RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1314
(275 letters)
>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 = 205 bits (525), Expect = 2e-67
Identities = 56/162 (34%), Positives = 95/162 (58%), Gaps = 2/162 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ K+F+GGL+ +T E + +YF +YG V + I DP TG+SRGF F++F +VD++
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
+ H + K IDPKR R K KIFVGG+ ++ ++ ++FSQ+G+I + Q
Sbjct: 62 VKT-QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
DK +GF F+++D + ++V N +++++KR
Sbjct: 121 LDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKR 162
Score = 101 bits (255), Expect = 7e-27
Identities = 30/83 (36%), Positives = 46/83 (55%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
++ K+FVGG+ + KE ++FSQ+G + + D TGQSRGF FVT+ + AVD
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Query: 73 DLLAAGDHYIGNKKIDPKRVTKR 95
+ ++KI+ KR R
Sbjct: 144 RVCQNKFIDFKDRKIEIKRAEPR 166
>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 = 204 bits (520), Expect = 3e-66
Identities = 61/186 (32%), Positives = 98/186 (52%), Gaps = 8/186 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGS 126
+ A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG
Sbjct: 71 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
I + D+ K+GF F++FDD + ++++ + G +V++ E M S
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE-MASA 189
Query: 187 SGAVRG 192
S + RG
Sbjct: 190 SSSQRG 195
Score = 101 bits (253), Expect = 2e-26
Identities = 30/92 (32%), Positives = 48/92 (52%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
R + +K+FVGG+ +T E + DYF QYG++E I I D +G+ RGFAFV
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 64 TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
TF +VD ++ H + + ++ +
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183
Score = 83.9 bits (208), Expect = 8e-20
Identities = 20/87 (22%), Positives = 44/87 (50%)
Query: 89 PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
K + + K+F+GGL+ E +++ +R +F Q+G++T+ D + +GF F++
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKR 175
+ + + + G+ V+ KR
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKR 88
>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 = 144 bits (366), Expect = 2e-43
Identities = 34/166 (20%), Positives = 71/166 (42%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTTQKAV 71
R+L+VG + E+ + D+F+ + ++ Q + FAF+ F +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEISEQDVRDYFSQYGSITEF 130
+A + + +R K+F+GGL +++ V++ + +G + F
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR 175
D + + KG+ F + D NV +Q +A + K++ V+R
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Score = 81.9 bits (203), Expect = 2e-19
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF + D +A
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 78 GD-HYIGNKKIDPKRVT 93
+ +G+KK+ +R +
Sbjct: 156 LNGMQLGDKKLLVQRAS 172
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 134 bits (339), Expect = 7e-39
Identities = 37/194 (19%), Positives = 77/194 (39%), Gaps = 16/194 (8%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV + +A
Sbjct: 23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82
Query: 71 VDDLLAA-GDHYIGNKKIDPKRVTKRVNPLKC------------KIFVGGLTTEISEQDV 117
L +G + I R + +I+V + ++S+ D+
Sbjct: 83 AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 118 RDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV 176
+ F +G I D + KG+ FI ++ ++ +++ + G+ + V +
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Query: 177 --KFNPETMGSVSG 188
P + G
Sbjct: 203 VTPPMPLLTPATPG 216
Score = 65.4 bits (160), Expect = 6e-13
Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ + +++VG + E+ E +R F+ +G I +D KGF F+
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 148 SFDDQNVAEQVLANPKQV-ICGKEVDVKR 175
++ A+ L V + G+ + V R
Sbjct: 76 EYEVPEAAQLALEQMNSVMLGGRNIKVGR 104
>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 = 130 bits (328), Expect = 9e-38
Identities = 45/176 (25%), Positives = 80/176 (45%), Gaps = 19/176 (10%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTT---- 67
+D K+FVG + R EK++ + F QYG V I++ D QS+G FVTF T
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-----CKIFVGGLTTEISEQDVRDYFS 122
+A + L + + P ++ + K+F+G ++ + +E D+R FS
Sbjct: 61 LEAQNAL---HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFS 117
Query: 123 QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVI--CGKEVDVK 174
+G I E + +G F++F + +A+ + + Q + C + VK
Sbjct: 118 SFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172
>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 = 121 bits (306), Expect = 2e-34
Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 8/151 (5%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAV 71
+ L V L +N ++E F GE+ES + D TGQS G+ FV + +KA+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
+ L + K I ++ ++V GL ++++++ FSQYG I
Sbjct: 62 NTL---NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS 118
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ D+ + +G FI FD + AE+ +
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Score = 71.5 bits (176), Expect = 2e-15
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ L+V GL + +KE+ FSQYG + + I D TG SRG F+ F + +
Sbjct: 85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 73 D 73
+
Sbjct: 145 E 145
>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 = 115 bits (291), Expect = 5e-33
Identities = 39/90 (43%), Positives = 50/90 (55%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+G G ++ KLFVGGL +T ++ + YFSQYGEV I D T QSRGF FV F
Sbjct: 6 SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
V +LA+ H + + IDPK T R
Sbjct: 66 KDPNCVGTVLASRPHTLDGRNIDPKPCTPR 95
Score = 83.1 bits (206), Expect = 1e-20
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVGGL +++ +R YFSQYG + + DK+ N +GF F+ F D N VLA
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 161 NPKQVICGKEVDVKR 175
+ + G+ +D K
Sbjct: 77 SRPHTLDGRNIDPKP 91
>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 = 117 bits (296), Expect = 5e-33
Identities = 32/169 (18%), Positives = 63/169 (37%), Gaps = 10/169 (5%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
LF+G L+ N E+ S+ +++ D TG +R F +V F + + ++
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLK---CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
L + +I ++ R + + L+ I+E ++++ F I
Sbjct: 69 KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR- 127
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK 177
KG +I F + AE+ L + I G+ V +
Sbjct: 128 ----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172
Score = 65.7 bits (161), Expect = 2e-13
Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 6/93 (6%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ G R L L N E E+ + F E+ G+S+G A++
Sbjct: 87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYI 141
Query: 64 TFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
F ++ + L I + + ++
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 114 bits (288), Expect = 9e-33
Identities = 35/83 (42%), Positives = 54/83 (65%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
A D K+FVGGL +T +K++ DYF+++GEV +IK DP+TG+SRGF F+ F
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63
Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
+V+ +L +H + + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86
Score = 82.2 bits (204), Expect = 2e-20
Identities = 25/75 (33%), Positives = 45/75 (60%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVGGL+ + S++D++DYF+++G + + D + +GF FI F D E+VL
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71
Query: 161 NPKQVICGKEVDVKR 175
+ + G+ +D K+
Sbjct: 72 QKEHRLDGRVIDPKK 86
>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 = 114 bits (287), Expect = 2e-32
Identities = 31/89 (34%), Positives = 50/89 (56%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G + K+FVGG+ N GE E+ +YF ++G V + + D + RGF F+TF
Sbjct: 1 GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
Query: 67 TQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+++VD + H I KK++ KR R
Sbjct: 61 DEQSVDQAVNMHFHDIMGKKVEVKRAEPR 89
Score = 95.3 bits (238), Expect = 3e-25
Identities = 29/74 (39%), Positives = 45/74 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGG+ E ++R+YF ++G +TE +D K +GF FI+F+D+ +Q +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 PKQVICGKEVDVKR 175
I GK+V+VKR
Sbjct: 72 HFHDIMGKKVEVKR 85
>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 = 117 bits (295), Expect = 2e-32
Identities = 34/186 (18%), Positives = 71/186 (38%), Gaps = 27/186 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTTQKAV 71
R+L+VG + E+ + D+F+ + ++ Q + FAF+ F +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC---------------------KIFVGGLTT 110
+A + + +R K+F+GGL
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGK 169
+++ V++ + +G + F D + + KG+ F + D NV +Q +A + K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 170 EVDVKR 175
++ V+R
Sbjct: 185 KLLVQR 190
Score = 73.9 bits (182), Expect = 3e-16
Identities = 21/95 (22%), Positives = 45/95 (47%), Gaps = 1/95 (1%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
Y + + KLF+GGL + ++ + + +G +++ ++ D TG S+G+A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159
Query: 62 FVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
F + D +A + +G+KK+ +R +
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194
Score = 57.7 bits (140), Expect = 3e-10
Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 5/105 (4%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVA 155
+++VG + I+E+ + D+F+ + Q N K F F+ F +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 156 EQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASA 200
Q +A + G+ + ++R G V++
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTV 109
>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 = 116 bits (292), Expect = 2e-32
Identities = 36/150 (24%), Positives = 67/150 (44%), Gaps = 8/150 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
L V L ++ ++E+ F G + + I D TG S G+AFV FT+ Q+A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
L + NK++ +K ++V L I++ + F +YGSI +
Sbjct: 64 VL---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
DK +G F+ ++ + A++ ++
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Score = 68.0 bits (167), Expect = 3e-14
Identities = 16/61 (26%), Positives = 30/61 (49%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ L+V L R + +++ F +YG + +I D TG+ RG AFV + ++
Sbjct: 86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 145
Query: 73 D 73
+
Sbjct: 146 E 146
>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 = 114 bits (287), Expect = 2e-32
Identities = 35/85 (41%), Positives = 49/85 (57%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+ K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVTF Q
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
VD +LA H + +K IDPK R
Sbjct: 80 VDKVLAQSRHELDSKTIDPKVAFPR 104
Score = 99.3 bits (248), Expect = 1e-26
Identities = 27/100 (27%), Positives = 53/100 (53%), Gaps = 2/100 (2%)
Query: 76 AAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD 135
++ H+ + + P+ + CK+F+GGL+ + +++ +R+YF Q+G + E D
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGSSG--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60
Query: 136 KSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+GF F++F DQ ++VLA + + K +D K
Sbjct: 61 PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV 100
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 110 bits (278), Expect = 2e-31
Identities = 28/74 (37%), Positives = 44/74 (59%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL NT +++ YF Q+G+V+ + D T + RGF FVTF ++ V+ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 GDHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 97.9 bits (245), Expect = 1e-26
Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL+ + +DV+ YF Q+G + + FDK+ N +GF F++F+ +++ E+V
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 162 PKQVICGKEVDVKR 175
I K V+ K+
Sbjct: 61 HFHEINNKMVECKK 74
>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 = 111 bits (279), Expect = 3e-31
Identities = 32/85 (37%), Positives = 50/85 (58%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+ RKLF+GGL T E+ + +Y+ Q+G++ + DP + +SRGF FVTF++
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
VD +AA H I + ++PKR R
Sbjct: 82 VDAAMAARPHSIDGRVVEPKRAVAR 106
Score = 85.8 bits (213), Expect = 2e-21
Identities = 26/91 (28%), Positives = 46/91 (50%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
+ P KR K+F+GGL+ E +E+ +R+Y+ Q+G +T+ D + +GF
Sbjct: 12 LETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGF 71
Query: 145 CFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
F++F + +A I G+ V+ KR
Sbjct: 72 GFVTFSSMAEVDAAMAARPHSIDGRVVEPKR 102
>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 = 109 bits (275), Expect = 5e-31
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL +T E++I +YF +GEVESI + D T + RGF F+TF ++ V ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 GDHYIGNKKIDPKR 91
H +G K + K
Sbjct: 61 KYHNVGLSKCEIKV 74
Score = 101 bits (254), Expect = 7e-28
Identities = 22/74 (29%), Positives = 43/74 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 162 PKQVICGKEVDVKR 175
+ + ++K
Sbjct: 61 KYHNVGLSKCEIKV 74
