEQMD 140
A + + R + ++ + + + AL +
Sbjct: 149 SAARAKSDLLG--KPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRA- 205
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ + + G +GFA +E++ +
Sbjct: 206 -LSAVHSPTFCQLACG-QDGQLKGFAVLEYETAE 237
Score = 79.6 bits (197), Expect = 2e-17
Identities = 23/160 (14%), Positives = 55/160 (34%), Gaps = 35/160 (21%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGF 89
+ + + + RK+ I GL + + + +K + +G F
Sbjct: 9 RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAF 61
Query: 90 ITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRR---------------VTKVQI 134
+T + + A++ + + E+ V+ +T+ Q
Sbjct: 62 VTLLNGEQAEAAIN----AFHQSRLRER-----ELSVQLQPTDALLCVANLPPSLTQQQF 112
Query: 135 ALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ +G++E +V ++ TG +G+ F E+ D
Sbjct: 113 E----ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Score = 65.4 bits (160), Expect = 2e-12
Identities = 16/115 (13%), Positives = 32/115 (27%), Gaps = 5/115 (4%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTND-DSLKAFFEQWGEIVDVVVMKDPVTKRSRG 86
++ R L + L ND D+L + + +G
Sbjct: 169 VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKG 227
Query: 87 FGFITYSESKMVDEAMS--NRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM 139
F + Y ++M +EA + + G + P + + A
Sbjct: 228 FAVLEYETAEMAEEAQQQADG-LSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281
>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 = 94.8 bits (236), Expect = 2e-24
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ P+ L + GL T + L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPR 122
EA N E+DGR + ++ +
Sbjct: 101 AKEAKERANG-MELDGRRIRVDFSITK 126
Score = 52.8 bits (127), Expect = 6e-09
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F +YG I V++V ++++ RGFAF+ F++ D
Sbjct: 65 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
>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 = 96.6 bits (241), Expect = 1e-23
Identities = 26/165 (15%), Positives = 60/165 (36%), Gaps = 20/165 (12%)
Query: 29 NKAMEDSQCS-EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
+K + ++ + L++ +++ + + + + SR F
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161
Query: 88 GFITYSESKMVDEAMS--NRPHEIDGRVVETKRAVPREVKVR-RVTKVQ----------- 133
+I + + + N +I+G + TK + P E R ++
Sbjct: 162 AYIDVTSKEDARYCVEKLNG-LKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLST 220
Query: 134 -IALEQM--DYFGQYGTIESVNMVTN-KETGAKRGFAFIEFDDYD 174
+ E + + F +G+IE +N+ KE AF+ F++ D
Sbjct: 221 ELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKD 265
Score = 86.2 bits (214), Expect = 1e-19
Identities = 21/152 (13%), Positives = 46/152 (30%), Gaps = 15/152 (9%)
Query: 30 KAMEDSQCSEPESLRK-----LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRS 84
A S+ + R + + L N + + +F+ G I+ V V K++
Sbjct: 23 AAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKN 80
Query: 85 RGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKV----RRVTKVQIALEQMD 140
F I ++ A++ + + + + T+ I D
Sbjct: 81 FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNI----RD 136
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ + + R FA+I+
Sbjct: 137 LLQDINVVALSIRLPSLRFNTSRRFAYIDVTS 168
Score = 67.3 bits (165), Expect = 5e-13
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 2/81 (2%)
Query: 44 RKLFIGGLDYRTND-DSLKAFFEQWGEIVDVVVMKD-PVTKRSRGFGFITYSESKMVDEA 101
R++ I L D + L+ FE +G I + + + F+ + + A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 102 MSNRPHEIDGRVVETKRAVPR 122
+ + R + A +
Sbjct: 271 LQMNRSLLGNREISVSLADKK 291
Score = 41.1 bits (97), Expect = 2e-04
Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 9/57 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
YF G I V++ FA IEF YD + +V+
Sbjct: 60 KYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALA-------AITKTHKVVGQ 107
>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 = 91.1 bits (227), Expect = 2e-23
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 1/86 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 104 N-RPHEIDGRVVETKRAVPREVKVRR 128
N E+ GR + A P +K
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIKESG 98
Score = 52.6 bits (127), Expect = 3e-09
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I + + + ET RGFAF+EF+
Sbjct: 31 AAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
>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 = 90.7 bits (226), Expect = 3e-23
Identities = 26/91 (28%), Positives = 48/91 (52%), Gaps = 1/91 (1%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
+ + + L + L YRT+ DSL+ FE++G + DV + ++P TK RGF F+ + + +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 99 DEAMSNRP-HEIDGRVVETKRAVPREVKVRR 128
+A + E+DGR + + A +
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYGRRDLSG 99
Score = 53.8 bits (130), Expect = 1e-09
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YG + V + T A RGFAF+ F D
Sbjct: 32 RVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 90.6 bits (225), Expect = 1e-22
Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 3/87 (3%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
+ E + L + L YRT+ D+L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 99 DEAMS--NRPHEIDGRVVETKRAVPRE 123
++AM + +DGR + + A
Sbjct: 103 EDAMDAMDG-AVLDGRELRVQMARYGR 128
Score = 53.2 bits (128), Expect = 3e-09
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YG + V + ++ T RGFAF+ F D
Sbjct: 66 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 88.8 bits (221), Expect = 1e-22
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ P+ L + GL T + L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 98 VDEAMS--NRPHEIDGRVV 114
EA N E+DGR +
Sbjct: 70 AKEAKERANG-MELDGRRI 87
Score = 51.0 bits (123), Expect = 1e-08
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F +YG I V++V ++++ RGFAF+ F++ D
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 88.9 bits (221), Expect = 1e-22
Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 5/91 (5%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S LR +F+ G + L +F +G + VV+ KD F + +
Sbjct: 3 SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGA 57
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPREVKVRR 128
+ +S H + G + + +E +
Sbjct: 58 REAVLSQSQHSLGGHRLRVRPREQKEFQSPA 88
Score = 49.6 bits (119), Expect = 3e-08
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YF +G + SV V +K+ G FA +E D + ++
Sbjct: 27 EYFLAFGPVASV--VMDKDKG---VFAIVEMGDVGAREAVLSQS 65
>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 = 89.3 bits (222), Expect = 1e-22
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
S + KLFIG + ++ LK FE++G+I ++ V+KD T +G F+TY E
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 95 SKMVDEAMSN----RPHEIDGRVVETKRAVPRE 123
+ +A S + R ++ K A
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSES 97
Score = 48.1 bits (115), Expect = 1e-07
Identities = 9/39 (23%), Positives = 21/39 (53%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F ++G I + ++ ++ TG +G AF+ + + + K
Sbjct: 32 PLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70
>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 = 90.7 bits (225), Expect = 2e-22
Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ E + L + L YRT+ D+L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPRE 123
++AM + +DGR + + A
Sbjct: 125 AEDAMDAMDG-AVLDGRELRVQMARYGR 151
Score = 54.5 bits (131), Expect = 3e-09
Identities = 20/114 (17%), Positives = 35/114 (30%), Gaps = 26/114 (22%)
Query: 85 RGFGFITYSESKMVDEA-------MSNRPHEIDGR-VVETKRAVPREVKVRRVTKVQIAL 136
G + ++ VD A + +DG + + + +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 137 EQM------------------DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
E M F +YG + V + ++ T RGFAF+ F D
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 89.1 bits (221), Expect = 4e-22
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++
Sbjct: 58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 117
Query: 98 VDEAMSN-RPHEIDGRVVETKRA 119
A+ N E+ GR + A
Sbjct: 118 AAAAIDNMNESELFGRTIRVNLA 140
Score = 50.9 bits (122), Expect = 3e-08
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I + + + ET RGFAF+EF+
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114
>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 = 87.2 bits (217), Expect = 4e-22
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+G L+ +D++L+ F+ + + VM D T SRG+GF++++ AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 105 -RPHEIDGRVVETKRAVPRE 123
+ +++GR + A E
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
Score = 42.9 bits (102), Expect = 6e-06
Identities = 8/33 (24%), Positives = 19/33 (57%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F + + S +++ + +TG+ RG+ F+ F
Sbjct: 20 NAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 52
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 88.8 bits (220), Expect = 7e-22
Identities = 14/101 (13%), Positives = 39/101 (38%), Gaps = 3/101 (2%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFG 88
A+ + +++G + T D L G ++V++ ++ +S+G+
Sbjct: 43 AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102
Query: 89 FITYSESKMVDEAMSNRP-HEIDGRVVETKRAVPREVKVRR 128
+ + V + + P ++G V+ + A + +
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFE 143
Score = 45.7 bits (108), Expect = 2e-06
Identities = 7/41 (17%), Positives = 14/41 (34%), Gaps = 2/41 (4%)
Query: 140 DYFGQYGTIE--SVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
G + + N+ G +G+A + + V K
Sbjct: 74 QVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
>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 = 87.0 bits (216), Expect = 1e-21
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+ Q + + +F+G L + +KA F +G I D V+KD T +S+G+GF+
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 91 TYSESKMVDEAMSN-RPHEIDGRVVETKRAVPRE 123
++ + A+ + GR + T A +
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 96
Score = 43.9 bits (104), Expect = 6e-06
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +G I +V + TG +G+ F+ F +
Sbjct: 34 AAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 68
>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 = 85.7 bits (213), Expect = 2e-21
Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L++G L + +D L+ FE +G+I ++V+MKD T RS+G+GFIT+S+S+ A+
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 105 -RPHEIDGRVVETKRAVPRE 123
E+ GR + R
Sbjct: 67 LNGFELAGRPMRVGHVTERL 86
Score = 52.2 bits (126), Expect = 4e-09
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +G I+++ ++ + +TG +G+ FI F D +
Sbjct: 24 GIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 85.8 bits (213), Expect = 2e-21
Identities = 16/83 (19%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYS---ESKMV 98
+ + + T DS+ + + ++ ++KD T+++RGF F+ S ++ +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 99 DEAMSNR--PHEIDGRVVETKRA 119
+ + + P +IDG+ + A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
Score = 45.4 bits (108), Expect = 9e-07
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 139 MDYFGQYGT--IESVNMVTNKETGAKRGFAFIEFDDYD 174
M Y + + ++ ++ +K+T RGFAF++
Sbjct: 27 MTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
>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 = 86.2 bits (214), Expect = 2e-21
Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 1/94 (1%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
AM ++ +L++G L + +D L+ FE +G I + +M D T RS+G+GFI
Sbjct: 14 AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73
Query: 91 TYSESKMVDEAMSN-RPHEIDGRVVETKRAVPRE 123
T+S+S+ +A+ E+ GR ++ R
Sbjct: 74 TFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
Score = 50.0 bits (120), Expect = 3e-08
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G IES+ ++ + ETG +G+ FI F D
Sbjct: 45 GIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 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 = 89.0 bits (220), Expect = 3e-21
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 3/87 (3%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L+IG L + T D+ L G +I+++ ++ +S+GF + + M
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 103 SNRP-HEIDGRVVETKRAVPREVKVRR 128
P E+ G+ + +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFE 156
Score = 47.0 bits (111), Expect = 2e-06
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 140 DYFGQYGTIE--SVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ G + + N+ G +GFA + K
Sbjct: 87 EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127
>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 = 85.4 bits (212), Expect = 4e-21
Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ ++L + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ S
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSAD 67
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPRE 123
D A ++GR +E A R
Sbjct: 68 ADRAREKLHGTVVEGRKIEVNNATARV 94
Score = 44.6 bits (106), Expect = 2e-06
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
FGQ+G I V ++ N+ +GF F+ F++ D+
Sbjct: 34 QMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADR 70
>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 = 85.0 bits (211), Expect = 4e-21
Identities = 17/86 (19%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS- 103
+LF+ L Y ++++ L+ F +G + ++ D +TK+ +GF F+T+ + +A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 104 -NRPHEIDGRVVETKRAVPREVKVRR 128
+ GR++ + ++ +
Sbjct: 70 VDG-QVFQGRMLHVLPSTIKKEASQS 94
Score = 52.6 bits (127), Expect = 3e-09
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F YG + ++ + T +GFAF+ F
Sbjct: 27 KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59
>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 = 84.5 bits (210), Expect = 5e-21
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 104 N-RPHEIDGRVV 114
N E+ GR +
Sbjct: 68 NMNESELFGRTI 79
Score = 50.6 bits (122), Expect = 9e-09
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I + + + ET RGFAF+EF+
Sbjct: 26 AAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58
>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 = 84.6 bits (210), Expect = 6e-21
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S +++ L + ++ L F ++G++V V +MKD T++S+G FI + +
Sbjct: 11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 98 VDEAMSN-RPHEIDGRVVETKRAV 120
++ GRV++ A+
Sbjct: 71 AQNCTRAINNKQLFGRVIKASIAI 94
Score = 53.0 bits (128), Expect = 2e-09
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F +YG + V ++ +K+T +G AFI F D D
Sbjct: 35 RIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
>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 = 84.2 bits (209), Expect = 8e-21
Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 1/92 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ SLR +F+G + Y ++ LK F + G +V ++ D T + +G+GF Y + +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPREVKVRR 128
AM N E GR + A + K
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNKEEL 94
Score = 54.2 bits (131), Expect = 1e-09
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
D F + G + S +V ++ETG +G+ F E+ D + +
Sbjct: 27 DIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
>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 = 83.8 bits (208), Expect = 1e-20
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
SE +++GGLD + ++ L F Q G +V+ + KD VT + +G+GF+ + +
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPREVKVRR 128
D A+ ++ G+ + +A +
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 49.6 bits (119), Expect = 4e-08
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F Q G + + +M ++ TG +G+ F+EF
Sbjct: 34 ELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66
>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 = 83.8 bits (208), Expect = 1e-20
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 3/88 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + + L T + L+ F +G I + + KD T +S+GF FI++ +
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPRE 123
A++ + D ++ + A P
Sbjct: 70 AARAIAGVSG-FGYDHLILNVEWAKPST 96
Score = 52.2 bits (126), Expect = 4e-09
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F +G+I + + +K TG +GFAFI F +
Sbjct: 34 ELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
>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 = 83.1 bits (206), Expect = 2e-20
Identities = 16/83 (19%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G + Y ++ + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 104 N-RPHEIDGRVVETKRAVPREVK 125
N +++ R ++ + ++
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDIS 85
Score = 54.5 bits (132), Expect = 5e-10
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D G + ++ M+ + +TG +G+AFIEF D +
Sbjct: 21 DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55
>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 = 82.7 bits (205), Expect = 3e-20
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 4/92 (4%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + + LF+ GL T +++LK F V ++ D T S+GFGF+ ++ +
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPREVKVRR 128
A EIDG V A P+
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSG 98
Score = 41.1 bits (97), Expect = 4e-05
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F +VT++ETG+ +GF F++F+ +
Sbjct: 34 ESFDGSV---RARIVTDRETGSSKGFGFVDFNSEE 65
>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 = 82.3 bits (204), Expect = 4e-20
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+ + SE + LFIG L+ + LK + D+ V+ T +R FG++ +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDF 65
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
++ +++A+ ++ G ++ ++ R+
Sbjct: 66 ESAEDLEKALELTGLKVFGNEIKLEKPKGRD 96
Score = 43.8 bits (104), Expect = 4e-06
Identities = 7/39 (17%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ + V + TG R F +++F+ + ++K
Sbjct: 36 VAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEK 73
>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 = 81.8 bits (203), Expect = 4e-20
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+F+G L ++ A F +G I D V+KD T +S+G+GF+++ + A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 105 -RPHEIDGRVVETKRAVPR 122
+ GR + T A +
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 40.6 bits (96), Expect = 4e-05
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I +V + TG +G+ F+ F +
Sbjct: 27 FAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
>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 = 83.7 bits (208), Expect = 6e-20
Identities = 31/149 (20%), Positives = 63/149 (42%), Gaps = 19/149 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++G LD +D LK +F+ G I ++ +M D ++ + F+ Y +S + A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 104 --NRPHEIDGRVVETKRAVPREVKVRRVTKVQI------------ALEQMDYFGQYGTIE 149
N +I+ +V+ A + + + L F + +
Sbjct: 60 TLNG-KQIENNIVKINWAFQSQ-QSSSDDTFNLFVGDLNVNVDDETLRNA--FKDFPSYL 115
Query: 150 SVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
S +++ + +TG+ RG+ F+ F D
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Score = 67.2 bits (165), Expect = 8e-14
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
IN A + Q S + LF+G L+ +D++L+ F+ + + VM D T SRG+
Sbjct: 73 INWAFQSQQ-SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY 131
Query: 88 GFITYSESKMVDEAMSN-RPHEIDGRVVETKRA 119
GF++++ AM + + +++GR + A
Sbjct: 132 GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 82.9 bits (205), Expect = 9e-20
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
EP+ LR L + + ++ L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPRE 123
+A++ N I + ++ A
Sbjct: 97 AQQAIAGLNG-FNILNKRLKVALAASGH 123
Score = 49.4 bits (118), Expect = 1e-07
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
L Q+ F +YG IESV +V ++ET RG+ F++F
Sbjct: 59 LRQL--FERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
>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 = 80.6 bits (200), Expect = 1e-19
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 5/85 (5%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
L+I GL T D L + +G+IV + D T + +G+GF+ +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 100 EAMS--NRPHEIDGRVVETKRAVPR 122
+A++ + ++ K++ P
Sbjct: 62 KAVTALKA-SGVQAQMA--KQSGPS 83
Score = 49.4 bits (119), Expect = 3e-08
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ YG I S + +K T +G+ F++FD
Sbjct: 23 VKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58
>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 = 81.6 bits (202), Expect = 1e-19
Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 1/85 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+ G+ ++ + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 105 -RPHEIDGRVVETKRAVPREVKVRR 128
++ G+ + R +
Sbjct: 84 LNGQDLMGQPISVDWCFVRGPPKGK 108
Score = 55.5 bits (134), Expect = 6e-10
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D F +YG I+++++ ++ TG +G+ +E++ Y
Sbjct: 40 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
>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 = 80.8 bits (200), Expect = 2e-19
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK---RSRGFGFITYSESKMVDEA 101
LFI L++ T +++LK F + G I + K S GFGF+ Y + + +A
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 102 MSN-RPHEIDGRVVETKRAVPRE 123
+ + H +DG +E + +
Sbjct: 67 LKQLQGHTVDGHKLEVRISERAT 89
Score = 42.2 bits (100), Expect = 1e-05
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 140 DYFGQYGTIESVNMVTNKETGAK---RGFAFIEFDD 172
F + G I+S + K GF F+E+
Sbjct: 24 GVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
>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 = 80.3 bits (199), Expect = 2e-19
Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 3/87 (3%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L+IG L + T D+ L G +I+++ ++ +S+GF + + M
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 103 SNRP-HEIDGRVVETKRAVPREVKVRR 128
P E+ G+ + E
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHHHHH 89
Score = 44.9 bits (107), Expect = 1e-06
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 140 DYFGQYGTIE--SVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ G + + N+ G +GFA + K
Sbjct: 20 EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
>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 = 79.5 bits (197), Expect = 3e-19
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+R +++G L Y + +K F Q+G++ +V ++ D TK+ +GFGF+ E + EA+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAI 59
Query: 103 SN-RPHEIDGRVVETKRAVPREVKVRR 128
+ + GR + A P++
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSLEHH 86
Score = 51.0 bits (123), Expect = 9e-09
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F Q+G + +V ++ ++ET +GF F+E +
Sbjct: 20 ELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 80.1 bits (198), Expect = 4e-19
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
++L + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ S
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSAD 81
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPR 122
D A ++GR +E A R
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 43.8 bits (104), Expect = 4e-06
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
FGQ+G I V ++ N+ +GF F+ F++ D+
Sbjct: 48 QMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADR 84
>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 = 79.1 bits (196), Expect = 5e-19
Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV-TKRSRGFGFITYSESKMVDEAMS 103
K+ IG L D + F +G+I + + + + S+G+ ++ + ++A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 104 NRP-HEIDGRVVETKRAVPRE 123
+ +IDG+ + +
Sbjct: 66 HMDGGQIDGQEITATAVLAPW 86
Score = 48.3 bits (116), Expect = 8e-08
Identities = 10/35 (28%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 139 MDYFGQYGTIESVNMVTNK-ETGAKRGFAFIEFDD 172
M+ F YG I+ ++M + +G+A++EF++
Sbjct: 22 MEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFEN 56
>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 = 79.1 bits (196), Expect = 6e-19
Identities = 17/80 (21%), Positives = 37/80 (46%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G +DY + L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 104 NRPHEIDGRVVETKRAVPRE 123
GR ++
Sbjct: 67 LDESLFRGRQIKVIPKRTNR 86
Score = 57.5 bits (140), Expect = 4e-11
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+F G++ V ++ +K +G +GFA+IEF D + V +
Sbjct: 25 AHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>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 = 79.7 bits (197), Expect = 6e-19
Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 3/94 (3%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDP-VTKRSRGFGFIT 91
Q + ++ K+ + + ++ N ++ F +GE+ V + K T RGFGF+
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 92 YSESKMVDEAMSNRPH--EIDGRVVETKRAVPRE 123
+ + +A + H + GR + + A
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV 98
Score = 47.7 bits (114), Expect = 2e-07
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 140 DYFGQYGTIESVNMVTNKE-TGAKRGFAFIEFDDYD 174