>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 = 110 bits (276), Expect = 7e-31
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 1/91 (1%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
+ L V GL T E+++ +YFS +GEV + +K D TG S+GF FV
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
FT + +++ H I + D K +
Sbjct: 64 FTEYETQVKVMSQ-RHMIDGRWCDCKLPNSK 93
Score = 83.4 bits (207), Expect = 9e-21
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ V GL + +EQD+++YFS +G + Q D KGF F+ F + +V++
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 161 NPKQVICGKEVDVKR 175
+I G+ D K
Sbjct: 76 QR-HMIDGRWCDCKL 89
>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 = 110 bits (276), Expect = 9e-31
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 4/111 (3%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ K+FVGGL +T + + YF +G++E + D TG+SRG+ FV
Sbjct: 5 SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
Query: 64 TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKC----KIFVGGLTT 110
T + A + + I +K + P I V G ++
Sbjct: 65 TMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115
Score = 78.5 bits (194), Expect = 1e-18
Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 2/95 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
KIFVGGL ++ +R YF +G I E D+ +G+ F++ D+ AE+
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 161 NPKQVICGKEVDVKR--VKFNPETMGSVSGAVRGA 193
+P +I G++ +V + P ++ +
Sbjct: 78 DPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSG 112
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 108 bits (273), Expect = 1e-30
Identities = 34/74 (45%), Positives = 47/74 (63%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVTF Q VD +LA
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPKR 91
H + +K IDPK
Sbjct: 62 SRHELDSKTIDPKV 75
Score = 89.1 bits (222), Expect = 4e-23
Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+F+GGL+ + +++ +R+YF Q+G + E D +GF F++F DQ ++VLA
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVKR 175
+ + K +D K
Sbjct: 61 QSRHELDSKTIDPKV 75
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 112 bits (283), Expect = 4e-30
Identities = 33/169 (19%), Positives = 61/169 (36%), Gaps = 15/169 (8%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+LFVG L + E++ F +YGE + I D RGF F+ ++ +
Sbjct: 19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE 72
Query: 73 DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
A D + ++ + + T + V L+ +S + + FSQ+G + +
Sbjct: 73 IAKAELDGTILKSRPLRIRFATHGAA-----LTVKNLSPVVSNELLEQAFSQFGPVEKAV 127
Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEVDVKRVKF 178
D G F+ F + A + L + V+
Sbjct: 128 VVVDDR-GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175
>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 = 108 bits (273), Expect = 2e-28
Identities = 34/176 (19%), Positives = 70/176 (39%), Gaps = 17/176 (9%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
E L++ + ++ I D V SR FA++ T+
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Query: 68 QKAVDDLLAAGDHYIGNKKI-----DPKRVTKRVNPLKC---KIFVGGLTTEIS-EQDVR 118
+ V+ L I + +P +KR + +I + L+TE+ E +R
Sbjct: 173 RYCVEKL---NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLR 229
Query: 119 DYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLANPKQVICGKEVDV 173
+ F +GSI + P + ++ F+ F++++ AE+ L + ++ +E+ V
Sbjct: 230 ESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISV 285
Score = 107 bits (270), Expect = 7e-28
Identities = 19/146 (13%), Positives = 50/146 (34%), Gaps = 10/146 (6%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ + V L ++ + ++ YF G + + + + ++ FA + F
Sbjct: 38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGAL 95
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
+ +G +I V+ L C +++ +++++RD +
Sbjct: 96 AAITKTHKVVGQNEI-------IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQ 157
+ N + F +I + A
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARY 174
Score = 66.9 bits (164), Expect = 4e-13
Identities = 22/124 (17%), Positives = 37/124 (29%), Gaps = 7/124 (5%)
Query: 57 SRGFAFVTFT-TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQ 115
S + +++ +D+ A G R N + V L ++
Sbjct: 1 SMEYGHHARPDSKRPLDEGSPAA---AGLTSKKANEALTR-NRELTTVLVKNLPKSYNQN 56
Query: 116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
V YF G I KN F I F + A + +V+ E+ V
Sbjct: 57 KVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAITKTHKVVGQNEIIVSH 114
Query: 176 VKFN 179
+
Sbjct: 115 LTEC 118
>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 = 108 bits (271), Expect = 4e-28
Identities = 33/175 (18%), Positives = 64/175 (36%), Gaps = 16/175 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
L V L + +++ + +G +E + TGQS+G+ F + +A D
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 74 LLAAGDHYIGNKKI-----DPKRVTKRVNPLKCKIFVGGLTTEISEQD-VRDYFSQYGSI 127
L +G + + D ++T + +C + V L ++ D + S S
Sbjct: 157 L---LGKPLGPRTLYVHWTDAGQLTPALLHSRC-LCVDRLPPGFNDVDALCRALSAVHSP 212
Query: 128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPE 181
T Q + KGF + ++ +AE+ + G + V P
Sbjct: 213 TFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266
Score = 101 bits (254), Expect = 1e-25
Identities = 25/164 (15%), Positives = 65/164 (39%), Gaps = 20/164 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
RK+ + GL + +E++D S Y ++ + +G AFVT + A++
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-LKYC------FVDKYKGTAFVTLLNGEQAEAAIN 75
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
++ + ++ ++ P + V L +++Q + +GS+
Sbjct: 76 AF--------HQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVKR 175
+ + KG+ F + ++ A + ++ + + + + V
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
Score = 53.1 bits (128), Expect = 2e-08
Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 80 HYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK 138
H + ++I + T+R + KI + GL +++ Q+V D S Y F
Sbjct: 1 HMLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCF-------V 53
Query: 139 NMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEVDVKR 175
+ KG F++ + AE + + + + +E+ V+
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFH-QSRLRERELSVQL 91
>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 = 102 bits (256), Expect = 1e-26
Identities = 47/185 (25%), Positives = 76/185 (41%), Gaps = 15/185 (8%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
L+VG LH + E + + FS G + SI + D T +S G+A+V F +
Sbjct: 12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 73 DLLAAGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQY 124
L + I K + DP V IF+ L I + + D FS +
Sbjct: 72 RALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAF 127
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVKRVKFNPETM 183
G+I + D +N KG+ F+ F+ Q AE+ + ++ ++V V R K E
Sbjct: 128 GNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185
Query: 184 GSVSG 188
+
Sbjct: 186 AELGA 190
Score = 66.1 bits (162), Expect = 3e-13
Identities = 27/117 (23%), Positives = 52/117 (44%), Gaps = 6/117 (5%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
++ +F+ L ++ K + D FS +G + S + D S+G+ FV F TQ+A +
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157
Query: 73 DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT 128
+ + + ++K+ V + + + + +G E DV DY G I
Sbjct: 158 RAIEKMNGMLLNDRKV---FVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGRIV 211
>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 = 98.8 bits (247), Expect = 9e-26
Identities = 34/166 (20%), Positives = 67/166 (40%), Gaps = 14/166 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R L+VG L + E + YF G + +I I D ++ +AFV + + L
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 77 AGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT 128
+ I N + + + +FVG L + ++ +R+ F + S
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTF----NLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDV 173
+D +G+ F+SF Q+ A+ + + Q + G+ + +
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Score = 65.2 bits (160), Expect = 3e-13
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
A + +D LFVG L+ N ++ + + F + S + D TG SRG+ FV
Sbjct: 75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134
Query: 64 TFTTQKAVDDLLAAGD-HYIGNKKI 87
+FT+Q + + + + + +
Sbjct: 135 SFTSQDDAQNAMDSMQGQDLNGRPL 159
>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 = 95.0 bits (237), Expect = 3e-25
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G + +FVG + E E+ ++FSQYG+V + I R FAFVTF +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
L D I + +
Sbjct: 56 QSLCGE-DLIIKGISVHISNAEPK 78
Score = 87.7 bits (218), Expect = 2e-22
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG T +++E ++R++FSQYG + + P + F F++F D +A+ +
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE 61
Query: 162 PKQVICGKEVDVKR 175
+I G V +
Sbjct: 62 D-LIIKGISVHISN 74
>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 = 93.1 bits (232), Expect = 1e-24
Identities = 23/88 (26%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
+ + K+FVG + +E+ +F QYGEV + I R FAFVTF
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
K L D I + +
Sbjct: 58 DKVAQSLC-GEDLIIKGISVHISNAEPK 84
Score = 91.1 bits (227), Expect = 1e-23
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVG T +++ ++++ +F QYG + + P + F F++F D VA+ +
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG 66
Query: 161 NPKQVICGKEVDVKR 175
+I G V +
Sbjct: 67 ED-LIIKGISVHISN 80
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex;
1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 88.4 bits (220), Expect = 1e-22
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 2/84 (2%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G+ +FVGG+ E EI +F++YG V+ + I D TG S+G+ FV+F V
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDV 63
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
++ + KK+ ++
Sbjct: 64 QKIVESQ-INFHGKKLKLGPAIRK 86
Score = 76.9 bits (190), Expect = 3e-18
Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF + ++++ +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVES 69
Query: 162 PKQVICGKEVDVKR 175
GK++ +
Sbjct: 70 QIN-FHGKKLKLGP 82
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 86.2 bits (214), Expect = 7e-22
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 5/87 (5%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
G + R +FV G R ++++YF +G V S+ + D FA V
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV 55
Query: 69 KAVDDLLAAGDHYIGNKKIDPKRVTKR 95
A + +L+ H +G ++ + ++
Sbjct: 56 GAREAVLSQSQHSLGGHRLRVRPREQK 82
Score = 81.6 bits (202), Expect = 5e-20
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 6/91 (6%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FV G + + +YF +G + D K F + D E VL+
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGAREAVLSQ 64
Query: 162 PKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
+ + G + V+ + E S + +G
Sbjct: 65 SQHSLGGHRLRVRP-REQKEFQSPASKSPKG 94
>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 = 83.9 bits (208), Expect = 8e-21
Identities = 25/103 (24%), Positives = 50/103 (48%), Gaps = 3/103 (2%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
++G++G +D KLF+G + RN EK++ F ++G++ +++ D TG +G AF+T
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGG 107
+ +++ A K + +V P + G
Sbjct: 62 YCERESAL---KAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101
Score = 64.3 bits (157), Expect = 1e-13
Identities = 17/82 (20%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ K+F+G + + E+D++ F ++G I E D+ M KG F+++ ++ A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 157 QVLA--NPKQVI--CGKEVDVK 174
+ + + ++ + + + VK
Sbjct: 70 KAQSALHEQKTLPGMNRPIQVK 91
>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 = 83.1 bits (206), Expect = 2e-20
Identities = 19/84 (22%), Positives = 37/84 (44%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
D R +F L +++ D+FS G+V + I +D ++ +S+G A+V F ++V
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVN 97
+ + I + N
Sbjct: 83 AIGLTGQRLLGVPIIVQASQAEKN 106
Score = 68.9 bits (169), Expect = 4e-15
Identities = 17/106 (16%), Positives = 37/106 (34%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
+ +P +F L I +D+ D+FS G + + + D++ KG
Sbjct: 9 SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
Query: 144 FCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGA 189
++ F + + Q + G + V+ + + S
Sbjct: 69 IAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114
>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 = 82.3 bits (204), Expect = 3e-20
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 1/92 (1%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
+ + +DE KLFVGGL +T E+ + FS+YG++ + + D T +SRGF FVT
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 65 FTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
F D + A + + ++I + K
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92
Score = 59.2 bits (144), Expect = 1e-11
Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVGGL+ + +EQ + FS+YG I+E D+ +GF F++F++ + A+ +
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 161 NP-KQVICGKEVDVKR 175
+ + G+++ V +
Sbjct: 73 AMNGKSVDGRQIRVDQ 88
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 80.8 bits (199), Expect = 1e-19
Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEV--ESISIKNDPHTGQSRGFAFVTFT 66