+ F +G +++V + TGA RGF F++F
Sbjct: 34 ELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 79.7 bits (197), Expect = 6e-19
Identities = 13/90 (14%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
L+++ L+ + LK ++GE+ +V ++ P T++ G + ++ ++
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 100 EAMSN-RPHEIDGRVVETKRAVPREVKVRR 128
E + N + G ++ + + + +++
Sbjct: 63 ETVKNLHLTSVMGNIIHAQLDIKGQQRMKY 92
Score = 49.7 bits (119), Expect = 4e-08
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D +YG +E V ++ + T G A + F
Sbjct: 25 DMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTR 59
>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 = 78.9 bits (195), Expect = 7e-19
Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + L + L Y +++L+ FE+ + + +S+G+ FI ++ +
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFED 65
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPREVKVRR 128
EA+++ EI+GR + + PR
Sbjct: 66 AKEALNSCNKREIEGRAIRLELQGPRGSPNSG 97
Score = 42.7 bits (101), Expect = 1e-05
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F + I+ V + G +G+AFIEF ++
Sbjct: 34 EVFEKATFIK----VPQNQNGKSKGYAFIEFASFE 64
>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 = 82.3 bits (204), Expect = 7e-19
Identities = 30/154 (19%), Positives = 62/154 (40%), Gaps = 18/154 (11%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + L++G L + L F G I+ + V +D +T+RS G+ ++ + +
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPREVKVRRVTKVQI------------ALEQMDYFGQ 144
+ A+ I G+ V + R+ +R+ I AL F
Sbjct: 70 AERALDTMNFDVIKGKPVRIMWS-QRDPSLRKSGVGNIFIKNLDKSIDNKALYDT--FSA 126
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+G I S +V + +G+ F+ F+ + ++
Sbjct: 127 FGNILSCKVVC--DENGSKGYGFVHFETQEAAER 158
Score = 66.9 bits (164), Expect = 2e-13
Identities = 26/127 (20%), Positives = 50/127 (39%), Gaps = 7/127 (5%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
I + D + +FI LD ++ +L F +G I+ V+ D S+G+
Sbjct: 89 IMWSQRDPS-LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGY 145
Query: 88 GFITYSESKMVDEAMSN-RPHEIDGRVVETKRAVPREVKVRRV--TKVQIALEQM-DYFG 143
GF+ + + + A+ ++ R V R R+ + + + + DY G
Sbjct: 146 GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAG 205
Query: 144 QYGTIES 150
G I +
Sbjct: 206 SSGRIVT 212
>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 = 79.8 bits (197), Expect = 8e-19
Identities = 18/91 (19%), Positives = 40/91 (43%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
++ + R +++G +DY + L+A F G I + ++ D + +G+ +I +
Sbjct: 26 LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+E VD A++ GR ++
Sbjct: 86 AERNSVDAAVAMDETVFRGRTIKVLPKRTNM 116
Score = 57.8 bits (140), Expect = 6e-11
Identities = 13/41 (31%), Positives = 25/41 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+F G+I + ++ +K +G +G+A+IEF + + VD V
Sbjct: 55 AHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 78.9 bits (195), Expect = 1e-18
Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 2/87 (2%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S KLFI GL + + L+ + G + D+ ++ + + +G ++ Y
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPRE 123
+A+ I +++ +
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAISNSGP 97
Score = 47.3 bits (113), Expect = 2e-07
Identities = 9/33 (27%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ +GT++ + +VTN+ G +G A++E+++
Sbjct: 36 EICKAHGTVKDLRLVTNR-AGKPKGLAYVEYEN 67
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 78.9 bits (194), Expect = 1e-18
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 4/94 (4%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKD--PVTKRSRGFGFITYSES 95
S RK+F+GGL ++D + A F ++G +V K +G+ F+ + E
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 96 KMVDEAMSNRPHEIDGRV--VETKRAVPREVKVR 127
V + E V + + V++R
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIR 96
Score = 37.3 bits (86), Expect = 9e-04
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 140 DYFGQYGTIESVNMV--TNKETGAKRGFAFIEFDDYDVVDKIV 180
F ++G + +K +G+AF+ F + V ++
Sbjct: 27 ASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 78.5 bits (194), Expect = 2e-18
Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 1/79 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+ G+ ++ + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 105 -RPHEIDGRVVETKRAVPR 122
++ G+ + R
Sbjct: 85 LNGQDLMGQPISVDWCFVR 103
Score = 55.3 bits (134), Expect = 4e-10
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D F +YG I+++++ ++ TG +G+ +E++ Y
Sbjct: 41 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 77.7 bits (192), Expect = 2e-18
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + KL+IG L D L+ F + V+ G+ F+ Y +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNW 56
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPRE 123
A+ + E+ G+++E +V ++
Sbjct: 57 AIRAIETLSGKVELHGKIMEVDYSVSKK 84
Score = 38.0 bits (89), Expect = 4e-04
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
FG + + K G+AF+++ D + +
Sbjct: 27 QLFGDRKLPLAG------QVLLKSGYAFVDYPDQNWAIR 59
>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 = 79.5 bits (196), Expect = 2e-18
Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 2/92 (2%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
E+ + +S L++G L + T ++ + F + G+I +++ D + K + GF F+ Y
Sbjct: 30 EEQEKLLKKS-CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 93 SESKMVDEAMSNRP-HEIDGRVVETKRAVPRE 123
+ AM +D R++ T +
Sbjct: 89 YSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120
Score = 49.8 bits (119), Expect = 8e-08
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F + G I+ + M +K GF F+E+
Sbjct: 58 ELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 92
>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 = 76.6 bits (189), Expect = 6e-18
Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
+ S+ RKLF+G L+ + +++ + F+ +G I + V++ P S+G
Sbjct: 2 SSGSSGSESRGGRD-RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59
Query: 89 FITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
F+ +S A+ + G + VK
Sbjct: 60 FVKFSSHTEAQAAIH----ALHGSQTMPGASSSLVVK 92
Score = 40.7 bits (96), Expect = 4e-05
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ ++ F +G I+ ++ G+ +G AF++F
Sbjct: 32 VLRL--FQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65
>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 = 75.4 bits (186), Expect = 2e-17
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 4/95 (4%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+ LDY+ LK F G +V +++D +SRG G +T+
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTF 63
Query: 93 SESKMVDEAMS--NRPHEIDGRVVETKRAVPREVK 125
+S +A+S N + R + K K
Sbjct: 64 EQSIEAVQAISMFNG-QLLFDRPMHVKMDERALPK 97
Score = 36.5 bits (85), Expect = 0.002
Identities = 7/33 (21%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F G + +++ +K+ G RG + F+
Sbjct: 34 EVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQ 65
>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 = 74.9 bits (185), Expect = 2e-17
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDV-VVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 104 N-RPHEIDGRVVETKRAVPREVK 125
+ R + A ++ K
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
Score = 38.3 bits (90), Expect = 3e-04
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 140 DYFGQYGTIESV-NMVTNKETGAKRGFAFIEFDDYD 174
D F +G I ++ + +TG +G+AFI F +D
Sbjct: 24 DTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD 59
>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 = 74.6 bits (184), Expect = 3e-17
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
++ E+ R +F+G L+ R ++ L F Q G + V + KD + + FGF+ + +
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPES 69
Query: 98 VDEAMSN-RPHEIDGR 112
V A++ + GR
Sbjct: 70 VSYAIALLNGIRLYGR 85
Score = 43.0 bits (102), Expect = 6e-06
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ F Q G + V + ++E G + F F+ F + V
Sbjct: 35 ELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72
>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 = 75.0 bits (185), Expect = 3e-17
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 1/80 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+ + +D ++ F +GEI ++ + D T S+G+ + Y K A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 105 -RPHEIDGRVVETKRAVPRE 123
EI G+ ++ +
Sbjct: 88 LNGAEIMGQTIQVDWCFVKG 107
Score = 55.4 bits (134), Expect = 3e-10
Identities = 9/36 (25%), Positives = 23/36 (63%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F YG I+++++ ++ TG +G+A +E++ +
Sbjct: 44 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
>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 = 74.2 bits (183), Expect = 3e-17
Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 7/97 (7%)
Query: 29 NKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
+ +ED S+ + R L L + +D LK FE E + +S+G
Sbjct: 1 SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGI 55
Query: 88 GFITYSESKMVDEAMSNRP-HEIDGRVVETKRAVPRE 123
+I + ++ + + EIDGR V +
Sbjct: 56 AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 92
Score = 39.6 bits (93), Expect = 1e-04
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 5/39 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ F I V+ + G +G A+IEF +K
Sbjct: 35 EVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEK 68
>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 = 76.4 bits (188), Expect = 4e-17
Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 1/85 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+ + +D ++ F +GEI ++ + D T S+G+ + Y K A
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 105 -RPHEIDGRVVETKRAVPREVKVRR 128
EI G+ ++ + K +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVK 158
Score = 54.8 bits (132), Expect = 2e-09
Identities = 9/35 (25%), Positives = 23/35 (65%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F YG I+++++ ++ TG +G+A +E++ +
Sbjct: 91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
>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 = 74.2 bits (183), Expect = 5e-17
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS- 103
L++ LD +D+ L+ F +G I VM + RS+GFGF+ +S + +A++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 104 -NRPHEIDGRVVETKRAVPREVK 125
N + + + A +E +
Sbjct: 75 MNG-RIVATKPLYVALAQRKEER 96
Score = 38.0 bits (89), Expect = 4e-04
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F +GTI S ++ E G +GF F+ F + K
Sbjct: 34 KAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATK 70
>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 = 74.3 bits (183), Expect = 6e-17
Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 9/86 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LFI L D L F +G +V V D T S+ FGF++Y A+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ- 85
Query: 105 RPHEIDGRVVETKR-----AVPREVK 125
++G + KR +
Sbjct: 86 ---SMNGFQIGMKRLKVQLKRSKNDS 108
Score = 48.1 bits (115), Expect = 2e-07
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
L QM F +G + S + +K+T + F F+ +D+
Sbjct: 42 LLQM--FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 73.9 bits (182), Expect = 8e-17
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LFI L D L + F +G ++ V D T S+ FGF+++ A+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK- 100
Query: 105 RPHEIDGRVVETKR 118
++G V TKR
Sbjct: 101 ---AMNGFQVGTKR 111
Score = 47.7 bits (114), Expect = 3e-07
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
L F +G + S + +K+T + F F+ FD+ D
Sbjct: 57 LAST--FLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
>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 = 73.6 bits (181), Expect = 1e-16
Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 2/92 (2%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E+ KL + LD+ +D ++ F ++G + V D + RS G + +
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 88
Query: 98 VDEAMSN-RPHEIDGRVVETKRAVPREVKVRR 128
+AM + +DGR ++ + +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 120
Score = 36.2 bits (84), Expect = 0.003
Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F ++GT++ + + +G G A + F+
Sbjct: 54 ELFAEFGTLKKAAVDYD-RSGRSLGTADVHFER 85
>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 = 73.1 bits (180), Expect = 2e-16
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 5/86 (5%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P +FI LD ++ +L F +G I+ V+ D S+G+GF+ + + +
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 59
Query: 100 EAMS--NRPHEIDGRVVETKRAVPRE 123
A+ N ++ R V R R+
Sbjct: 60 RAIEKMNG-MLLNDRKVFVGRFKSRK 84
Score = 36.8 bits (86), Expect = 0.001
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D F +G I S +V + +G+ F+ F+ + ++
Sbjct: 24 DTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 72.2 bits (178), Expect = 2e-16
Identities = 14/88 (15%), Positives = 35/88 (39%), Gaps = 5/88 (5%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S ++F+ L + LK F + G ++ + + +S+G G + + ++
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEV 60
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPRE 123
+ A N ++ GR ++ +
Sbjct: 61 AERACRMMNG-MKLSGREIDVRIDRNAS 87
Score = 37.2 bits (87), Expect = 8e-04
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
D F + G + ++ E G +G ++F+
Sbjct: 27 DKFNECGHVLYADIKM--ENGKSKGCGVVKFES 57
>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 = 72.3 bits (178), Expect = 3e-16
Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+ L++ L R + L + F ++ E + +T R RG FIT+ ++ +A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 104 --NRPHEIDGRVVETKRAVPRE 123
N +++ G+++ + ++
Sbjct: 86 LVNG-YKLYGKILVIEFGKNKK 106
Score = 45.7 bits (109), Expect = 1e-06
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F ++ + + TG RG AFI F + +
Sbjct: 43 VSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE 78
>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 = 71.9 bits (177), Expect = 4e-16
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS---ESKMVDEA 101
L+I L ++ L+ + +G+++ +++D + SRG GF + + V
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH 85
Query: 102 MSNRPHEIDGRVVETKRAVPREVK 125
+ + I + P K
Sbjct: 86 FNGK--FIKTPPGVSAPTEPLLCK 107
Score = 41.1 bits (97), Expect = 4e-05
Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
LE M +G + S ++ + +G RG F + + + ++
Sbjct: 42 LENM--LKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
>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 = 71.5 bits (176), Expect = 4e-16
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 7/85 (8%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+G L ++ ++ FE++G+ +V + KD +GFGFI + + A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 105 RP-HEIDGRVVETKRAVPREVKVRR 128
+ G+ + + A
Sbjct: 71 LDNMPLRGKQLRVRFACHSASLTSG 95
Score = 37.6 bits (88), Expect = 5e-04
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 6/35 (17%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +YG V + +K GF FI +
Sbjct: 34 KLFEKYGKAGEVFIHKDK------GFGFIRLETRT 62
>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 = 70.6 bits (173), Expect = 1e-15
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 5/85 (5%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIV-DVVVMKDPV-TKRSRGFGFITYSESKMVDEA 101
+LFIGG+ + + + E V DV+V ++RGF F+ Y + A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 102 ---MSNRPHEIDGRVVETKRAVPRE 123
+ ++ G + A P
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEI 93
Score = 33.6 bits (77), Expect = 0.020
Identities = 8/50 (16%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 127 RRVTKVQIALEQMDYFGQYGT-IESVNMVTN-KETGAKRGFAFIEFDDYD 174
+ + +I ++ + + V + + + RGFAF+E++ +
Sbjct: 18 KMKKREEI----LEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 70.0 bits (172), Expect = 2e-15
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++G L + T + A F+ I V +++D T + +GF ++ + E + EA++
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 104 NRPHEIDGRVVETKRAVPRE 123
+ R + A R+
Sbjct: 75 YDGALLGDRSLRVDIAEGRK 94
Score = 48.4 bits (116), Expect = 1e-07
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F I SV +V +K+T +GF ++EFD+ D + + +
Sbjct: 34 AIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 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 = 70.0 bits (172), Expect = 2e-15
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ E+ KL + LD+ +D ++ F ++G + V D + RS G + +
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKAD 82
Query: 98 VDEAMS---NRPHEIDGR 112
+AM +DGR
Sbjct: 83 ALKAMKQYNGV--PLDGR 98
Score = 36.5 bits (85), Expect = 0.002
Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F ++GT++ + + +G G A + F+
Sbjct: 48 ELFAEFGTLKKAAVHYD-RSGRSLGTADVHFER 79
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 70.1 bits (172), Expect = 2e-15
Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 9/89 (10%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEI--------VDVVVMKDPVTKRSRGFGFITYSES 95
+F+ GL +S+ +F+Q G I + + D T + +G +++ +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 96 KMVDEAMSN-RPHEIDGRVVETKRAVPRE 123
A+ E G ++ A R
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
Score = 46.2 bits (110), Expect = 6e-07
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 140 DYFGQYGTIES--------VNMVTNKETGAKRGFAFIEFDDYDVVDK 178
DYF Q G I++ +N+ T++ETG +G A + FDD
Sbjct: 26 DYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKA 72
>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 = 74.9 bits (183), Expect = 3e-15
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+ LF+ ++Y T + L+ FE +G I + ++ + + RG+ FI Y + + A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 104 NRPH-EIDGRVVETKRAVPREVK 125
+ +IDGR V R VK
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVK 185
Score = 52.2 bits (124), Expect = 7e-08
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD-------YDVVDKIVLDKVVVLEVDQEVI 194
F YG I+ ++MV +K +G RG+AFIE++ Y D +D VL +
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
Query: 195 NGEDHRTHGTHQE 207
+ R
Sbjct: 183 TVKGWRPRRLGGG 195
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 69.6 bits (170), Expect = 3e-15
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 13/93 (13%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQW-----GEIVDVVVMKDPVTKRSRGFGFITY 92
S + + GL D+ L +FE G ++ +R G +T+
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTF 54
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
E + ++ HE+ G + + A PR
Sbjct: 55 REPADAERVLAQADHELHGAQLSLRPAPPRAPA 87
Score = 30.3 bits (68), Expect = 0.20
Identities = 4/35 (11%), Positives = 10/35 (28%), Gaps = 7/35 (20%)
Query: 162 KRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+ F + ++ VL ++G
Sbjct: 46 LGCGGVLTFREPADAER-------VLAQADHELHG 73
>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 = 68.8 bits (169), Expect = 3e-15
Identities = 13/87 (14%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ K+F+G + L++ FE+ G +++ V+K + F+ +
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEAD 55
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPRE 123
A++ E+ G+ + + + +
Sbjct: 56 AKAAIAQLNGKEVKGKRINVELSTKGQ 82
Score = 38.0 bits (89), Expect = 4e-04
Identities = 4/35 (11%), Positives = 12/35 (34%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F + G + ++ + +AF+ +
Sbjct: 28 SLFERRGRVIECDV--------VKDYAFVHMEKEA 54
>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 = 68.8 bits (169), Expect = 4e-15
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 11/93 (11%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
S S ++ LF+ L ++ L+ F Q+G++ V +KD + FI + E
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDE 54
Query: 95 SKMVDEAMS--NRPHEIDGRVVETKRAVPREVK 125
+AM N +++G +E A P + K
Sbjct: 55 RDGAVKAMEEMNG-KDLEGENIEIVFAKPPDQK 86
Score = 36.1 bits (84), Expect = 0.002
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F Q+G +E V + + +AFI FD+ D
Sbjct: 30 KAFSQFGKLERVKKL--------KDYAFIHFDERD 56
>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 = 68.4 bits (168), Expect = 6e-15
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVT-KRSRGFGFITYSESKMVDEAM 102
F+G L Y ++S+K FF I V + ++P +R +GFG+ + + + A+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
Query: 103 SNRPHEIDGRVVETKRAVPRE 123
S + R + A +
Sbjct: 79 SLNEESLGNRRIRVDVADQAQ 99
Score = 42.2 bits (100), Expect = 1e-05
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 9/58 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAK-RGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
++F I +V + + +GF + EF+D D + L +++E +
Sbjct: 38 EFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-------LSLNEESLGN 87
>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 = 68.4 bits (168), Expect = 7e-15
Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV-TKRSRGFGFITYSESKMVDEAM 102
F+G L Y ++S+K FF I V + ++P +R +GFG+ + + + A+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 103 SNRPHEIDGRVVETKRAVPRE 123
S + + + A +
Sbjct: 75 SLNEESLGNKRIRVDVADQAQ 95
Score = 42.2 bits (100), Expect = 2e-05
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 9/58 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAK-RGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
++F I +V + + +GF + EF+D D + L +++E +
Sbjct: 34 EFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-------LSLNEESLGN 83
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 70.3 bits (172), Expect = 7e-15
Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 4/93 (4%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E+ KL + LD+ +D ++ F ++G + V D + RS G + +
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 141
Query: 98 VDEAMS--NRPHEIDGRVVETKRAVPREVKVRR 128
+AM +DGR ++ + +
Sbjct: 142 ALKAMKQYKG-VPLDGRPMDIQLVASQIDLEHH 173
Score = 39.1 bits (91), Expect = 7e-04
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F ++GT++ + + +G G A + F+
Sbjct: 106 QELFAEFGTLKKAAVDYD-RSGRSLGTADVHFER 138
>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 = 67.7 bits (166), Expect = 1e-14
Identities = 11/68 (16%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV-VMKDPVTKRSRGFGFITYSESK 96
L++G L+ +++ + F GE V V ++++ +T G+ F+ +++
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 97 MVDEAMSN 104
++ +
Sbjct: 64 TAEKCLHK 71
Score = 43.8 bits (104), Expect = 4e-06
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 140 DYFGQYG-TIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F G T+ SV ++ N+ TG G+ F+EF D +K
Sbjct: 28 RAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
>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 = 67.5 bits (165), Expect = 2e-14
Identities = 14/93 (15%), Positives = 38/93 (40%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+ + + + GL + + + + FF + + + + RS G F+ +
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
+ ++ ++A+ I R +E ++ EV+
Sbjct: 65 ASQEIAEKALKKHKERIGHRYIEIFKSSRAEVR 97
Score = 35.5 bits (82), Expect = 0.003
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
V++R +K +I + +F + + + G G AF++F ++ +K
Sbjct: 18 VRLRGLPFGCSKEEI----VQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72
>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 = 68.0 bits (166), Expect = 2e-14
Identities = 13/97 (13%), Positives = 39/97 (40%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
+ S ++ + + + GL + + + FF + + + + + G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87
Query: 89 FITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
F+ ++ ++ ++A+ I R +E ++ EV+
Sbjct: 88 FVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEVR 124
Score = 36.4 bits (84), Expect = 0.002
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 121 PREVKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVV 176
V++R TK +I + +F + + + G G AF++F ++
Sbjct: 42 DGFVRLRGLPFGCTKEEI----VQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97
Query: 177 DK 178
+K
Sbjct: 98 EK 99
>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 = 66.5 bits (163), Expect = 2e-14
Identities = 16/95 (16%), Positives = 39/95 (41%), Gaps = 9/95 (9%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
S S ++ KL +G + + L+A FE++G +++ ++ + + F+
Sbjct: 2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMER 53
Query: 95 SKMVDEAMSNR-PHEIDGRVVETKRAVPREVKVRR 128
++ EA+ E G+ + + + R
Sbjct: 54 AEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 38.8 bits (91), Expect = 2e-04
Identities = 5/35 (14%), Positives = 14/35 (40%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +YG + ++ + +AF+ + +
Sbjct: 29 AKFEEYGPVIECDI--------VKDYAFVHMERAE 55
>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 = 67.0 bits (164), Expect = 3e-14
Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 9/95 (9%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
PE R L+I L Y+ + + F ++G I + V P +RG ++ Y +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAK 61
Query: 100 EAMSNRPH-EIDGR--VVE---TKRAVPREVKVRR 128
A+ + + R VV RA + ++
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKK 96
Score = 42.0 bits (99), Expect = 3e-05
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D FG+YG I + + ET RG A++ ++D