G + RK+FVGGL + E EI F ++G + + +G+AF+ F
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 67 TQKAVDDLLAAGDHYIGN-------KKIDPKRV 92
+ +V L+ A G I K V
Sbjct: 61 EESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
Score = 66.5 bits (162), Expect = 3e-14
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK--KGFCFISFDDQNVAEQV 158
K+FVGGL +I E ++ F ++G + +SK+ KG+ F+ F +++ + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 159 LANPKQV-------ICGKEVDVKRVKFNP 180
+ + + + K V+ P
Sbjct: 69 IDACLEEDGKLYLCVSSPTIKDKPVQIRP 97
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 81.7 bits (202), Expect = 1e-19
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+G +G +R L+VGGL +K ++ F +G++ I I D T + RGFA
Sbjct: 49 GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108
Query: 62 FVTFTT----QKAVDDL 74
FV F A+D++
Sbjct: 109 FVEFELAEDAAAAIDNM 125
Score = 59.8 bits (145), Expect = 1e-11
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A +
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 160 AN 161
N
Sbjct: 123 DN 124
>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 = 80.3 bits (199), Expect = 2e-19
Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++GP + L V L T + F +YG V + I +PHT RGFAFV F
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 67 T----QKAVDDL 74
Q A +
Sbjct: 64 DRRDAQDAEAAM 75
Score = 56.1 bits (136), Expect = 1e-10
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ V LT S +R F +YG + + P + +GF F+ F D+ A+
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
>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 = 78.7 bits (195), Expect = 4e-19
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-- 67
G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV F
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 68 --QKAVDDL 74
A+D++
Sbjct: 61 DAAAAIDNM 69
Score = 60.6 bits (148), Expect = 2e-12
Identities = 19/64 (29%), Positives = 31/64 (48%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 158 VLAN 161
+ N
Sbjct: 65 AIDN 68
>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 = 78.4 bits (194), Expect = 7e-19
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ + L V GL T E+++ + FS+YG + +SI D + +SRGFAFV
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 64 TFTT----QKAVDDL 74
F ++A +
Sbjct: 63 YFENVDDAKEAKERA 77
Score = 57.2 bits (139), Expect = 5e-11
Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ + A++
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 161 NPKQVICGKEVDVKRVKFN 179
G E+D +R++ +
Sbjct: 76 R----ANGMELDGRRIRVS 90
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein
1; RRM domain, RBD, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 94
Score = 78.4 bits (194), Expect = 7e-19
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+G +G + ++V L + ++ FS+YG+V ++I D T +S+G AF+ F
Sbjct: 6 SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
Query: 66 TT----QKAVDDL 74
Q +
Sbjct: 66 LDKDSAQNCTRAI 78
Score = 59.9 bits (146), Expect = 4e-12
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P K ++V L ++ D+ FS+YG + + DK KG FI F D++ A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 158 VLAN 161
Sbjct: 74 CTRA 77
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 78.2 bits (193), Expect = 2e-18
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ G P L V L T + F +YG V + I D +T +SRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 64 TFTT----QKAVDDL 74
F + A+D +
Sbjct: 95 RFHDKRDAEDAMDAM 109
Score = 55.5 bits (134), Expect = 4e-10
Identities = 17/57 (29%), Positives = 26/57 (45%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+ V LT S +R F +YG + + P D+ +GF F+ F D+ AE
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
>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 = 78.2 bits (193), Expect = 2e-18
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ + L V GL T E+++ + FS+YG + +SI D + +SRGFAFV
Sbjct: 34 SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
Query: 64 TFTT----QKAVDDL 74
F ++A +
Sbjct: 94 YFENVDDAKEAKERA 108
Score = 57.4 bits (139), Expect = 1e-10
Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ + A++
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 161 NPKQVICGKEVDVKRVKFN 179
G E+D +R++ +
Sbjct: 107 R----ANGMELDGRRIRVD 121
>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 = 76.5 bits (189), Expect = 3e-18
Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVD 72
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ F ++ AV
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 73 DL 74
+L
Sbjct: 63 NL 64
Score = 63.0 bits (154), Expect = 4e-13
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+++G + + +E+ + D S G + + FD KG+ FI F D + +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 161 N 161
N
Sbjct: 63 N 63
>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 = 76.9 bits (190), Expect = 3e-18
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 7 GTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
G++G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 65 FTT----QKAVDDL 74
F A+D++
Sbjct: 61 FELAEDAAAAIDNM 74
Score = 59.2 bits (144), Expect = 9e-12
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A +
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 160 AN 161
N
Sbjct: 72 DN 73
>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 = 76.0 bits (188), Expect = 4e-18
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
G + L++ GL T ++++ YG++ S D T + +G+ FV F +
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 68 QKAVDDL 74
QKAV L
Sbjct: 61 QKAVTAL 67
Score = 56.0 bits (136), Expect = 1e-10
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
+++ GL ++QD+ YG I + DK+ N KG+ F+ FD + A++ +
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 161 -NPKQVICGKEVDVKRVK 177
V + K
Sbjct: 67 LK------ASGVQAQMAK 78
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 77.1 bits (190), Expect = 4e-18
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
+++ L+ N E + D +YGEVE + I P T + G A V FT+ ++ V
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 73 DL 74
+L
Sbjct: 67 NL 68
Score = 58.9 bits (143), Expect = 1e-11
Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 1/74 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ L + E ++D +YG + E + G + F A++ + N
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 162 P-KQVICGKEVDVK 174
+ G + +
Sbjct: 68 LHLTSVMGNIIHAQ 81
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 76.9 bits (190), Expect = 4e-18
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
+ GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+
Sbjct: 10 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 63 VTFTT----QKAVDDL 74
V + T Q A++ L
Sbjct: 70 VEYETYKEAQAAMEGL 85
Score = 58.8 bits (143), Expect = 1e-11
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++ A+
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 76.4 bits (189), Expect = 4e-18
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
G + L+VG LH N E + F +G++++I + D TG+S+G+ F+TF+
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 68 QKAVDDL 74
++A++ L
Sbjct: 61 RRALEQL 67
Score = 56.8 bits (138), Expect = 7e-11
Identities = 18/60 (30%), Positives = 26/60 (43%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++VG L I+E +R F +G I D KG+ FI+F D A + L
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
>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 = 76.6 bits (189), Expect = 4e-18
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ + +F+ L ++ E+ + + Q+G+++ + + P T S+G AF F TQ+A
Sbjct: 12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71
Query: 73 DLLAAGDH 80
LAA
Sbjct: 72 KCLAAASL 79
Score = 60.4 bits (147), Expect = 5e-12
Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL- 159
+F+ L+ + E+ + + Q+G + + KG F F Q A++ L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 160 -ANPKQVICGKEVDVKRVKFNP 180
A+ + G ++D +++K +
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDL 97
>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 = 76.5 bits (189), Expect = 5e-18
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++GP +D + V L +T E ++ + F +G + I + D TGQS+GFAF
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 63 VTFTT----QKAVDDL 74
++F +A+ +
Sbjct: 62 ISFHRREDAARAIAGV 77
Score = 56.8 bits (138), Expect = 7e-11
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
I V L+ + E D+++ F +GSI+ DK+ KGF FISF + A +
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
>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 = 77.0 bits (190), Expect = 5e-18
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
+ GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+
Sbjct: 9 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68
Query: 63 VTFTT----QKAVDDL 74
V + T Q A++ L
Sbjct: 69 VEYETYKEAQAAMEGL 84
Score = 57.8 bits (140), Expect = 6e-11
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++ A+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
>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 = 75.6 bits (187), Expect = 6e-18
Identities = 18/62 (29%), Positives = 34/62 (54%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D +G +GFA++ F+ +++V
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 75 LA 76
LA
Sbjct: 65 LA 66
Score = 56.4 bits (137), Expect = 7e-11
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
I+VG + + +++ +F GS+ DK KGF +I F D+ LA
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
>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 = 76.2 bits (188), Expect = 7e-18
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+ KLF+GGL+R T EK + F ++G + + + D T +SRGFAF+TF +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKN 63
Query: 74 LLAAGD-HYIGNKKIDPKRVTKR 95
+ + K I ++ K
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAKKP 86
Score = 62.3 bits (152), Expect = 1e-12
Identities = 25/105 (23%), Positives = 50/105 (47%), Gaps = 2/105 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+F+GGL E +E+ ++ F ++G I+E D++ + +GF FI+F++ A+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKNAAK 66
Query: 161 NP-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAY 204
+ + + GK + V++ K G + R S +
Sbjct: 67 DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111
>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 = 76.3 bits (188), Expect = 8e-18
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D+R ++VG + + +++ +FS G + I+I D +G +G+A++ F + +VD
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 75 LAAGDHYIGNK--KIDPKR 91
+A + + K+ PKR
Sbjct: 95 VAMDETVFRGRTIKVLPKR 113
Score = 59.7 bits (145), Expect = 1e-11
Identities = 23/86 (26%), Positives = 40/86 (46%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K ++VG + + QD+ +FS GSI DK KG+ +I F ++N + +
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 160 ANPKQVICGKEVDVKRVKFNPETMGS 185
A + V G+ + V + N + S
Sbjct: 96 AMDETVFRGRTIKVLPKRTNMPGISS 121
>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 = 75.8 bits (187), Expect = 1e-17
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++GP RN + ++VGGL E + + F Q G V + + D TGQ +G+ F
Sbjct: 2 SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61
Query: 63 VTFTT----QKAVDDL 74
V F + A+ +
Sbjct: 62 VEFLSEEDADYAIKIM 77
Score = 53.4 bits (129), Expect = 1e-09
Identities = 15/62 (24%), Positives = 29/62 (46%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++VGGL ++SE + + F Q G + P D+ +G+ F+ F + A+ +
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 160 AN 161
Sbjct: 75 KI 76
>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 = 77.2 bits (190), Expect = 1e-17
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ L V L T + F +YG V + I D +T +SRGFAFV
Sbjct: 58 SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117
Query: 64 TFTT----QKAVDDL 74
F + A+D +
Sbjct: 118 RFHDKRDAEDAMDAM 132
Score = 57.2 bits (138), Expect = 2e-10
Identities = 26/119 (21%), Positives = 39/119 (32%), Gaps = 20/119 (16%)
Query: 58 RGFAFVTFTTQKAVDDLLA--AGDHYIGNKKIDPKRVTKRVNPLK--------------- 100
G TT +AVD A Y + +D +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 101 ---CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ V LT S +R F +YG + + P D+ +GF F+ F D+ AE
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 75.1 bits (185), Expect = 1e-17
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ + + +T I S Y V +I + D T Q+RGFAFV ++ L
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
L KID K + V+
Sbjct: 70 LQILQSLHPPLKIDGKTI--GVD 90
Score = 58.9 bits (143), Expect = 1e-11
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 7/79 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
I + + + S Y ++ + DK +GF F+ A Q+L
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 160 AN-----PKQVICGKEVDV 173
P I GK + V
Sbjct: 71 QILQSLHPPLKIDGKTIGV 89
>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 = 74.5 bits (184), Expect = 2e-17
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKND-PHTGQSRGFAFVTFTT----QKAVD 72
K+ +G L RN + I + FS YG+++ I + + H S+G+A+V F +KA+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 73 DL 74
+
Sbjct: 66 HM 67
Score = 57.9 bits (141), Expect = 2e-11
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVL 159
K+ +G LT +++ + + FS YG I P ++ KG+ ++ F++ + AE+ L
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 160 A--NPKQVICGKEVDVKRVK 177
+ Q I G+E+ V
Sbjct: 65 KHMDGGQ-IDGQEITATAVL 83
>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 = 74.6 bits (184), Expect = 3e-17
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 1 MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
MA G +L+VG LH N E + F +G +ESI + D TG+S+G+
Sbjct: 11 MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70
Query: 61 AFVTFTT----QKAVDDL 74
F+TF+ +KA++ L
Sbjct: 71 GFITFSDSECAKKALEQL 88
Score = 55.0 bits (133), Expect = 4e-10
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+++VG L I+E +R F +G I Q D KG+ FI+F D A++ L
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 161 N 161
Sbjct: 87 Q 87
>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 = 74.6 bits (184), Expect = 3e-17
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A V + T
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 68 ---QKAVDDL 74
A + L
Sbjct: 79 KQALAAKEAL 88
Score = 58.8 bits (143), Expect = 2e-11
Identities = 12/60 (20%), Positives = 23/60 (38%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FV + E E ++++ F YG I D+ KG+ + ++ A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
>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 = 75.3 bits (185), Expect = 6e-17
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 63 VTFTT----QKAVDDL 74
V + T A + L
Sbjct: 119 VEYETHKQALAAKEAL 134
Score = 57.9 bits (140), Expect = 1e-10
Identities = 12/56 (21%), Positives = 23/56 (41%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+FV + E E ++++ F YG I D+ KG+ + ++ A
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
>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 = 73.4 bits (181), Expect = 6e-17
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
G + +LFV L + E+++ FS YG + + D T + +GFAFVTF
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 68 -QKAVDDL 74
KA ++
Sbjct: 63 AVKAYAEV 70
Score = 55.7 bits (135), Expect = 2e-10
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++FV L+ SE+D+ FS YG ++E P D KGF F++F A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 74.6 bits (183), Expect = 9e-17
Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 3/98 (3%)
Query: 1 MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIK--NDPHTGQSR 58
T RN ++VG T ++++ G + + +K + GQS+
Sbjct: 40 KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99
Query: 59 GFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
G+A V ++ +V LL + +K+D + T++
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
Score = 54.9 bits (132), Expect = 1e-09
Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGS--ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++VG + ++Q + G + E + +++ KG+ + +N ++L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 160 AN-PKQVICGKEVDVK 174
P +V+ G++VDV+
Sbjct: 117 ELLPGKVLNGEKVDVR 132
>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 = 73.6 bits (181), Expect = 1e-16
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 1 MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
+ P + R L V + E ++ F +YG +ES+ I D T QSRG+
Sbjct: 27 QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 61 AFVTFTT----QKAVDDL 74
FV F + Q+A+ L
Sbjct: 87 GFVKFQSGSSAQQAIAGL 104
Score = 54.8 bits (132), Expect = 1e-09
Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 8/98 (8%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
++ P + + V + T + E +R F +YG I + D+ +G
Sbjct: 26 QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85
Query: 144 FCFISFDDQNVAEQVLA--NPKQVICGKEVDVKRVKFN 179
+ F+ F + A+Q +A N G + KR+K
Sbjct: 86 YGFVKFQSGSSAQQAIAGLN------GFNILNKRLKVA 117
>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 = 72.3 bits (178), Expect = 2e-16
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH-TGQSRGFAF 62
+ P + K+ V + ++EI + FS +GE++++ + TG RGF F
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 63 VTFTT----QKAVDDL 74
V F T +KA + L
Sbjct: 63 VDFITKQDAKKAFNAL 78
Score = 53.8 bits (130), Expect = 1e-09
Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 4/81 (4%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQV 158
KI V + + +++++R+ FS +G + + P + +GF F+ F + A++
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 159 LANPKQVICGKEVDVKRVKFN 179
+ +R+
Sbjct: 75 FNALCH---STHLYGRRLVLE 92
>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 = 71.9 bits (177), Expect = 2e-16
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQK 69
R +FVG + E+++ D FS+ G V S + D TG+ +G+ F + T
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 70 AVDDL 74
A+ +L
Sbjct: 66 AMRNL 70
Score = 59.2 bits (144), Expect = 1e-11
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG + E +E+ ++D FS+ G + F+ +D+ KG+ F + DQ A + N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
>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 = 71.4 bits (176), Expect = 3e-16
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---QKAVDD 73
R ++VG L + +++ + FSQ+G+V ++ + D T + +GF FV +A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 74 L 74
L
Sbjct: 62 L 62
Score = 52.6 bits (127), Expect = 2e-09
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
I+VG L + + V++ FSQ+G + + +D+ KGF F+ ++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE 53
>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 = 71.5 bits (176), Expect = 3e-16
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKA 70
+RKLFVG L++ E+++ F +G ++ ++ P G S+G AFV F++ Q A
Sbjct: 14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAA 72
Query: 71 VDDL 74
+ L
Sbjct: 73 IHAL 76
Score = 55.4 bits (134), Expect = 3e-10
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
++ K+FVG L + SE+DV F +G I E + KG F+ F
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSH 66
Query: 153 NVAEQVLA--NPKQVI--CGKEVDVK 174
A+ + + Q + + VK
Sbjct: 67 TEAQAAIHALHGSQTMPGASSSLVVK 92
>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 = 70.4 bits (173), Expect = 7e-16
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 1/88 (1%)
Query: 8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
G LF+G L+ N E+ S+ +++ D TG +R F +V F +
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFES 67
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ ++ L + +I ++ R
Sbjct: 68 AEDLEKALELTGLKVFGNEIKLEKPKGR 95
Score = 49.6 bits (119), Expect = 3e-08
Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 1/77 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+F+G L S +++ S+ + + D + F ++ F+ E+ L
Sbjct: 18 FNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE 76
Query: 161 NPKQVICGKEVDVKRVK 177
+ G E+ +++ K
Sbjct: 77 LTGLKVFGNEIKLEKPK 93
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 70.2 bits (172), Expect = 9e-16
Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 1/73 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
R +++ G + +I ++ G+V +I ++ H +G FV F + ++
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKF 68
Query: 75 LAAGDHYIGNKKI 87
+ +
Sbjct: 69 VETPGQKYKETDL 81
Score = 66.7 bits (163), Expect = 2e-14
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+++ G T+ + D++++ G + Q K KG F+ FD A++ +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVET 71
Query: 162 PKQVICGKEVDVKR 175
P Q ++ +
Sbjct: 72 PGQKYKETDLLILF 85
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 69.6 bits (171), Expect = 1e-15
Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ ++ KLF+ GL + ++E+ + +G V+ + + + G+ +G A+V
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYV 63
Query: 64 TFTT----QKAVDDL 74
+ +AV +
Sbjct: 64 EYENESQASQAVMKM 78
Score = 56.9 bits (138), Expect = 6e-11
Identities = 10/62 (16%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K K+F+ GL +++++ + +G++ + + +++ KG ++ +++++ A Q +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQAV 75
Query: 160 AN 161
Sbjct: 76 MK 77
>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 = 72.0 bits (176), Expect = 2e-15
Identities = 25/186 (13%), Positives = 51/186 (27%), Gaps = 45/186 (24%)
Query: 15 DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
D L V GL + + F YG VE + G A V AVD
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57
Query: 74 LLAAGDHY-IGNKKID--------------------------------------PKRVTK 94
+ ++ + +K++ +
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117
Query: 95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
R+ + E++E++ + + G K+ + + +D ++
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177
Query: 155 AEQVLA 160
A + L
Sbjct: 178 ALETLG 183
Score = 55.9 bits (134), Expect = 1e-09
Identities = 9/77 (11%), Positives = 22/77 (28%), Gaps = 1/77 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK-AVDDLLAA 77
L E+ + + G S+K + + + ++ A++ L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 78 GDHYIGNKKIDPKRVTK 94
+ + N K
Sbjct: 186 NHYQMKNPNGPYPYTLK 202
Score = 41.2 bits (96), Expect = 1e-04
Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ V GL ++ V + F YG++ + + K G + D ++ +
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59
Query: 160 AN 161
+
Sbjct: 60 TH 61
>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 = 69.2 bits (170), Expect = 2e-15
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 16 FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTAD 74
Query: 63 VTFTT----QKAVDDL 74
V F KA+
Sbjct: 75 VHFERKADALKAMKQY 90
Score = 45.0 bits (107), Expect = 1e-06
Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K+ V L +S+ D+++ F+++G++ + +D+S G + F+ + A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALK 85
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 68.5 bits (168), Expect = 5e-15
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
R + ++ ++L V + + ++ F Q+G++ + I + S+GF FV
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFV 74
Query: 64 TFTT----QKAVDDL 74
TF +A + L
Sbjct: 75 TFENSADADRAREKL 89
Score = 51.2 bits (123), Expect = 1e-08
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ V + + D+R F Q+G I + + F++ KGF F++F++ A++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 162 PKQVICGKEVDVKRVKFN 179
+ G V+ ++++ N
Sbjct: 89 ----LHGTVVEGRKIEVN 102
>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 = 68.7 bits (168), Expect = 5e-15
Identities = 17/102 (16%), Positives = 40/102 (39%), Gaps = 9/102 (8%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--PFDKSKNMKKGFCFISFDDQNVAE- 156
C++F+GG+ +++ + ++ K +GF F+ ++ A
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 157 --QVLANPKQVICGKEVDVK----RVKFNPETMGSVSGAVRG 192
+ L + + G ++ V + + + M +VSG G
Sbjct: 68 ARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSSG 109
Score = 64.8 bits (158), Expect = 1e-13
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 10/87 (11%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDP-HTGQSRGFAFVTFTTQKAVD 72
+LF+GG+ + +EI + ++ E V + + ++RGFAFV + + +A
Sbjct: 7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66
Query: 73 D---LLAAGDHYIGNKKI-----DPKR 91
L G + +I +P+
Sbjct: 67 MARRKLMPGRIQLWGHQIAVDWAEPEI 93
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 68.0 bits (167), Expect = 5e-15
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
L++G L T ++++ + G ++ I + GQS+GFA V ++ + L+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 76 AA 77
Sbjct: 63 DL 64
Score = 49.5 bits (119), Expect = 2e-08
Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+++G LT +++D+ + G I E + +++ KGF + + +++++
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 160 A 160
Sbjct: 63 D 63
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 68.0 bits (167), Expect = 5e-15
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
G + ++FV L + K + D F++ G V IK + G+S+G V F +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 68 ---QKAVDDL 74
++A +
Sbjct: 59 EVAERACRMM 68
Score = 46.8 bits (112), Expect = 2e-07
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
C+IFV L + + + ++D F++ G + + K+ KG + F+ VAE+
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKS--KGCGVVKFESPEVAER 63
>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 = 67.6 bits (166), Expect = 6e-15
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+FVG L I F+ +G + + D TG+S+G+ FV+F + ++ +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 78 -GDHYIGNKKIDPKRVTKRVN 97
G ++G ++I R N
Sbjct: 68 MGGQWLGGRQI-------RTN 81
Score = 51.0 bits (123), Expect = 6e-09
Identities = 17/59 (28%), Positives = 32/59 (54%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FVG L+ EI+ + F+ +G I++ + D + KG+ F+SF ++ AE +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>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 = 67.7 bits (166), Expect = 8e-15
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
++G +R +FVG L E+ + + F Q G + ++I D G+ + F FV
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVC 63
Query: 65 FTT----QKAVDDL 74
F A+ L
Sbjct: 64 FKHPESVSYAIALL 77
Score = 50.3 bits (121), Expect = 1e-08
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+FVG L + E+ + + F Q G +T+ D+ K F F+ F
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 67.7 bits (166), Expect = 8e-15
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
++ ++L V + + ++ F Q+G++ + I + S+GF FVTF
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSAD 67
Query: 68 -QKAVDDL 74
+A + L
Sbjct: 68 ADRAREKL 75