Sbjct: 27 DIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIF 58
>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 = 66.5 bits (163), Expect = 3e-14
Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 9/95 (9%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+ S++ L++ L T+++ ++ F V K+ R + F+
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFV 56
Query: 91 TYSESKMVDEAMS--NRPHEIDGRVVETKRAVPRE 123
+S + EAM N +DG +E A P +
Sbjct: 57 HFSNREDAVEAMKALNG-KVLDGSPIEVTLAKPVD 90
Score = 31.9 bits (73), Expect = 0.051
Identities = 5/33 (15%), Positives = 8/33 (24%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F R +AF+ F +
Sbjct: 34 KEFNNIKPGAVE------RVKKIRDYAFVHFSN 60
>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 = 66.7 bits (163), Expect = 3e-14
Identities = 16/99 (16%), Positives = 35/99 (35%), Gaps = 11/99 (11%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEI--------VDVVVMKDPVTKRSRG 86
E +++ GL+ D L FF+Q G + + + D T + +G
Sbjct: 7 GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66
Query: 87 FGFITYSESKMVDEAMS--NRPHEIDGRVVETKRAVPRE 123
++Y + A+ + + G ++ A +
Sbjct: 67 DATVSYEDPPTAKAAVEWFDG-KDFQGSKLKVSLARKKP 104
Score = 46.6 bits (111), Expect = 5e-07
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 140 DYFGQYGTIES--------VNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D+F Q G ++ +++ +KETG +G A + ++D
Sbjct: 34 DFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKA 80
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 66.3 bits (162), Expect = 4e-14
Identities = 10/76 (13%), Positives = 29/76 (38%), Gaps = 1/76 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R ++I G D +K + E G+++++ + + K +G F+ + + + +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70
Query: 104 NRPHEIDGRVVETKRA 119
+ +
Sbjct: 71 TPGQKYKETDLLILFK 86
Score = 44.3 bits (105), Expect = 3e-06
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
++ G + ++ M A +G F+ FD + K V
Sbjct: 30 EWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV 69
>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 = 67.6 bits (165), Expect = 4e-14
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
K+++G L N L+ F +G + V V ++P GF F+ + + + +A+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVR 128
Query: 104 NRP-HEIDGR--VVETKRAVPR 122
+ G VE R
Sbjct: 129 ELDGRTLCGCRVRVELSNGEKR 150
Score = 40.6 bits (95), Expect = 1e-04
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG YG + SV + N GFAF+EF+D
Sbjct: 92 RAFGYYGPLRSVWVARNP-----PGFAFVEFEDPR 121
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 66.2 bits (162), Expect = 4e-14
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+++G L L+ F +G + V + ++P GF F+ + + + ++A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 105 RP-HEIDGR--VVETKRAVPREVKVRR 128
I G VE +PR + R
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDR 83
Score = 41.1 bits (97), Expect = 3e-05
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F YG + +V + N GFAF+EF+D + V
Sbjct: 19 RAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAV 54
>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 = 65.7 bits (161), Expect = 4e-14
Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + KLFIG L + +++ FEQ+G++++ ++K +GF+ +
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTA 54
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPRE 123
++A+ N +++ G + + + +
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKNKS 81
Score = 39.5 bits (93), Expect = 9e-05
Identities = 6/41 (14%), Positives = 15/41 (36%), Gaps = 8/41 (19%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F QYG + ++ + + F+ +D + +
Sbjct: 27 SLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAI 59
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++++G L ++ F ++G I D+ + F F+ + + + ++A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 79
Query: 104 NRP-HEIDGR--VVE 115
R ++ DG VE
Sbjct: 80 GRDGYDYDGYRLRVE 94
Score = 43.1 bits (102), Expect = 8e-06
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D F +YG I +++ K FAF+EF+D
Sbjct: 41 DVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPR 72
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 63.5 bits (155), Expect = 4e-13
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGF 89
+A++ S P + +IG + + + L F+ +G I+D + +G F
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCF 67
Query: 90 ITYS---ESKMVDEAMSNRPHEIDGRVV 114
I Y ++ + A++N GR +
Sbjct: 68 IKYDTHEQAAVCIVALANF--PFQGRNL 93
Score = 38.8 bits (91), Expect = 2e-04
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 6/34 (17%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F +G I K G FI++D
Sbjct: 45 IPLFQNFGFILDFKHYPEK------GCCFIKYDT 72
>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 = 64.1 bits (156), Expect = 5e-13
Identities = 12/93 (12%), Positives = 34/93 (36%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
S E+ +++ GL + + + FF++ + D + + ++ G GF+ +
Sbjct: 15 RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 74
Query: 93 SESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
A+ + R ++ + +
Sbjct: 75 RNEADYKAALCRHKQYMGNRFIQVHPITKKGML 107
Score = 37.1 bits (86), Expect = 0.001
Identities = 10/82 (12%), Positives = 22/82 (26%), Gaps = 8/82 (9%)
Query: 101 AMSNRPHEIDGRVVETKRAVPREVKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTN 156
+ P + V ++ + +D+F + +E +
Sbjct: 5 SSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHV----IDFFKKLDIVEDSIYIAY 60
Query: 157 KETGAKRGFAFIEFDDYDVVDK 178
G G F+EF +
Sbjct: 61 GPNGKATGEGFVEFRNEADYKA 82
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 63.4 bits (155), Expect = 5e-13
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFF-EQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS- 103
LF+G L +D L FF + + V+ D T S+G+GF+ +++ A++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 104 -NRPHEIDGRVVETKRAVPREVKVRRVTKVQIA 135
+ + V A+P+ +V+ V +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103
Score = 29.9 bits (68), Expect = 0.34
Identities = 9/34 (26%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 140 DYFGQ-YGTIESVNMVTNKETGAKRGFAFIEFDD 172
++F + Y + +V ++ TG +G+ F++F D
Sbjct: 28 EFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
>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 = 63.0 bits (154), Expect = 6e-13
Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 3/92 (3%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
+ R L++G L + + F Q G ++ + + + F+ + E
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYE 64
Query: 95 SKMVDEAMSN-RPHEIDGRVVETKRAVPREVK 125
+ A++ +I G+ V+ A +
Sbjct: 65 HRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 96
Score = 42.6 bits (101), Expect = 1e-05
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F Q G +S M+T + + F+EF +
Sbjct: 34 QLFSQIGPCKSCKMITEHTSN--DPYCFVEFYE 64
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 62.3 bits (152), Expect = 1e-12
Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 9/99 (9%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGF 89
+ + S +LF+ + L F +G + +V ++ GF F
Sbjct: 18 GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAF 69
Query: 90 ITYSESKMVDEAMSNRP-HEIDGRVVETKRAVPREVKVR 127
+ + E++ +A+ + +E + + R
Sbjct: 70 VEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 38.0 bits (89), Expect = 5e-04
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ FG +G ++ V + GFAF+EF++ +
Sbjct: 50 EIFGPFGPMKEVKI--------LNGFAFVEFEEAE 76
>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 = 61.1 bits (149), Expect = 2e-12
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E +++ L++GGL + L+ F Q+GEI + V++ + FI ++ +
Sbjct: 7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQA 60
Query: 98 VDEAMSNRPH--EIDGRVV 114
+ A + ++GR +
Sbjct: 61 AEVAAEKSFNKLIVNGRRL 79
Score = 37.3 bits (87), Expect = 5e-04
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
++F Q+G I ++ +V + AFI+F
Sbjct: 31 NHFYQFGEIRTITVVQRQ------QCAFIQFAT 57
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 9/90 (10%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVD--------VVVMKDPVTKRSRGFGFI 90
+F+ GL +S+ +F+Q G I + + D T + +G +
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 91 TYSESKMVDEAMSN-RPHEIDGRVVETKRA 119
++ + A+ E G ++ A
Sbjct: 69 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 46.9 bits (112), Expect = 3e-07
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 140 DYFGQYGTIES--------VNMVTNKETGAKRGFAFIEFDDYDVVDK 178
DYF Q G I++ +N+ T++ETG +G A + FDD
Sbjct: 32 DYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKA 78
>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 = 61.2 bits (149), Expect = 4e-12
Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 11/85 (12%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
ED ++ GG+ D ++ F +G+I+++ V + +G+ F+ +
Sbjct: 15 EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRF 68
Query: 93 S---ESKMVDEAMSNRPHEIDGRVV 114
S + +++ I+G VV
Sbjct: 69 STHESAAHAIVSVNGT--TIEGHVV 91
Score = 35.8 bits (83), Expect = 0.003
Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 8/38 (21%)
Query: 137 EQM--DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+Q+ F +G I + + K G++F+ F
Sbjct: 39 DQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFST 70
>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 = 60.4 bits (147), Expect = 4e-12
Identities = 12/87 (13%), Positives = 25/87 (28%), Gaps = 1/87 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + + + + + D + FF + I V +K G + +
Sbjct: 10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 98 VDEAMSNRP-HEIDGRVVETKRAVPRE 123
A+ + I R V+
Sbjct: 70 ATAAVIDLNDRPIGSRKVKLVLGSGPS 96
Score = 37.3 bits (87), Expect = 7e-04
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 121 PREVKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVV 176
P +KV+ V+ +I +D+F Y I + E G G A + F+ D
Sbjct: 15 PTIIKVQNMPFTVSIDEI----LDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70
Query: 177 DK 178
Sbjct: 71 TA 72
>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 = 60.9 bits (148), Expect = 5e-12
Identities = 7/91 (7%), Positives = 25/91 (27%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
+ + I + + + F E + V + + G + +
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN 66
Query: 95 SKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
++ +++GR +++
Sbjct: 67 EDDARKSERLHRKKLNGREAFVHVVTLEDMR 97
Score = 35.5 bits (82), Expect = 0.004
Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 17/78 (21%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIE-SVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ +TK+ + + + E +V+++ + G G A ++F + D K
Sbjct: 18 AHITNIPFSITKMDV----LQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARK 72
Query: 179 IVLDKVVVLEVDQEVING 196
+ ++ +NG
Sbjct: 73 -------SERLHRKKLNG 83
>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 = 60.9 bits (148), Expect = 6e-12
Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 16/100 (16%)
Query: 21 VVPLAMIINKAMEDSQCSEPESLRK---LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMK 77
+VP + E + RK L++ G D L+ F +G I+D+ +
Sbjct: 14 LVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP 71
Query: 78 DPVTKRSRGFGFITYSESKMVDEA---MSNRPHEIDGRVV 114
R F+TY + + D+A ++ +++ +
Sbjct: 72 P------RNCAFVTYEKMESADQAVAELNGT--QVESVQL 103
Score = 37.8 bits (88), Expect = 6e-04
Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I ++M + AF+ ++
Sbjct: 56 GAFSPFGNIIDLSMDPPR------NCAFVTYEK 82
>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 = 60.0 bits (146), Expect = 6e-12
Identities = 16/92 (17%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
+ P L++ G D L+ F +G I+D+ + R F+TY +
Sbjct: 7 GERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEK 58
Query: 95 SKMVDEAMSNR-PHEIDGRVVETKRAVPREVK 125
+ D+A++ +++ ++ A + +
Sbjct: 59 MESADQAVAELNGTQVESVQLKVNIARKQPML 90
Score = 36.9 bits (86), Expect = 0.001
Identities = 6/34 (17%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I ++M + AF+ ++
Sbjct: 31 RGAFSPFGNIIDLSMDPPR------NCAFVTYEK 58
>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 = 59.5 bits (145), Expect = 9e-12
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 44 RKLFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
++I L+ + D LK A F ++G+I+D++V + + RG F+ + E
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 65
Query: 100 EAMSNRPHEIDGRVVETK 117
A+ + G K
Sbjct: 66 NAL----RSMQGFPFYDK 79
Score = 40.3 bits (95), Expect = 6e-05
Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 128 RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
++ K ++ F ++G I + + + RG AF+ F +
Sbjct: 19 KIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKE 60
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 59.8 bits (145), Expect = 1e-11
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+ + G+ + ++ ++ FF + V ++KD R+ G G + + + EA+
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 106 PHEIDGRVVETKRAVPRE 123
+ R VE A R+
Sbjct: 77 RMLMIQRYVEVSPATERQ 94
Score = 32.8 bits (75), Expect = 0.030
Identities = 9/77 (11%), Positives = 27/77 (35%), Gaps = 17/77 (22%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
V V + + D+F +++V+++ + G G ++F +
Sbjct: 19 VSVHGMPFSAMENDV----RDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFE- 71
Query: 180 VLDKVVVLEVDQEVING 196
L+ ++ ++
Sbjct: 72 ------ALKRNRMLMIQ 82
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 58.5 bits (142), Expect = 2e-11
Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 1/79 (1%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + + + + + D + FF + I V +K G + +
Sbjct: 10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 98 VDEAMSNRP-HEIDGRVVE 115
A+ + I R V+
Sbjct: 70 ATAAVIDLNDRPIGSRKVK 88
Score = 38.4 bits (90), Expect = 3e-04
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+KV+ V+ +I +D+F Y I + E G G A + F+ D
Sbjct: 18 IKVQNMPFTVSIDEI----LDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
>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 = 61.0 bits (147), Expect = 6e-11
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 11/78 (14%)
Query: 44 RKLFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
++I L+ + D LK A F Q+G+I+D++V + + + RG F+ + E
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 100 EAMSNRPHEIDGRVVETK 117
A+ + G K
Sbjct: 67 NAL----RSMQGFPFYDK 80
Score = 40.6 bits (94), Expect = 4e-04
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 128 RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
++ K ++ F Q+G I + + + RG AF+ F +
Sbjct: 20 KIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKE 61
Score = 38.3 bits (88), Expect = 0.002
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
F+ L TN+ L F Q+ +V ++ F+ + A
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDA 263
Score = 36.4 bits (83), Expect = 0.008
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F Q+ + V +V + AF+EFD+
Sbjct: 228 FNQFPGFKEVRLVPGR-----HDIAFVEFDNEV 255
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 57.9 bits (140), Expect = 1e-10
Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 2/97 (2%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
+ + + + + + GL Y+ ++ + FF V V + P R G
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEA 89
Query: 89 FITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
+ ++ + AMS + R +E
Sbjct: 90 DVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGAS 126
Score = 32.9 bits (75), Expect = 0.045
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 10/62 (16%)
Query: 121 PREVKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVV 176
V +R + T+ I ++F V++ + G G A +EF ++
Sbjct: 46 GHCVHMRGLPYKATENDI----YNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEA 99
Query: 177 DK 178
Sbjct: 100 VA 101
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 13/86 (15%), Positives = 34/86 (39%), Gaps = 2/86 (2%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
S + + + G + + ++ F + V + ++++ G+ F+ +S +
Sbjct: 5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAP-LKPVAIRIVRNA-HGNKTGYIFVDFSNEEE 62
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPRE 123
V +A+ + GR +E R
Sbjct: 63 VKQALKCNREYMGGRYIEVFREKSGP 88
Score = 32.3 bits (74), Expect = 0.036
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
VK+R VT+ + M++ ++ +V N G K G+ F++F + + V +
Sbjct: 13 VKLRGAPFNVTEKNV----MEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQ 65
>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 = 56.3 bits (136), Expect = 2e-10
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 2/88 (2%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + + + GL YR ++ + FF + V + P R G + ++ +
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSP-LNPMRVHIEIGP-DGRVTGEADVEFATHED 67
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPREVK 125
AM+ + R VE
Sbjct: 68 AVAAMAKDKANMQHRYVELFLNSTAGTS 95
Score = 32.8 bits (75), Expect = 0.034
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 10/59 (16%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
V +R R T+ I ++F V++ + G G A +EF ++
Sbjct: 18 VHMRGLPYRATENDI----YNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVA 70
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 56.4 bits (136), Expect = 2e-10
Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 7/79 (8%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKR 83
++ S E + + I ++ + L+ A G+I+D+VV +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70
Query: 84 SRGFGFITYSESKMVDEAM 102
+ G +I ++ + +
Sbjct: 71 NSGKAYIVFATQESAQAFV 89
Score = 38.0 bits (88), Expect = 7e-04
Identities = 8/45 (17%), Positives = 14/45 (31%), Gaps = 3/45 (6%)
Query: 128 RVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
V K ++ G I + + + G A+I F
Sbjct: 40 EVPKEKLQALLYALASSQGDILDIVV---DLSDDNSGKAYIVFAT 81
>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 = 55.3 bits (134), Expect = 3e-10
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+L++GGL T+ +L F+++G I + + F +I Y A +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACA 71
Query: 104 N 104
Sbjct: 72 K 72
Score = 38.0 bits (89), Expect = 4e-04
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F ++G+I +++ V FA+I+++ D
Sbjct: 36 REFDRFGSIRTIDHVKG------DSFAYIQYESLD 64
>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 = 54.4 bits (131), Expect = 6e-10
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 5/80 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVM-KDPV----TKRSRGFGFITYSESKMV 98
R+L++G + + ++++ FF + + +PV + + F F+ +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 99 DEAMSNRPHEIDGRVVETKR 118
+AM+ G+ ++ +R
Sbjct: 67 TQAMAFDGIIFQGQSLKIRR 86
Score = 30.5 bits (69), Expect = 0.16
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 139 MDYFGQYG-----TIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
MD+F T N V + + FAF+EF D +
Sbjct: 24 MDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 54.5 bits (131), Expect = 9e-10
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 46 LFIGGLDYRTNDDSL---KAFFEQWGEIVDVVVMKDPVT---KRSRGFGFITYSESKMVD 99
+F+ GL R D + +F ++G+I VV+ + ++TY S+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 100 EAMSNRP-HEIDGRVVET 116
A+ +DGR ++
Sbjct: 78 RAIQCVNNVVVDGRTLKA 95
Score = 38.3 bits (89), Expect = 4e-04
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKR---GFAFIEFDDYD 174
L++ +YFG++G I V + + + A++ + +
Sbjct: 33 LKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 56.6 bits (136), Expect = 9e-10
Identities = 21/175 (12%), Positives = 44/175 (25%), Gaps = 51/175 (29%)
Query: 46 LFIGGLDY-RTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM-- 102
L + GLD + N D + F +G + V MK G + ++ VD A+
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61
Query: 103 ---------------SNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM-------- 139
S +P + G+ + + + +
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 140 --------------------DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ + G ++ + +E+D
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176
Score = 45.5 bits (107), Expect = 6e-06
Identities = 6/77 (7%), Positives = 18/77 (23%), Gaps = 3/77 (3%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS-- 103
L +++ ++ G V G + + E +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 104 NRPHEIDGRVVETKRAV 120
N +++ +
Sbjct: 186 NH-YQMKNPNGPYPYTL 201
Score = 31.6 bits (71), Expect = 0.20
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F YG +E V + + K G A +E D VD+
Sbjct: 26 FCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 54.1 bits (130), Expect = 1e-09
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 3/96 (3%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEI---VDVVVMKDPVTKRSRGFGF 89
E +Q E+ + + GL + + + AFF Q I + ++ R G F
Sbjct: 13 EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAF 72
Query: 90 ITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
+ ++ + A+ + R +E R+ EV+
Sbjct: 73 VLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQ 108
Score = 33.3 bits (76), Expect = 0.025
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 13/63 (20%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQYGTI----ESVNMVTNKETGAKRGFAFIEFDDYDV 175
V++R T ++ + +FGQ+ I E + VT + G G AF+ F +
Sbjct: 26 VRMRGLPFTATAEEV----VAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACEEY 80
Query: 176 VDK 178
Sbjct: 81 AQN 83
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 52.8 bits (127), Expect = 2e-09
Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 11/85 (12%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+D + + I GL + L +++G I VVVM + + +
Sbjct: 13 DDPHKTPAS--PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEF 64
Query: 93 SESKMVDEAM---SNRPHEIDGRVV 114
+ A+ ++ I G
Sbjct: 65 EDVLGACNAVNYAADNQIYIAGHPA 89
Score = 33.6 bits (77), Expect = 0.014
Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 15/84 (17%)
Query: 102 MSNRPHEIDGRVVETKRAVP-REVKVR----RVTKVQIALEQMDYFGQYGTIESVNMVTN 156
M + H + + V +R V + + ++ ++G I V ++
Sbjct: 1 MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADL----VEALQEFGPISYVVVMPK 56
Query: 157 KETGAKRGFAFIEFDDYDVVDKIV 180
K A +EF+D V
Sbjct: 57 K------RQALVEFEDVLGACNAV 74
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 52.5 bits (126), Expect = 3e-09
Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 4/76 (5%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
+ + +RKL I + + L + Q+G + + +TYS
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQA 67
Query: 99 DEAMSNRP-HEIDGRV 113
+A+ +++
Sbjct: 68 RQALDKLNGFQLENFT 83
Score = 33.6 bits (77), Expect = 0.012
Identities = 7/35 (20%), Positives = 10/35 (28%), Gaps = 3/35 (8%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
QYG +ES V + + D
Sbjct: 34 SLLVQYGVVESCEQVNTDSET---AVVNVTYSSKD 65
>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 = 52.9 bits (127), Expect = 3e-09
Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 11/84 (13%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++ + GL + LK + G++ V +D G G + + + + A+
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR- 68
Query: 105 RPHEIDGRVVETKRAVPREVKVRR 128
++D + ++V+
Sbjct: 69 ---KLDNTKFRSHEGETAYIRVKV 89
Score = 29.8 bits (67), Expect = 0.37
Identities = 5/39 (12%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D+ + G + ++ + G +EF + +
Sbjct: 34 DHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTY 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
Length = 110
Score = 52.8 bits (127), Expect = 3e-09
Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 38 SEPESL-RKLFIGGLDY-RTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES 95
++P+S+ ++FIG L+ ++ F ++G + V K G+ F+ YS
Sbjct: 21 NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNE 72
Query: 96 KMVDEAMSNRP-HEIDGRVVETKRAVPR 122
+ A+ + G+ ++ A
Sbjct: 73 RHARAAVLGENGRVLAGQTLDINMAGEP 100
Score = 38.9 bits (91), Expect = 2e-04
Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F +YG + ++ +G+AF+++ + V
Sbjct: 47 TIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAV 79
>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 = 52.9 bits (127), Expect = 3e-09
Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 10/87 (11%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++ + GL + LK + G++ V +D G G + + + + A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 69
Query: 104 --NRPHEIDGRVVETKRAVPREVKVRR 128
+ + ET + R
Sbjct: 70 KLDN-TKFRSHEGETAYIRVKVDGPRS 95
Score = 28.6 bits (64), Expect = 0.94
Identities = 5/39 (12%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D+ + G + ++ + G +EF + +
Sbjct: 35 DHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTY 66
>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 = 54.6 bits (131), Expect = 5e-09
Identities = 22/173 (12%), Positives = 48/173 (27%), Gaps = 53/173 (30%)
Query: 46 LFIGGLD-YRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L + L+ R SL F +G++ V ++ + + + ++ AMS+
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 91