Score = 52.7 bits (127), Expect = 2e-09
Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
++ V + + D+R F Q+G I + + F++ + KGF F++F++ A+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADAD 69
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 67.1 bits (165), Expect = 9e-15
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
LFVG L+ N ++ + + F + S + D TG SRG+ FV+FT+Q + + +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 78 GD-HYIGNKKIDPKRVTKRVN 97
+ + + R+N
Sbjct: 63 MQGQDLNGRPL-------RIN 76
Score = 52.9 bits (128), Expect = 1e-09
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+FVG L + ++ +R+ F + S +D +G+ F+SF Q+ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 69.5 bits (170), Expect = 9e-15
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTA 132
Query: 62 FVTFTT----QKAVDDL 74
V F KA+
Sbjct: 133 DVHFERRADALKAMKQY 149
Score = 45.6 bits (108), Expect = 2e-06
Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K+ V L +S+ D+++ F+++G++ + +D+S G + F+ + A +
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALK 144
>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 = 68.2 bits (167), Expect = 1e-14
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 22 FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTAD 80
Query: 63 VTFTT----QKAVDDL 74
V F KA+
Sbjct: 81 VHFERRADALKAMKQY 96
Score = 45.1 bits (107), Expect = 2e-06
Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K+ V L +S+ D+++ F+++G++ + +D+S G + F+ + A +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALK 91
>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 = 66.8 bits (164), Expect = 1e-14
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKA 70
G + +F+G L EK + D FS +G + ++ I DP TG S+G+AF+ F + A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 71 VDDLLAAGD-HYIGNKKIDPKRVTKRVNP 98
D + A + Y+ N+ I V+
Sbjct: 61 SDAAIEAMNGQYLCNRPI-------TVSY 82
Score = 51.8 bits (125), Expect = 4e-09
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKGFCFISFDDQNVAEQVLA 160
IF+G L EI E+ + D FS +G I + + D KG+ FI+F + ++ +
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 161 NPK-QVICGKEVDV 173
Q +C + + V
Sbjct: 67 AMNGQYLCNRPITV 80
>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 = 66.9 bits (164), Expect = 2e-14
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ---SRGFAFVTFTT- 67
G + LF+ L+ +T E+ + FS+ G ++S +I + S GF FV +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 68 ---QKAVDDL 74
QKA+ L
Sbjct: 61 EQAQKALKQL 70
Score = 48.4 bits (116), Expect = 8e-08
Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK---KGFCFISFDDQNVAEQ 157
+F+ L +E+ ++ FS+ G+I K+K GF F+ + A++
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 158 VLAN-PKQVICGKEVDVKR 175
L + G +++V+
Sbjct: 66 ALKQLQGHTVDGHKLEVRI 84
>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 = 66.1 bits (162), Expect = 3e-14
Identities = 11/77 (14%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ + + L + L + E+ + + F + ++ G+S+G+A
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYA 56
Query: 62 FVTFTT----QKAVDDL 74
F+ F + ++A++
Sbjct: 57 FIEFASFEDAKEALNSC 73
Score = 48.8 bits (117), Expect = 5e-08
Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ + L+ +E+ +++ F + I Q KS KG+ FI F A++ L
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS----KGYAFIEFASFEDAKEALN 71
Query: 161 NPKQVICGKEVDVKRVKFNPET 182
+ +E++ + ++ +
Sbjct: 72 S----CNKREIEGRAIRLELQG 89
>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 = 68.8 bits (168), Expect = 3e-14
Identities = 31/200 (15%), Positives = 59/200 (29%), Gaps = 52/200 (26%)
Query: 19 LFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
L V L+ + + F YG+V+ + I + + A V Q A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 74 L---------------------------------LAAGDHYIGNKKIDPKRVTKRVNPLK 100
L G+ + K + + + P
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ + + +SE+D++ FS G + + + F K + I A Q L
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 176
Query: 161 --NPKQVICGKEVDVKRVKF 178
+ + + RV F
Sbjct: 177 DLHNHDLGENHHL---RVSF 193
Score = 41.4 bits (97), Expect = 9e-05
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ V L E ++ Q + F YG + + F+K K + D N A+ +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58
Query: 160 ANPK-QVICGKEVDVKRVK 177
++ + GK + + K
Sbjct: 59 SHLNGHKLHGKPIRITLSK 77
>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 = 66.2 bits (162), Expect = 3e-14
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
GP N++ +++VG L + K+I D F +YG + I +KN FAFV
Sbjct: 10 GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFV 66
Query: 64 TFTT----QKAVDDL 74
F + AV
Sbjct: 67 EFEDPRDAEDAVYGR 81
Score = 56.6 bits (137), Expect = 1e-10
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
C+I+VG L +I +D+ D F +YG+I + + F F+ F+D AE
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAE 75
>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 = 65.8 bits (161), Expect = 5e-14
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 7 GTAGPGRN-----DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
G++G + +FVG L ++I F+ +G + + D TG+S+G+
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 62 FVTFTT----QKAVDDL 74
FV+F + A+ +
Sbjct: 61 FVSFFNKWDAENAIQQM 77
Score = 52.0 bits (125), Expect = 6e-09
Identities = 18/56 (32%), Positives = 34/56 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+FVG L+ EI+ +D++ F+ +G I++ + D + KG+ F+SF ++ AE
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
>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 = 65.4 bits (160), Expect = 7e-14
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
+ L++ L E+++ F+++ E + I+ TG+ RG AF+TF +A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 73 DL 74
+
Sbjct: 86 LV 87
Score = 53.1 bits (128), Expect = 2e-09
Identities = 11/57 (19%), Positives = 27/57 (47%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+++ L+ ++E+D+ F+++ F +G FI+F ++ +A Q
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
>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 = 65.0 bits (159), Expect = 7e-14
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKA 70
R L L N E E+ + F E+ + G+S+G A++ F + +K
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKN 69
Query: 71 VDDL 74
+++
Sbjct: 70 LEEK 73
Score = 48.0 bits (115), Expect = 1e-07
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 5/60 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ L+ I+E ++++ F I KG +I F + AE+ L
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72
>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 = 65.6 bits (160), Expect = 1e-13
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QK 69
L+VG L T E++I + FS+ G+++ I + D + GF FV + + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 70 AVDDL 74
A+ +
Sbjct: 97 AMRYI 101
Score = 57.1 bits (138), Expect = 2e-10
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
C ++VG L+ +E+ + + FS+ G I + DK K GFCF+ + + AE +
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 161 NPKQVICGKEVD 172
I G +D
Sbjct: 100 Y----INGTRLD 107
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
LF+ L + G++++ F +G V S + D T S+ F FV++ Q A+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 74 LLAAGDHYIGNKKI 87
+ IG K++
Sbjct: 87 M---NGFQIGMKRL 97
Score = 48.5 bits (116), Expect = 1e-07
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 94 KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
++ P +F+ L E +QD+ F +G++ + DK N+ K F F+S+D+
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 154 VAEQVLA--NPKQVICGKEVDVKRVKFN 179
A+ + N G ++ +KR+K
Sbjct: 79 SAQAAIQSMN------GFQIGMKRLKVQ 100
>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 = 67.1 bits (163), Expect = 2e-13
Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFA 61
A L++G L T ++++ + G ++ I + GQS+GFA
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115
Query: 62 FVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
V ++ + L+ + + V K+
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150
Score = 62.4 bits (151), Expect = 7e-12
Identities = 25/162 (15%), Positives = 53/162 (32%), Gaps = 8/162 (4%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+++G LT +++D+ + G I E + +++ KGF + + +++++
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 160 AN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTY 218
PK+ + G+ V N + + R +G A PG
Sbjct: 130 DLLPKRELHGQNPVVT--PVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGG---SSRAA 184
Query: 219 AGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYG 260
G G+ +PA T +
Sbjct: 185 FPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHH 226
>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 = 64.2 bits (157), Expect = 2e-13
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
A D L++ L + E+E+ + +G+V S I D +G SRG F +
Sbjct: 18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMEST 76
Query: 68 ---QKAVDDL 74
+ +
Sbjct: 77 EKCEAVIGHF 86
Score = 48.0 bits (115), Expect = 1e-07
Identities = 16/101 (15%), Positives = 32/101 (31%), Gaps = 9/101 (8%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
++ K+ +++ L + EQ++ + +G + + D S +G
Sbjct: 10 ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGV 68
Query: 145 CFISFDDQNVAEQVLA--NPKQVICGKEVDV-----KRVKF 178
F + E V+ N K I KF
Sbjct: 69 GFARMESTEKCEAVIGHFNGKF-IKTPPGVSAPTEPLLCKF 108
>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 = 63.5 bits (155), Expect = 2e-13
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQ 56
+ +D +FV GL N + + DYF Q G +++ I++ D TG+
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
Query: 57 SRGFAFVTFTTQKAVD 72
+G A V+F +
Sbjct: 62 LKGEATVSFDDPPSAK 77
Score = 54.2 bits (131), Expect = 7e-10
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
IFV GL ++ + V DYF Q G I ++ D+ KG +SFDD
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 154 VAE 156
A+
Sbjct: 75 SAK 77
>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 = 63.5 bits (155), Expect = 2e-13
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFV 63
++G++G + L++G L E I+ F+ GE V S+ I + TG G+ FV
Sbjct: 2 SSGSSGMAAS----LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57
Query: 64 TFTTQKAVDDLLAA 77
F + L
Sbjct: 58 EFADLATAEKCLHK 71
Score = 52.3 bits (126), Expect = 3e-09
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ + +++G L + E + F+ G ++ + ++ + G+CF+ F D A
Sbjct: 6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65
Query: 156 EQVLANPK-QVICGKEVDVKRVKFN 179
E+ L + + G KR K N
Sbjct: 66 EKCLHKINGKPLPGATP-AKRFKLN 89
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 63.9 bits (156), Expect = 3e-13
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
LF+ L + + ++ F +G V S + D T S+ F FV+F Q A+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 74 LLAAGDHYIGNKKI 87
+ +G K++
Sbjct: 102 M---NGFQVGTKRL 112
Score = 47.7 bits (114), Expect = 2e-07
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P C +F+ L E ++ D+ F +G++ + DK ++ K F F+SFD+ + A+
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 158 VLA--NPKQVICGKEVDVKRVK 177
+ N G +V KR+K
Sbjct: 98 AIKAMN------GFQVGTKRLK 113
>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 = 63.8 bits (156), Expect = 3e-13
Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 17/118 (14%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G G G +F+ L ++ K + D FS +G + S + D S+G+ FV F
Sbjct: 1 GPLGSG-----NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFE 53
Query: 67 TQKAVDDLLAAGD-HYIGNKKI---------DPKRVTKRVNPLKCKIFVGGLTTEISE 114
TQ+A + + + + ++K+ + + +++ +
Sbjct: 54 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111
Score = 53.4 bits (129), Expect = 2e-09
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
IF+ L I + + D FS +G+I + D++ + KG+ F+ F+ Q AE+ +
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIE 63
Query: 161 --NPKQVICGKEVDVKRVKFNPETMGSVSG 188
N ++ ++V V R K E +
Sbjct: 64 KMN-GMLLNDRKVFVGRFKSRKEREAELGA 92
>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 = 63.0 bits (154), Expect = 4e-13
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 15/77 (19%)
Query: 7 GTAGPGRNDER-----KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
G++G ++ +LFVG L + E+E+ F +YG+ + I D +GF
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54
Query: 62 FVTFTT----QKAVDDL 74
F+ T + A +L
Sbjct: 55 FIRLETRTLAEIAKVEL 71
Score = 57.3 bits (139), Expect = 4e-11
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++FVG L +I+E+++R F +YG E D KGF FI + + +AE
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 66
>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 = 62.4 bits (152), Expect = 9e-13
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
R L++ L +E+ D F +YG + I + N T ++RG A+V + + AVD
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65
Query: 73 DL 74
L
Sbjct: 66 HL 67
Score = 52.0 bits (125), Expect = 6e-09
Identities = 10/55 (18%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+++ L +I+ +++ D F +YG I + + +G ++ ++D A+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE---TRGTAYVVYEDIFDAKN 62
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 61.5 bits (149), Expect = 1e-12
Identities = 19/105 (18%), Positives = 35/105 (33%), Gaps = 16/105 (15%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYF-----SQYGEVESISIKNDPHTGQSRGFAFV 63
G + + V GL ++ + YF S G V S + +