Query: 105 -RPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQ------------------------- 138
H++ G+ + + + V++ R + L +
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 139 -----------------MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F G + K R A I+ +
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 200
Score = 42.7 bits (100), Expect = 5e-05
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 4/57 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L + + +++ LK F G +V ++ R I + +A+
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL 206
>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 = 52.2 bits (125), Expect = 7e-09
Identities = 16/104 (15%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
M DS+ + S R + I L + + + +G++ +++++ + +
Sbjct: 18 GSHMGDSRSAGVPS-RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 70
Query: 89 FITY----SESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRR 128
FI + + MV+ S + G+ + + + +E+K
Sbjct: 71 FIEMNTEEAANTMVNYYTSV-TPVLRGQPIYIQFSNHKELKTDS 113
>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 = 52.5 bits (126), Expect = 8e-09
Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEI--------VDVVVMKDPVTKRSRGFGFITYSES 95
++++ L + LK F ++ + D+ +MK R +G FI
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPNE 102
Query: 96 KMVDEAMSNRPHEIDGRVVETK 117
K +A+ E +G V+ K
Sbjct: 103 KAAAKALK----EANGYVLFGK 120
Score = 34.8 bits (80), Expect = 0.012
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 5/36 (13%)
Query: 142 FGQYGTIESVNM-----VTNKETGAKRGFAFIEFDD 172
FG+Y S + + G +G AFI +
Sbjct: 66 FGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN 101
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 55.2 bits (132), Expect = 1e-08
Identities = 43/361 (11%), Positives = 101/361 (27%), Gaps = 121/361 (33%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG-FITYSES---K 96
F+ D + D K+ + EI +++ KD V+ R F ++ E K
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 97 MVDEAM--------------SNRPHEI-------------DGRVVETKRAVPREVKVRRV 129
V+E + +P + D +V K V R ++
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF-AKYNVSRLQPYLKL 140
Query: 130 TKV--------QIALEQM--------------DY--------------FGQYGTIESV-- 151
+ + ++ + Y + E+V
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200
Query: 152 ---------------------NMVTNKETGAKRGFAFIEFDDY--------DVVDKIVLD 182
N+ + ++ Y +V + +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260
Query: 183 ------KVVVLEVDQEVIN--GEDHRTHGTHQEAKVDGVTTTNQTHGTIREVVGMDNSKV 234
K+++ ++V + TH + + +T + + + + +
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHIS-LDHHSMTLTPD-EVKSLLLKYLDCRPQDL 318
Query: 235 VAGEIKEVG--VVSLVVDGVVAKVAT------VGVDKM--LIQSFILLLSIRDLLSYFMC 284
E+ +S++ + + +AT V DK+ +I+S + +L + F
Sbjct: 319 -PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 285 F 285
Sbjct: 378 L 378
>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 = 53.0 bits (127), Expect = 1e-08
Identities = 22/173 (12%), Positives = 48/173 (27%), Gaps = 53/173 (30%)
Query: 46 LFIGGLD-YRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L + L+ R SL F +G++ V ++ + + + ++ AMS+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 105 -RPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQ------------------------- 138
H++ G+ + + + V++ R + L +
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 139 -----------------MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F G + K R A I+ +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 169
Score = 41.0 bits (96), Expect = 1e-04
Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 4/57 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L + + +++ LK F G +V + R I + +A+
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQAL 175
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 49.8 bits (119), Expect = 2e-08
Identities = 13/85 (15%), Positives = 27/85 (31%), Gaps = 6/85 (7%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
+++G L LK + G + + + R F+ Y +S +A
Sbjct: 18 LAADVYVGNLPRDARVSDLKRALRELGSVPLRL-----TWQGPRRRAFLHYPDSAAAQQA 72
Query: 102 MSNRP-HEIDGRVVETKRAVPREVK 125
+S + + A + K
Sbjct: 73 VSCLQGLRLGTDTLRVALARQQRDK 97
Score = 30.2 bits (68), Expect = 0.20
Identities = 6/44 (13%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ + G++ + + R AF+ + D + V
Sbjct: 35 DLKRALRELGSV-PLRLTWQG----PRRRAFLHYPDSAAAQQAV 73
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 50.1 bits (120), Expect = 3e-08
Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR- 105
I +L + F + G++V++ D T +++GF F+ + + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 106 PHEIDGRVV 114
+D +
Sbjct: 76 GKRLDLKHR 84
Score = 43.2 bits (102), Expect = 6e-06
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV-------LDKVVVLEV 189
F + G + ++ ++ TG +GF F+E + KI+ LD L +
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFL 87
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 44 RKLFIGGLDYRT-NDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+LFIG L + + + L F +G I+ + + FGFI + + V +A+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 74
Query: 103 SNRP-HEIDGR--VVETKRAVPR 122
G+ ++E + R
Sbjct: 75 EXESQEMNFGKKLILEVSSSNAR 97
Score = 38.8 bits (91), Expect = 2e-04
Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 19/86 (22%)
Query: 102 MSNRPHEIDGRVVETKRAVPREVKV-------RRVTKVQIALEQMDYFGQYGTIESVNMV 154
M + H R + ++ + V+K + F YG I +N+
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDL----FRIFSPYGHIMQINI- 55
Query: 155 TNKETGAKRGFAFIEFDDYDVVDKIV 180
K F FI+FD+ V +
Sbjct: 56 -------KNAFGFIQFDNPQSVRDAI 74
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 49.8 bits (119), Expect = 4e-08
Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 6/86 (6%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P ++ + L + LK + T+ G G + + +++
Sbjct: 25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILV 81
Query: 100 EAMS--NRPHEIDGRVVETKRAVPRE 123
EA+ N E G V+ +R
Sbjct: 82 EALERLNN-IEFRGSVITVERDDNPP 106
Score = 27.5 bits (61), Expect = 2.4
Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 3/39 (7%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D + ++ T G +EF +++ +
Sbjct: 47 DLARENSL---ETTFSSVNTRDFDGTGALEFPSEEILVE 82
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 49.1 bits (118), Expect = 4e-08
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 12/82 (14%)
Query: 45 KLFIGGLDYRT-NDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+LFIG L + + + L F +G I+ + + FGFI + + V +A+
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 63
Query: 104 NRP-HEIDGR--VVETKRAVPR 122
G+ ++E + R
Sbjct: 64 CESQEMNFGKKLILEVSSSNAR 85
Score = 39.5 bits (93), Expect = 1e-04
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F YG I +N+ K F FI+FD+
Sbjct: 30 RIFSPYGHIMQINI--------KNAFGFIQFDNPQ 56
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 2/88 (2%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYSESK 96
E + + + GL + + + FF + + + RG I +
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
Query: 97 MVDEAMSNRPHEIDGRVVETKRAVPREV 124
V +A+ + R VE +V
Sbjct: 67 DVQKALEKHRMYMGQRYVEVYEINNEDV 94
Score = 31.0 bits (70), Expect = 0.13
Identities = 14/92 (15%), Positives = 28/92 (30%), Gaps = 17/92 (18%)
Query: 111 GRVVETKRAVPREVKVR----RVTKVQIALEQMDYFGQYGTIESVNMV--TNKETGAKRG 164
G +E + ++ + T + +++F N + G +RG
Sbjct: 1 GSKLEEEVDDVFLIRAQGLPWSCTMEDV----LNFFSDCRIRNGENGIHFLLNRDGKRRG 56
Query: 165 FAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
A IE + D LE + +
Sbjct: 57 DALIEMESEQ-------DVQKALEKHRMYMGQ 81
>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 = 8e-08
Identities = 10/88 (11%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R + I L + + + +G++ +++++K + FI + + + ++
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
Query: 104 ---NRPHEIDGRVVETKRAVPREVKVRR 128
+ + G+ + + + +E+K
Sbjct: 71 YYTSVTPVLRGQPIYIQFSNHKELKTDS 98
Score = 29.8 bits (67), Expect = 0.34
Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ +G + ++ M+ K AFIE + + + +V
Sbjct: 34 ISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMV 69
>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 = 47.6 bits (113), Expect = 2e-07
Identities = 13/90 (14%), Positives = 29/90 (32%), Gaps = 4/90 (4%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQ---WGEIVDVVVMKDPVTKRSRGFGFITYSES 95
E + + GL + + + ++ F + V + R G F+
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESE 71
Query: 96 KMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
V A+ + R +E ++ E+
Sbjct: 72 DDVKLALKKDRESMGHRYIEVFKSHRTEMD 101
Score = 32.2 bits (73), Expect = 0.063
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 19/80 (23%)
Query: 124 VKVR----RVTKVQIALEQMDYFGQY---GTIESVNMVTNKETGAKRGFAFIEFDDYDVV 176
VK+R + + ++ + V+ + +E G + G AF+E + D
Sbjct: 20 VKLRGLPWSCSIEDV----QNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESED-- 72
Query: 177 DKIVLDKVVVLEVDQEVING 196
D + L+ D+E +
Sbjct: 73 -----DVKLALKKDRESMGH 87
>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 = 48.7 bits (115), Expect = 4e-07
Identities = 10/86 (11%), Positives = 30/86 (34%), Gaps = 1/86 (1%)
Query: 32 MEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT 91
+ R ++I G D +K + E G+++++ + + K +G F+
Sbjct: 98 EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 156
Query: 92 YSESKMVDEAMSNRPHEIDGRVVETK 117
+ + + + + +
Sbjct: 157 FDSIESAKKFVETPGQKYKETDLLIL 182
Score = 39.4 bits (91), Expect = 4e-04
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
++ G + ++ M K G F+ FD + K V
Sbjct: 127 KEWLEDKGQVLNIQMRRTLHKAFK-GSIFVVFDSIESAKKFV 167
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 48.6 bits (115), Expect = 6e-07
Identities = 19/110 (17%), Positives = 42/110 (38%), Gaps = 18/110 (16%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDS---------LKAFFEQWGEIVDVVVMKDPV 80
+ S + + L++GG+D N ++ F + G+I + ++
Sbjct: 121 REDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE--- 177
Query: 81 TKRSRGFGFITY---SESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVR 127
S+ GF+ + + ++ EAMSN+ + R + V+
Sbjct: 178 ---SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVK 224
Score = 35.9 bits (82), Expect = 0.009
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F + G I+ + V +K F++F
Sbjct: 162 FVFSRLGDIDRIRYVESK------NCGFVKFKY 188
>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 = 46.9 bits (111), Expect = 7e-07
Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 4/91 (4%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQ---WGEIVDVVVMKDPVTKRSRGFGFITYSE 94
E + + GL + + + ++ F V + R G F+
Sbjct: 39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFVELGS 97
Query: 95 SKMVDEAMSNRPHEIDGRVVETKRAVPREVK 125
V A+ + R +E ++ E+
Sbjct: 98 EDDVKMALKKDRESMGHRYIEVFKSHRTEMD 128
Score = 33.1 bits (75), Expect = 0.042
Identities = 15/121 (12%), Positives = 29/121 (23%), Gaps = 19/121 (15%)
Query: 82 KRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRR----VTKVQIALE 137
G + + VK+R + +
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSMML--GPEGGEGFVVKLRGLPWSCSVEDV--- 61
Query: 138 QMDYFGQYGTIESVNMV--TNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVIN 195
++ + V G + G AF+E D D + L+ D+E +
Sbjct: 62 -QNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED-------DVKMALKKDRESMG 113
Query: 196 G 196
Sbjct: 114 H 114
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 45.9 bits (109), Expect = 7e-07
Identities = 10/76 (13%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 44 RKLFIGGLDYRTND------DSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ + + D + + F ++G+I + ++ +++G+ F+ Y+
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73
Query: 98 VDEAMSNR-PHEIDGR 112
+A+ N +++D +
Sbjct: 74 AVDAVKNADGYKLDKQ 89
Score = 37.0 bits (86), Expect = 0.001
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 9/58 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV-------LDKVVVLEVD 190
F ++G I + +E G +G+ F+E+ V LDK V+
Sbjct: 40 KIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 95
>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 = 45.6 bits (108), Expect = 1e-06
Identities = 12/84 (14%), Positives = 26/84 (30%), Gaps = 11/84 (13%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
+ + GL + L E++G I V++M + + +
Sbjct: 8 SHHKVSVS--PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFE 59
Query: 94 ESKMVDEAMS---NRPHEIDGRVV 114
E ++ + P I G+
Sbjct: 60 NIDSAKECVTFAADVPVYIAGQQA 83
Score = 30.9 bits (70), Expect = 0.12
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
++ ++GTI V M+ K A +EF++ D + V