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVL 52
Query: 64 TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGL 108
TF + +LA DH + ++ + R ++ + GL
Sbjct: 53 TFREPADAERVLAQADHELHGAQLSLRPAPPRAP---ARLLLQGL 94
Score = 59.2 bits (143), Expect = 1e-11
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 13/82 (15%)
Query: 101 CKIFVGGLTTEISEQDVRDYF-----SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ V GL + ++ + YF S G + +Q+ ++F + A
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL--------GCGGVLTFREPADA 60
Query: 156 EQVLANPKQVICGKEVDVKRVK 177
E+VLA + G ++ ++
Sbjct: 61 ERVLAQADHELHGAQLSLRPAP 82
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 61.6 bits (150), Expect = 2e-12
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFT 66
D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V+F
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 67 TQKAVD 72
+
Sbjct: 66 DPPSAK 71
Score = 52.0 bits (125), Expect = 5e-09
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
IFV GL ++ + V DYF Q G I ++ D+ KG +SFDD
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 154 VAE 156
A+
Sbjct: 69 SAK 71
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 61.5 bits (150), Expect = 2e-12
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K++VG L G+ E+ FS YG + ++ I +P GFAFV F + +D +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 78 GDHYIGNKKIDPKRVTKRVN 97
D K I RV RV
Sbjct: 57 LD----GKVICGSRV--RVE 70
Score = 55.0 bits (133), Expect = 3e-10
Identities = 26/101 (25%), Positives = 38/101 (37%), Gaps = 6/101 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K++VG L T + ++ FS YG + + GF F+ F+D AE +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 162 P-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
+VICG V V+ P R V G
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNG 97
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++G R L+VG L R+ E I FSQ G +S + + + + F
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCF 59
Query: 63 VTFTT----QKAVDDL 74
V F A+ +
Sbjct: 60 VEFYEHRDAAAALAAM 75
Score = 52.3 bits (126), Expect = 4e-09
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++VG L+ +++E + FSQ G + + + N +CF+ F + A LA
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74
>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 = 61.1 bits (149), Expect = 2e-12
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 8/67 (11%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G KL VG + +E+ F +YG V I + +AFV
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHME 52
Query: 67 TQKAVDD 73
+ +
Sbjct: 53 RAEDAVE 59
Score = 55.3 bits (134), Expect = 2e-10
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+ VG ++ + Q++R F +YG + E + K + F+ + A + +
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECD--------IVKDYAFVHMERAEDAVEAIR 62
Query: 161 N-PKQVICGKEVDV 173
GK + V
Sbjct: 63 GLDNTEFQGKRMHV 76
>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 = 61.6 bits (150), Expect = 2e-12
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++G + +FV L G K++ + FS G V I D G+SRG
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGT 60
Query: 63 VTFTT----QKAVDDL 74
VTF +A+
Sbjct: 61 VTFEQSIEAVQAISMF 76
Score = 45.8 bits (109), Expect = 1e-06
Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 4/87 (4%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
L +FV L ++ + +++ FS G + DK +G ++F+ A
Sbjct: 12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAV 70
Query: 157 QVLA--NPKQVICGKEVDVKRVKFNPE 181
Q ++ N Q++ + + VK +
Sbjct: 71 QAISMFN-GQLLFDRPMHVKMDERALP 96
>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 = 65.6 bits (159), Expect = 2e-12
Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 4/95 (4%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
+ + + + LFV ++ +T E ++ F YG ++ I + +G+ RG+AF
Sbjct: 89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
Query: 63 VTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
+ + ++ D+ +A H KKID +RV V
Sbjct: 149 IEYEHER---DMHSAYKH-ADGKKIDGRRVLVDVE 179
Score = 53.7 bits (128), Expect = 2e-08
Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 1/88 (1%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
K DP +FV + + +E +R F YG I + K +G+
Sbjct: 87 KMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Query: 145 CFISFDDQNVAEQVLANPKQV-ICGKEV 171
FI ++ + + I G+ V
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRV 174
>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 = 60.4 bits (147), Expect = 2e-12
Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 7 GTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
G++G D+ L+VGGL E ++ ++F Q+GE+ +I++ + AF+
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54
Query: 65 FTT----QKAVDDLLAAGDHYIGNKKI 87
F T + A + + +++
Sbjct: 55 FATRQAAEVAAEKSF--NKLIVNGRRL 79
Score = 59.6 bits (145), Expect = 5e-12
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ ++VGGL I+E D+R++F Q+G I + FI F + AE
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAE 62
Query: 157 QVLANP--KQVICGKEVDVK 174
K ++ G+ ++VK
Sbjct: 63 VAAEKSFNKLIVNGRRLNVK 82
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 60.5 bits (147), Expect = 3e-12
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-- 67
P R RKL + + + + ++ QYG VES N VT+++
Sbjct: 9 VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKD 65
Query: 68 --QKAVDDLLAAGDHYIGNKKI 87
++A+D L + N +
Sbjct: 66 QARQALDKL---NGFQLENFTL 84
Score = 45.5 bits (108), Expect = 9e-07
Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K+ + + + + + QYG + +Q S + +++ ++ A Q
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQ 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 = 62.2 bits (151), Expect = 3e-12
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
+ K++VG L N + E+ F YG + S+ + +P GFAFV F +
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDA 123
Query: 72 DD 73
D
Sbjct: 124 AD 125
Score = 58.0 bits (140), Expect = 8e-11
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
PL CK++VG L ++ ++ F YG + + GF F+ F+D A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAA 124
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 60.4 bits (147), Expect = 3e-12
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 92 VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+ + P ++G + +E D+ F +G I +F+ + KG CFI +D
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDT 72
Query: 152 QNVAEQ 157
A
Sbjct: 73 HEQAAV 78
Score = 55.8 bits (135), Expect = 2e-10
Identities = 7/49 (14%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
++G + E ++ F +G + + +G F+ + T
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDT 72
>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 = 23/88 (26%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFV 63
+ A G+ + V + EI D+F Y + S+ +K + G G A V
Sbjct: 4 GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62
Query: 64 TFTT----QKAVDDLLAAGDHYIGNKKI 87
F + AV DL D IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87
Score = 46.1 bits (110), Expect = 5e-07
Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 1/81 (1%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P I V + +S ++ D+F Y I K M G ++F+ ++ A
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 158 VLAN-PKQVICGKEVDVKRVK 177
+ + + I ++V +
Sbjct: 73 AVIDLNDRPIGSRKVKLVLGS 93
>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 = 60.5 bits (147), Expect = 4e-12
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFT 66
D ++V GL+ + ++ D+F Q G V+ I I D TG+ +G A V++
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 67 TQKAVD 72
Sbjct: 74 DPPTAK 79
Score = 52.4 bits (126), Expect = 4e-09
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
I+V GL ++ D+ D+F Q G + ++ DK KG +S++D
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 154 VAE 156
A+
Sbjct: 77 TAK 79
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 60.0 bits (146), Expect = 4e-12
Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 91 RVTKRVNPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+ R + +K ++F+G L + +S++D+ FS YG I + N+K F FI F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQF 64
Query: 150 DDQNVAEQVLANP-KQVICGKEVDV 173
D+ + +++ GK++ +
Sbjct: 65 DNPQSVRDAIEXESQEMNFGKKLIL 89
Score = 55.8 bits (135), Expect = 2e-10
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 3 YRANGTAGPGRNDERKLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ ++G G + + +LF+G L +N ++++ FS YG + I+IK F
Sbjct: 9 HHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFG 60
Query: 62 FVTFTTQKAVDD 73
F+ F ++V D
Sbjct: 61 FIQFDNPQSVRD 72
>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 = 63.1 bits (153), Expect = 5e-12
Identities = 32/213 (15%), Positives = 59/213 (27%), Gaps = 52/213 (24%)
Query: 6 NGTAGPGRNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
G L V L+ + + F YG+V+ + I + + A V
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQ 78
Query: 65 FTT----QKAVDDL-----------------------------LAAGDHYIGNK----KI 87
Q A+ L Y + K
Sbjct: 79 MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ + + P + + + +SE+D++ FS G + + + F K + I
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALI 194
Query: 148 SFDDQNVAEQVLA--NPKQVICGKEVDVKRVKF 178
A Q L + + + RV F
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHL---RVSF 224
>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 = 59.6 bits (145), Expect = 6e-12
Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 12/72 (16%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G KL++G L ++ F G+AFV +
Sbjct: 1 GSSGSSGM--NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYP 52
Query: 67 T----QKAVDDL 74
+A++ L
Sbjct: 53 DQNWAIRAIETL 64
Score = 58.8 bits (143), Expect = 1e-11
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
K+++G L+ ++ D+R F P +K G+ F+ + DQN A + +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 161 -NPKQVICGKEVDVKRVK 177
+ K + GK ++V
Sbjct: 64 LSGKVELHGKIMEVDYSV 81
>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 = 60.0 bits (146), Expect = 6e-12
Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
K++ + V + +P C ++ GG+ + +++Q +R FS +G I E + + KG+
Sbjct: 10 KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGY 63
Query: 145 CFISFDDQNVAEQVLAN-PKQVICGKEVDVKRVKFNPET 182
F+ F A + + I G V K +P+
Sbjct: 64 SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 102
Score = 54.3 bits (131), Expect = 9e-10
Identities = 12/60 (20%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
++ GG+ ++ + FS +G++ I + + +G++FV F+T A+ +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
>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 = 59.5 bits (145), Expect = 7e-12
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
G + KLF+G L R E+EI F QYG+V I + + FV + A
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54
Query: 71 VDDLLAAGDHY 81
+D + HY
Sbjct: 55 AEDAIRNLHHY 65
Score = 58.0 bits (141), Expect = 2e-11
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+F+G L E +EQ++R F QYG + E + K + F+ +D+ AE +
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIR 60
Query: 161 N-PKQVICGKEVDV 173
N + G ++V
Sbjct: 61 NLHHYKLHGVNINV 74
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 15/77 (19%)
Query: 7 GTAGPGRNDE-----RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
G++G +++ + L+V L +T E+ I F+ +K + R +A
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYA 54
Query: 62 FVTFTT----QKAVDDL 74
FV F+ +A+ L
Sbjct: 55 FVHFSNREDAVEAMKAL 71
Score = 48.4 bits (116), Expect = 6e-08
Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 10/76 (13%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++V L SE+ + F+ + + + F+ F ++ A + +
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70
Query: 162 PKQVICGKEVDVKRVK 177
+ GK +D ++
Sbjct: 71 ----LNGKVLDGSPIE 82
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 59.2 bits (144), Expect = 1e-11
Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+VG L NT + +I+ F + S+ + D T + +GF +V F ++ + L
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 77 AGDHYIGNKKIDPKRVTKRVN 97
+G++ + RV+
Sbjct: 75 YDGALLGDRSL-------RVD 88
Score = 50.7 bits (122), Expect = 1e-08
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 1/72 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+VG L + D+ F I + DK + KGFC++ FD+ + ++ L
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 162 PKQVICGKEVDV 173
++ + + V
Sbjct: 76 DGALLGDRSLRV 87
>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 = 59.9 bits (145), Expect = 1e-11
Identities = 19/92 (20%), Positives = 38/92 (41%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
G+ ++ + + GL ++EI +FS V + G+ G AFV
Sbjct: 30 MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89
Query: 64 TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
F +Q+ + L IG++ I+ + ++
Sbjct: 90 QFASQELAEKALGKHKERIGHRYIEVFKSSQE 121
Score = 52.2 bits (125), Expect = 6e-09
Identities = 14/75 (18%), Positives = 32/75 (42%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ + GL +++++ +FS + + G F+ F Q +AE+ L
Sbjct: 43 GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102
Query: 161 NPKQVICGKEVDVKR 175
K+ I + ++V +
Sbjct: 103 KHKERIGHRYIEVFK 117
>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 = 58.9 bits (143), Expect = 1e-11
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFV 63
+ + G+ + V + EI D+F Y + S+ +K + G G A V
Sbjct: 4 GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62
Query: 64 TFTT----QKAVDDLLAAGDHYIGNKKI 87
F + AV DL D IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87
Score = 45.8 bits (109), Expect = 6e-07
Identities = 13/64 (20%), Positives = 25/64 (39%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P I V + +S ++ D+F Y I K M G ++F+ ++ A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 158 VLAN 161
+ +
Sbjct: 73 AVID 76
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 9/96 (9%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ + LFV GL +T E+ + + F I D TG S+GF
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFG 57
Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
FV F +++ A + + +ID +V ++
Sbjct: 58 FVDFNSEEDAKAAKEAME----DGEIDGNKV--TLD 87
Score = 42.6 bits (101), Expect = 9e-06
Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FV GL+ + +E+ +++ F + D+ KGF F+ F+ + A+
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 161 NPKQVICGKEVDVKRVKFN 179
+ E+D +V +
Sbjct: 73 A----MEDGEIDGNKVTLD 87
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 58.4 bits (142), Expect = 1e-11
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 9/67 (13%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G N K+FVG + +E+ F + G V + + +AFV
Sbjct: 1 GSSGSSGN-TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHME 51
Query: 67 TQKAVDD 73
+
Sbjct: 52 KEADAKA 58
Score = 57.6 bits (140), Expect = 3e-11
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
KIFVG ++ + Q++R F + G + E + K + F+ + + A+ +A
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECD--------VVKDYAFVHMEKEADAKAAIA 61
Query: 161 N-PKQVICGKEVDVKRVKFNPETMGSVSG 188
+ + GK ++V+ + G SG
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKKSGPSSG 90
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 20/90 (22%), Positives = 39/90 (43%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+ P ++ + + GL ++EI +FS V + G+S G AFV F
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64
Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+Q+ + L IG++ I+ + ++
Sbjct: 65 ASQEIAEKALKKHKERIGHRYIEIFKSSRA 94
Score = 55.1 bits (133), Expect = 3e-10
Identities = 14/75 (18%), Positives = 32/75 (42%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+ + GL S++++ +FS + + G F+ F Q +AE+ L
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 163 KQVICGKEVDVKRVK 177
K+ I + +++ +
Sbjct: 78 KERIGHRYIEIFKSS 92
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 11/88 (12%), Positives = 28/88 (31%), Gaps = 2/88 (2%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTT 67
G + + + + + + ++ + E ++ + D + GQ G A V F
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN-GQGLGQALVQFKN 66
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ + ++ VT
Sbjct: 67 EDDARKSERLHRKKLNGREAFVHVVTLE 94
Score = 53.2 bits (128), Expect = 2e-09
Identities = 18/113 (15%), Positives = 35/113 (30%), Gaps = 2/113 (1%)
Query: 89 PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
VN K + + I++ DV + + G +
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
F +++ A + ++ + G+E V V E M + G S+G
Sbjct: 64 FKNEDDARKSERLHRKKLNGREAFVHVV--TLEDMREIEKNPPAQGKSGPSSG 114
>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 = 58.4 bits (142), Expect = 2e-11
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
L+V L ++ + FS +G + S + + G+S+GF FV F++ KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 74 LLAAGDHYIGNKKI 87
+ + K +
Sbjct: 75 M---NGRIVATKPL 85
Score = 45.7 bits (109), Expect = 7e-07
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
++V L I ++ +R FS +G+IT + + ++ KGF F+ F A + +
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKAVT 73
Query: 161 --NPKQVICGKEVDV 173
N +++ K + V
Sbjct: 74 EMN-GRIVATKPLYV 87
>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 = 58.2 bits (141), Expect = 3e-11
Identities = 17/94 (18%), Positives = 41/94 (43%), Gaps = 2/94 (2%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ ++G P D+ + V G+ + E ++ D+F V+++ + D G++ G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNG 59
Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
V F + + + L + + ++ T+R
Sbjct: 60 LVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER 93
Score = 47.4 bits (113), Expect = 2e-07
Identities = 17/98 (17%), Positives = 31/98 (31%), Gaps = 4/98 (4%)
Query: 96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+NP + V G+ E DVRD+F + D G + F
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR-NNGNGLVKFLSPQDT 69
Query: 156 EQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
+ L + ++ + V+V + G +
Sbjct: 70 FEALKRNRMLMIQRYVEVSPA--TERQWVAAGGHITSG 105
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 58.1 bits (141), Expect = 3e-11
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
G +LFV + E E+N+ F +G ++ + I GFAFV F
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESA 78
Query: 68 QKAVDDL 74
KA++++
Sbjct: 79 AKAIEEV 85
Score = 51.9 bits (125), Expect = 5e-09
Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 11/90 (12%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ ++FV ++ E ++ + F +G + E + + GF F+
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFV 70
Query: 148 SFDDQNVAEQVLA--NPKQVICGKEVDVKR 175
F++ A + + + K + ++V
Sbjct: 71 EFEEAESAAKAIEEVHGKS-FANQPLEVVY 99
>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 = 58.7 bits (142), Expect = 3e-11
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTT 67
+ +++ GL K + D+F + VE SI I P+ G++ G FV F
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPN-GKATGEGFVEFRN 76
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ L Y+GN+ I +TK+
Sbjct: 77 EADYKAALCRHKQYMGNRFIQVHPITKK 104
Score = 53.3 bits (128), Expect = 3e-09
Identities = 17/99 (17%), Positives = 36/99 (36%), Gaps = 2/99 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+++ GL E + V D+F + + + G F+ F ++ + L
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 163 KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
KQ + + + V + + M +R S+G
Sbjct: 88 KQYMGNRFIQVHPI--TKKGMLEKIDMIRKRLQSGPSSG 124
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 57.8 bits (140), Expect = 3e-11
Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
+ +K + FS+ G+V ++ D TG+++GF FV + ++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 80 HYIGNKKIDPKRVTKRVNPLK 100
K++D + + +K
Sbjct: 76 ----GKRLD-LKHRLFLYTMK 91
Score = 45.9 bits (109), Expect = 5e-07
Identities = 11/58 (18%), Positives = 27/58 (46%)
Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ + ++ + FS+ G + + P D++ KGF F+ N A++++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 57.2 bits (139), Expect = 4e-11
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 98 PLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
P K ++F+G L + +S++D+ FS YG I + N+K F FI FD+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQFDNPQSVR 59
Query: 157 QVLANP-KQVICGKEVDV 173
+ +++ GK++ +
Sbjct: 60 DAIECESQEMNFGKKLIL 77
Score = 53.8 bits (130), Expect = 8e-10
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 15 DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+ +LF+G L +N ++++ FS YG + I+IK F F+ F ++V D
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRD 60
>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 = 56.9 bits (138), Expect = 8e-11
Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
F+G L + E+ I ++F + + + +GF + F ++ L+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 77 AGDHYIGNKKIDPKRVTKRVN 97
+ +GN++I RV+
Sbjct: 80 LNEESLGNRRI-------RVD 93
Score = 48.8 bits (117), Expect = 6e-08
Identities = 15/73 (20%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLA 160
F+G L +++E+ ++++F I+ + P + S + KGF + F+D + L+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 161 NPKQVICGKEVDV 173
++ + + + V
Sbjct: 80 LNEESLGNRRIRV 92
>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 = 56.2 bits (136), Expect = 1e-10
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G + + G N EK + ++ + V +I I + H G G+ FV F+
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAH-GNKTGYIFVDFS 58
Query: 67 TQKAVDDLLAAGDHYIGNKKI 87
++ V L Y+G + I
Sbjct: 59 NEEEVKQALKCNREYMGGRYI 79
Score = 44.2 bits (105), Expect = 2e-06
Identities = 14/83 (16%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ + G ++E++V ++ + + + K G+ F+ F ++ +Q L
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALKC 69
Query: 162 PKQVICGKEVDVKRVKFNPETMG 184
++ + G+ ++V R K + + G
Sbjct: 70 NREYMGGRYIEVFREK-SGPSSG 91
>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 = 56.1 bits (136), Expect = 1e-10
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 10 GPGRND-ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
G G+ + +L+VGGL NT + F ++G + +I FA++ + +
Sbjct: 10 GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESL 63
Query: 68 ---QKAVDDL 74
Q A +
Sbjct: 64 DAAQAACAKM 73
Score = 49.5 bits (119), Expect = 3e-08
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 7/63 (11%)
Query: 95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
+ NP ++VGGL S + F ++GSI F +I ++ +
Sbjct: 13 KANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDA 65
Query: 155 AEQ 157
A+
Sbjct: 66 AQA 68
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 97 NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ ++F+G L T + + DV FS+YG + ++ KG+ F+ + ++ A
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC--------SVHKGYAFVQYSNERHA 75
Query: 156 EQVLANP-KQVICGKEVDV 173
+ +V+ G+ +D+
Sbjct: 76 RAAVLGENGRVLAGQTLDI 94
Score = 52.4 bits (126), Expect = 3e-09
Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 13 RNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
++ ++F+G L+ + ++ FS+YG V S+ +G+AFV ++ ++
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHA 75
Query: 72 DDLLAAGDHY-IGNKKID 88
+ + + + +D
Sbjct: 76 RAAVLGENGRVLAGQTLD 93
>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 = 56.1 bits (136), Expect = 1e-10
Identities = 14/71 (19%), Positives = 30/71 (42%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
F+G L + E+ I ++F + + + +GF + F ++ L+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 77 AGDHYIGNKKI 87
+ +GNK+I
Sbjct: 76 LNEESLGNKRI 86
Score = 48.8 bits (117), Expect = 5e-08
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLA 160
F+G L +++E+ ++++F I+ + P + S + KGF + F+D + L+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 161 NPKQVICGKEVDV 173
++ + K + V
Sbjct: 76 LNEESLGNKRIRV 88
>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 = 55.4 bits (134), Expect = 3e-10
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
+ LFV L E+ + FSQ+G++E + + +AF+ F KA++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAME 63
Query: 73 DL 74
++
Sbjct: 64 EM 65
Score = 53.1 bits (128), Expect = 2e-09
Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FV L ++E+ + FSQ+G + + K + FI FD+++ A + +
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 64
Query: 162 -PKQVICGKEVDVKRVK 177
+ + G+ +++ K
Sbjct: 65 MNGKDLEGENIEIVFAK 81
>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 = 54.2 bits (131), Expect = 7e-10
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
A P +++ L+ + E ++ FS++G++ I + + + RG AFV
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVI 57
Query: 65 FTT----QKAVDDL 74
F A+ +
Sbjct: 58 FKEVSSATNALRSM 71
Score = 45.3 bits (108), Expect = 1e-06
Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 100 KCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
I++ L +I + +++ FS++G I + +S M+ G F+ F + + A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMR-GQAFVIFKEVSSA 64
Query: 156 EQVLANPK-QVICGKEVDV 173
L + + K + +
Sbjct: 65 TNALRSMQGFPFYDKPMRI 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 = 54.4 bits (131), Expect = 1e-09
Identities = 15/107 (14%), Positives = 40/107 (37%), Gaps = 9/107 (8%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN 139
++G + +R ++V G +++ +R FS +G+I +
Sbjct: 19 SHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP---- 72
Query: 140 MKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVKRVKFNPETMGS 185
+ F++++ A+Q +A + ++ V + P +
Sbjct: 73 --RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAA 117
Score = 51.3 bits (123), Expect = 1e-08
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 12/62 (19%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
L+V G + + FS +G + +S+ R AFVT+ +AV
Sbjct: 40 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVA 91
Query: 73 DL 74
+L
Sbjct: 92 EL 93
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 53.3 bits (128), Expect = 1e-09
Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 6/91 (6%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
P PL ++VG L + D++ + GS+ P + + F+
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFL 61
Query: 148 SFDDQNVAEQVLANPKQV-ICGKEVDVKRVK 177
+ D A+Q ++ + + + + V +
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 44.8 bits (106), Expect = 1e-06
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 2 AYRANGTAGPGRND--ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG 59
+ + + PG ++VG L R+ ++ + G V P R
Sbjct: 3 SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RR 57
Query: 60 FAFVTFTTQKAVDDLLAA 77
AF+ + A ++
Sbjct: 58 RAFLHYPDSAAAQQAVSC 75