Sbjct: 33 VEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECV 68
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 12/86 (13%), Positives = 34/86 (39%), Gaps = 11/86 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY----SESKMVD 99
R L I L + + A +G++ +++++K + F+ + MV+
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69
Query: 100 EAMSNRPHEIDGRVVETKRAVPREVK 125
+ + + + + + +E+K
Sbjct: 70 YYSAV-TPHLRNQPIYIQYSNHKELK 94
Score = 29.8 bits (67), Expect = 0.36
Identities = 7/42 (16%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ +G + ++ M+ K AF+E + +V
Sbjct: 33 IALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMV 68
>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 = 43.9 bits (104), Expect = 3e-06
Identities = 8/70 (11%), Positives = 22/70 (31%), Gaps = 8/70 (11%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+ + L +N + + + +K R++ F+T + A+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 104 NR-PHEIDGR 112
+ G+
Sbjct: 59 MFHQYSFRGK 68
Score = 27.0 bits (60), Expect = 2.5
Identities = 5/42 (11%), Positives = 10/42 (23%), Gaps = 7/42 (16%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
E D Y + + AF+ + +
Sbjct: 21 EVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQN 55
>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 = 44.1 bits (104), Expect = 4e-06
Identities = 16/109 (14%), Positives = 36/109 (33%), Gaps = 10/109 (9%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGF 89
+ S + GGL + + L E+ G + +++ + + + F
Sbjct: 14 RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSF 67
Query: 90 ITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQ 138
Y ++ A ++G+ V + + V KVQ +
Sbjct: 68 ARYRTTEESKRAYV----TLNGKEVVDDLGQKITLYLNFVEKVQWSGPS 112
Score = 33.0 bits (75), Expect = 0.030
Identities = 5/33 (15%), Positives = 13/33 (39%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ G ++++ M NK ++F +
Sbjct: 46 PVLEKCGLVDALLMPPNK------PYSFARYRT 72
>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 = 43.6 bits (103), Expect = 5e-06
Identities = 10/70 (14%), Positives = 22/70 (31%), Gaps = 6/70 (8%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
S S S + L T ++ F ++G + V++ + + E
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55
Query: 95 SKMVDEAMSN 104
+A +
Sbjct: 56 PLEARKAFRH 65
Score = 32.1 bits (73), Expect = 0.058
Identities = 6/33 (18%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F ++G++ V + A +EF +
Sbjct: 29 ETFSRFGSLGRVLL------PEGGITAIVEFLE 55
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 44.7 bits (105), Expect = 3e-05
Identities = 51/295 (17%), Positives = 98/295 (33%), Gaps = 111/295 (37%)
Query: 50 GLDYRTNDDSLKAFFEQ----WGE-----IVDVVVMKDPVTKRSRGFG-----FITYSES 95
G+D + + + + + + I+D+V + +PV FG I + S
Sbjct: 1632 GMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIV-INNPVNLTIH-FGGEKGKRIRENYS 1689
Query: 96 KMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKV---------------QIAL---- 136
M+ E + DG++ K + +E+ T Q AL
Sbjct: 1690 AMIFETIV------DGKLKTEK--IFKEIN-EHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 137 ----EQM---------DYF-----GQYG---------TIES-VNMVTNKETGAKRGFAFI 168
E + F G+Y +IES V +V RG
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVV------FYRGMTMQ 1794
Query: 169 EF--------DDYDVVDKIVLDKVVVLEVDQEVINGEDHRTHGTHQEAKVDGVTTTNQTH 220
+Y ++ + V QE + + V+ V +
Sbjct: 1795 VAVPRDELGRSNYGMIA--INPGRVAASFSQEAL------------QYVVERV---GKRT 1837
Query: 221 GTIREVVGMDNSK----VVAGEIKEVGVVSLVVDGVVAKVATVGVDKMLIQSFIL 271
G + E+V N + V AG+++ + V+ V++ + K+ + + + L +S L
Sbjct: 1838 GWLVEIVN-YNVENQQYVAAGDLRALDTVTNVLNFI--KLQKIDIIE-LQKSLSL 1888
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 40.5 bits (95), Expect = 4e-05
Identities = 8/45 (17%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 60 LKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+ F ++G+I + ++ +++G+ F+ Y+ +A+ N
Sbjct: 24 IHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKN 66
Score = 36.2 bits (84), Expect = 0.001
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 9/57 (15%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV-------LDKVVVLEV 189
F ++G I + +E G +G+ F+E+ V LDK V
Sbjct: 26 KIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV 80
>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 = 35.8 bits (82), Expect = 0.006
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 6/83 (7%)
Query: 25 AMIINKAMEDSQCSEPESLRKLF--IGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK 82
A+ + A D+ + L + L Y D L F ++G ++ ++ TK
Sbjct: 26 ALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TK 81
Query: 83 RSRGFGFITYSESKMVDEAMSNR 105
++ + Y++ A +
Sbjct: 82 NNQFQALLQYADPVSAQHAKLSL 104
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 34.9 bits (80), Expect = 0.006
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 39 EPESLRKLFIGGLDY-RTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
+ E R + + L + +D ++ E +G+I + ++M+ + FI +
Sbjct: 21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRED 74
Query: 98 VDEAMS---NRPHEIDGRVV 114
+ + GR V
Sbjct: 75 AMAMVDHCLKKALWFQGRCV 94
Score = 27.2 bits (60), Expect = 3.5
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YG I++ ++ K AFIE + + +V
Sbjct: 47 AEPYGKIKNYILMRMK------SQAFIEMETREDAMAMV 79
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 32.7 bits (74), Expect = 0.050
Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 6/84 (7%)
Query: 24 LAMIINKAMEDSQCSEPESLRKLF--IGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVT 81
LA+ + A D+ + L + L Y D L F ++G ++ ++ T
Sbjct: 7 LALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----T 62
Query: 82 KRSRGFGFITYSESKMVDEAMSNR 105
K ++ + Y++ A +
Sbjct: 63 KNNQFQALLQYADPVSAQHAKLSL 86
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.2 bits (72), Expect = 0.094
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 6 QYIFKLVPGLEV-AGTVVPLAMIINKAME 33
Q + KL L++ A P A+ I ME
Sbjct: 20 QALKKLQASLKLYADDSAP-ALAIKATME 47
Score = 31.1 bits (69), Expect = 0.23
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 9/33 (27%)
Query: 39 EPESLRKLFIGGLD-YRTNDDS-----LKAFFE 65
E ++L+KL L Y DDS +KA E
Sbjct: 18 EKQALKKL-QASLKLYA--DDSAPALAIKATME 47
>2hzl_A Trap-T family sorbitol/mannitol transporter, periplasmic binding
protein, SMOM; trap transporter, periplasmic subunit,
ligand binding; 1.40A {Rhodobacter sphaeroides 2} PDB:
2hzk_A
Length = 365
Score = 32.8 bits (75), Expect = 0.14
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 6/70 (8%)
Query: 15 LEVAGTVVPLAMIINKAMEDSQCSEPESLRKLFIGGLD-YRTNDDSLKAFFEQWGEIVDV 73
L A M+ ++ P +++ L G + + L+A FE E+
Sbjct: 265 LRTACHAADANMLQLYDWKN-----PTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAE 319
Query: 74 VVMKDPVTKR 83
+ +P K+
Sbjct: 320 MEASNPAFKK 329
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.4 bits (65), Expect = 0.46
Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YG + ++ + + K G A +EF + V
Sbjct: 37 LLQKYGEVLNLVLSSK-----KPGTAVVEFATVKAAELAV 71
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT,
cytoplasmic vesicle, membrane, Ca structural protein;
7.94A {Bos taurus}
Length = 190
Score = 29.7 bits (66), Expect = 0.95
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 31 AMEDSQCSEPESLRK 45
A D EPES+RK
Sbjct: 75 AQADRLTQEPESIRK 89
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 29.0 bits (64), Expect = 2.0
Identities = 7/43 (16%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
+ + Y Q+G I + + +A +EF + + +
Sbjct: 68 KFLKYLSQFGPINNHFFYESFGL-----YAVVEFCQKESIGSL 105
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 27.1 bits (60), Expect = 3.4
Identities = 10/62 (16%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 57 DDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA---MSNRPHEIDGRV 113
++ E++GE+ ++ V D + G ++ + + ++A ++NR +G+
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNR--WFNGQP 97
Query: 114 VE 115
+
Sbjct: 98 IH 99
>2c0c_A Zinc binding alcohol dehydrogenase, domain containing 2;
oxidoreductase, quinone oxidoreductase, medium-chain
dehydrogenase/reductase; HET: NAP; 1.45A {Homo sapiens}
PDB: 2x1h_A* 2x7h_A* 2wek_A*
Length = 362
Score = 27.6 bits (62), Expect = 5.2
Identities = 6/24 (25%), Positives = 6/24 (25%), Gaps = 2/24 (8%)
Query: 1 MKGVMQ--YIFKLVPGLEVAGTVV 22
G G E G VV
Sbjct: 73 SAGRYDPSVKPPFDIGFEGIGEVV 96
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 26.1 bits (57), Expect = 5.2
Identities = 8/64 (12%), Positives = 23/64 (35%), Gaps = 7/64 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAF----FEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+ + +DYR + L+ F + G++ V + + + +
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDAIG 67
Query: 101 AMSN 104
A+++
Sbjct: 68 AVNS 71
>1iz0_A Quinone oxidoreductase; APO-enzyme, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 2.30A {Thermus thermophilus} SCOP: b.35.1.2
c.2.1.1 PDB: 1iyz_A 2cf2_D
Length = 302
Score = 27.5 bits (62), Expect = 5.3
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 12 VPGLEVAGTVV 22
+PG+EV G V
Sbjct: 58 IPGMEVVGVVE 68
>3ldu_A Putative methylase; structural genomics, PSI-2, protein structure
initiative, midwest center for structural genomics,
MCSG; HET: MSE GTP; 1.70A {Clostridium difficile}
Length = 385
Score = 27.7 bits (62), Expect = 6.1
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 146 GT--IESVNMVTNKETGAKRGFAFIEFDDYD 174
GT IE+ + N G R F ++ D
Sbjct: 207 GTILIEAAMIGINMAPGLNREFISEKWRTLD 237
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 26.6 bits (58), Expect = 6.3
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 57 DDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES 95
D S+K +F+++GEI DP + I Y+ S
Sbjct: 20 DISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASS 58
>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase,
transferase; HET: SAH; 1.96A {Streptococcus mutans}
Length = 384
Score = 27.3 bits (61), Expect = 6.5
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 146 GT--IESVNMVTNKETGAKRGFAFIEFDDYD 174
GT IE+ + N G R FAF E+ D
Sbjct: 206 GTFCIEAAMIGMNIAPGFNRDFAFEEWPWVD 236
>3pi7_A NADH oxidoreductase; groes-like fold, NAD(P)-binding rossmann
fold, structural GE joint center for structural
genomics, JCSG; HET: MSE; 1.71A {Mesorhizobium loti}
Length = 349
Score = 27.2 bits (61), Expect = 6.7
Identities = 5/11 (45%), Positives = 6/11 (54%)
Query: 12 VPGLEVAGTVV 22
G E GT+V
Sbjct: 82 PAGFEGVGTIV 92
>4a27_A Synaptic vesicle membrane protein VAT-1 homolog-L;
oxidoreductase; 2.10A {Homo sapiens}
Length = 349
Score = 27.2 bits (61), Expect = 7.5
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 12 VPGLEVAGTVV 22
VPG E +G V
Sbjct: 63 VPGFECSGIVE 73
>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170,
putative RNA methylase, PSI,MCSG, structu genomics;
1.50A {Listeria monocytogenes str}
Length = 393
Score = 27.3 bits (61), Expect = 8.0
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 146 GT--IESVNMVTNKETGAKRGFAFIEFDDYD 174
GT IE+ + N G R F +D
Sbjct: 213 GTIPIEAALIGQNIAPGFNREFVSETWDWMP 243
>4dup_A Quinone oxidoreductase; PSI-biology, structural genomics, protein
structure initiati structural genomics research
consortium, nysgrc; 2.45A {Rhizobium etli}
Length = 353
Score = 26.8 bits (60), Expect = 8.8
Identities = 5/11 (45%), Positives = 9/11 (81%)
Query: 12 VPGLEVAGTVV 22
+ GLE++G +V
Sbjct: 88 ILGLELSGEIV 98
>3tqh_A Quinone oxidoreductase; HET: NDP; 2.44A {Coxiella burnetii}
Length = 321
Score = 26.8 bits (60), Expect = 8.8
Identities = 3/22 (13%), Positives = 9/22 (40%)
Query: 1 MKGVMQYIFKLVPGLEVAGTVV 22
+ ++ G + +G V+
Sbjct: 59 VAKKLKNNLPSGLGYDFSGEVI 80
>2j8z_A Quinone oxidoreductase; medium-chain dehydrogenase- reductases,
QUIN oxidoreductase, oxidative stress response; HET:
NAP; 2.50A {Homo sapiens} PDB: 2oby_A*
Length = 354
Score = 26.8 bits (60), Expect = 9.8
Identities = 5/11 (45%), Positives = 7/11 (63%)
Query: 12 VPGLEVAGTVV 22
+ GLE +G V
Sbjct: 82 ILGLEASGHVA 92
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
0.321 0.138 0.392
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: 4,770,576
Number of extensions: 302919
Number of successful extensions: 1384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1136
Number of HSP's successfully gapped: 386
Length of query: 306
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 213
Effective length of database: 4,105,140
Effective search space: 874394820
Effective search space used: 874394820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.7 bits)