>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 = 53.3 bits (128), Expect = 1e-09
Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+D + GL + +++ ++FS I + G+ RG A + +++
Sbjct: 9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQD 67
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
V L Y+G + ++ +
Sbjct: 68 VQKALEKHRMYMGQRYVEVYEINNE 92
Score = 43.7 bits (103), Expect = 5e-06
Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 2/79 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVAEQV 158
I GL + +DV ++FS ++G I + + ++
Sbjct: 12 FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKA 71
Query: 159 LANPKQVICGKEVDVKRVK 177
L + + + V+V +
Sbjct: 72 LEKHRMYMGQRYVEVYEIN 90
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 53.4 bits (128), Expect = 3e-09
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 15/105 (14%)
Query: 5 ANGTAGPGRNDERK----------LFVGGLHRNTGEKEINDYFSQYGEV----ESISIKN 50
++G++G G ++E + + GL +E+ +F Q+ + E I
Sbjct: 2 SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61
Query: 51 DPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
P G+ G AFV F ++ + L +G + I+ R T
Sbjct: 62 YPD-GRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105
Score = 44.9 bits (106), Expect = 2e-06
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQP---FDKSKNMKKGFCFISFDDQNVAEQVL 159
+ + GL + ++V +F Q+ IT ++ G F+ F + A+ L
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 160 ANPKQVICGKEVDVKRVK 177
K ++ + +++ R
Sbjct: 86 RKHKDLLGKRYIELFRST 103
>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 = 53.0 bits (127), Expect = 3e-09
Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 4/94 (4%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGFA 61
+ GP + + + GL + +++ ++ S V + G+ G A
Sbjct: 6 SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEA 64
Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
FV ++ V L +G++ I+ + +
Sbjct: 65 FVELESEDDVKLALKKDRESMGHRYIEVFKSHRT 98
Score = 46.1 bits (109), Expect = 7e-07
Identities = 15/102 (14%), Positives = 40/102 (39%), Gaps = 6/102 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQY---GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ + GL S +DV+++ S + + + + + G F+ + ++ + L
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78
Query: 160 ANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
++ + + ++V + + M V A S+G
Sbjct: 79 KKDRESMGHRYIEVFKS--HRTEMDWVLKHSGPNSASGPSSG 118
>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 = 52.5 bits (126), Expect = 3e-09
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 11/77 (14%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
+ P R E ++ V GL + +++ D+ + G+V + D G
Sbjct: 1 GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 53
Query: 62 FVTFTT----QKAVDDL 74
V F AV L
Sbjct: 54 VVEFVRKEDMTYAVRKL 70
Score = 44.0 bits (104), Expect = 3e-06
Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 8/83 (9%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ ++ V GL S QD++D+ + G + + + G + F + +
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 67
Query: 160 AN-PKQVICGKEVDVKRVKFNPE 181
E + ++ +
Sbjct: 68 RKLDNTKFRSHEGETAYIRVKVD 90
>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 = 51.9 bits (125), Expect = 4e-09
Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 9/85 (10%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++V G +++ +R FS +G+I + + F++++ A+Q
Sbjct: 13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQ 64
Query: 158 VLAN-PKQVICGKEVDVKRVKFNPE 181
+A + ++ V + P
Sbjct: 65 AVAELNGTQVESVQLKVNIARKQPM 89
Score = 51.1 bits (123), Expect = 8e-09
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
L+V G + + FS +G + +S+ R AFVT+
Sbjct: 10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMES 61
Query: 68 -QKAVDDL 74
+AV +L
Sbjct: 62 ADQAVAEL 69
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 52.9 bits (127), Expect = 4e-09
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 2/84 (2%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+ + + GL E +I ++FS V + I+ P G+ G A V
Sbjct: 34 SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-GRVTGEADV 91
Query: 64 TFTTQKAVDDLLAAGDHYIGNKKI 87
F T + ++ + ++ I
Sbjct: 92 EFATHEEAVAAMSKDRANMQHRYI 115
Score = 43.7 bits (103), Expect = 7e-06
Identities = 12/92 (13%), Positives = 30/92 (32%), Gaps = 2/92 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ + GL + +E D+ ++FS G + F A ++
Sbjct: 47 HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAMS 104
Query: 161 NPKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
+ + + +++ + G+ S V
Sbjct: 105 KDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.0 bits (125), Expect = 4e-09
Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 13/91 (14%)
Query: 16 ERKLFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
+ + V + + I+ FS++G++ + + G+++G+ F+ + +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72
Query: 70 AVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK 100
D + D K+D K+ T RVN
Sbjct: 73 HAVDAVKNAD----GYKLD-KQHTFRVNLFT 98
Score = 42.4 bits (100), Expect = 1e-05
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 8/67 (11%)
Query: 101 CKIFVGGL------TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
I V + E + + FS++G IT P + K KG+ F+ +
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAH 73
Query: 155 AEQVLAN 161
A + N
Sbjct: 74 AVDAVKN 80
>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 = 51.3 bits (123), Expect = 5e-09
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVT 64
GP + R+L+VG + E+ + D+F+ + ++ Q + FAF+
Sbjct: 1 GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59
Query: 65 FTTQKAVDDLLA 76
F + +A
Sbjct: 60 FRSVDETTQAMA 71
Score = 50.1 bits (120), Expect = 1e-08
Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVAE 156
+++VG + I+E+ + D+F+ + Q N K F F+ F +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 157 QVLANPKQVICGKEVDVKR 175
Q +A + G+ + ++R
Sbjct: 68 QAMAFDGIIFQGQSLKIRR 86
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 51.3 bits (123), Expect = 6e-09
Identities = 10/62 (16%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
I V L + + Q+V D Y + + K F++ + A+ +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCY-------VDRNKRTAFVTLLNGEQAQNAI 57
Query: 160 AN 161
Sbjct: 58 QM 59
Score = 49.3 bits (118), Expect = 3e-08
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G + + V L +++ +E++D Y + +++ AFVT +
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYC-------YVDRNKRTAFVTLLNGEQA 53
Query: 72 DDLLAAGDHY 81
+ + Y
Sbjct: 54 QNAIQMFHQY 63
>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 = 51.2 bits (123), Expect = 7e-09
Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+ + + + GL E +I ++FS + I+ P G+ G A V F
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEF 62
Query: 66 TTQKAVDDLLAAGDHYIGNKKI 87
T + +A + ++ +
Sbjct: 63 ATHEDAVAAMAKDKANMQHRYV 84
Score = 41.2 bits (97), Expect = 3e-05
Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 2/73 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+ + GL +E D+ ++FS G + F A +A
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKD 75
Query: 163 KQVICGKEVDVKR 175
K + + V++
Sbjct: 76 KANMQHRYVELFL 88
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 50.7 bits (122), Expect = 1e-08
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 9/94 (9%)
Query: 103 IFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
+FVG LT ++ + + ++F + Y S + D++ + KG+ F+ F D+ ++ L
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQT-GVSKGYGFVKFTDELEQKRALTE 70
Query: 161 -NPKQVICGKEVDV-----KRVKFNPETMGSVSG 188
+ K V + K + P G SG
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSSG 104
Score = 46.9 bits (112), Expect = 3e-07
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
E LFVG L + + + ++F + Y + D TG S+G+ FV FT +
Sbjct: 4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL 62
Query: 70 AVDDLLAA--GDHYIGNKKI 87
L G +G+K +
Sbjct: 63 EQKRALTECQGAVGLGSKPV 82
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 50.7 bits (121), Expect = 2e-08
Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 1 MAYRANGTAGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPHTGQ 56
M G+ P + + + ++ +++ + S G++ I + +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70
Query: 57 SRGFAFVTFTT----QKAVDDL 74
+ G A++ F T Q V+
Sbjct: 71 NSGKAYIVFATQESAQAFVEAF 92
Score = 45.7 bits (108), Expect = 1e-06
Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 8/78 (10%)
Query: 101 CKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ + + E+ ++ ++ S G I + G +I F Q A+
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN---SGKAYIVFATQESAQ 86
Query: 157 QVLANPK-QVICGKEVDV 173
+ + G + +
Sbjct: 87 AFVEAFQGYPFQGNPLVI 104
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 50.4 bits (120), Expect = 3e-08
Identities = 18/106 (16%), Positives = 36/106 (33%), Gaps = 12/106 (11%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGF 60
R + GP + + + GL + +++ ++ S + G+ G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGE 90
Query: 61 AFVTFTTQKAVDDLLAAGDHYIGNKKI--------DPKRVTKRVNP 98
AFV ++ V L +G++ I + V K P
Sbjct: 91 AFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGP 136
Score = 41.9 bits (98), Expect = 4e-05
Identities = 10/80 (12%), Positives = 29/80 (36%), Gaps = 2/80 (2%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVAEQ 157
+ + GL S +DV+++ S + + G F+ ++ +
Sbjct: 44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKM 103
Query: 158 VLANPKQVICGKEVDVKRVK 177
L ++ + + ++V +
Sbjct: 104 ALKKDRESMGHRYIEVFKSH 123
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 48.9 bits (117), Expect = 3e-08
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 19 LFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ V + + I+ FS++G++ + + G+++G+ F+ + +
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVN 97
D + D K+D K+ T RVN
Sbjct: 62 DAVKNAD----GYKLD-KQHTFRVN 81
Score = 42.4 bits (100), Expect = 7e-06
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 8/65 (12%)
Query: 103 IFVGGL------TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
I V + E + + FS++G IT P + K KG+ F+ + A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAHAV 61
Query: 157 QVLAN 161
+ N
Sbjct: 62 DAVKN 66
>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 = 52.2 bits (124), Expect = 4e-08
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
A P +++ L+ + E+ FSQ+G++ I + + + RG AFV
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVI 58
Query: 65 FTT----QKAVDDL 74
F A+ +
Sbjct: 59 FKEVSSATNALRSM 72
Score = 52.2 bits (124), Expect = 5e-08
Identities = 27/177 (15%), Positives = 52/177 (29%), Gaps = 11/177 (6%)
Query: 103 IFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
I++ L +I + +++ FSQ+G I + +S M+ G F+ F + + A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMR-GQAFVIFKEVSSATNA 68
Query: 159 LAN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPST 217
L + K + ++ K + + + + G R + +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG---TFVERDRKREKRKPKSQETPATKKAV 125
Query: 218 YAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAP 274
G A G G P G A + P
Sbjct: 126 QGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPP 182
Score = 42.2 bits (98), Expect = 9e-05
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 5/61 (8%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+F+ L E +E + F+Q+ E + + F+ FD++ A
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEV-----RLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 161 N 161
Sbjct: 263 A 263
Score = 33.7 bits (76), Expect = 0.042
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 11/72 (15%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDLL 75
F+ L T E ++ F+Q+ + + + AFV F A D L
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDAL- 264
Query: 76 AAGDHYIGNKKI 87
G N +
Sbjct: 265 -QGFKITQNNAM 275
>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 = 48.8 bits (116), Expect = 8e-08
Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 13/105 (12%)
Query: 76 AAGDHYIGNKKIDPKRV----TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
++ H+ + + P+ ++ I + L +++E +V +G +T
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL 62
Query: 132 QPFDKSKNMKKGFCFISFDDQNVAE---QVLANPKQVICGKEVDV 173
K FI + + A + V+ G+ + +
Sbjct: 63 ------MLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 101
Score = 39.9 bits (93), Expect = 1e-04
Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
R + + L + E E+ +G+V ++ + + + AF+ T++A
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEA 79
>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 = 51.8 bits (123), Expect = 1e-07
Identities = 25/147 (17%), Positives = 44/147 (29%), Gaps = 39/147 (26%)
Query: 28 TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI 87
T K++ D+ S IS+ + S T V LL Y+ +
Sbjct: 272 TRFKQVTDFLSAATTTH-ISLDH-----HSMTL------TPDEVKSLLLK---YLDCRPQ 316
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVR-DYFSQYG----------SITEFQQPFDK 136
D R NP + I I + D + S+ +P +
Sbjct: 317 DLPREVLTTNPRRLSIIA----ESIRDGLATWDNWKHVNCDKLTTIIESSL-NVLEPAE- 370
Query: 137 SKNMKKGF--CFISF-DDQNVAEQVLA 160
+K F + F ++ +L+
Sbjct: 371 ---YRKMFDRLSV-FPPSAHIPTILLS 393
Score = 36.4 bits (83), Expect = 0.009
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 21/66 (31%)
Query: 108 LTTEISEQDVRDYFSQYGSITE-FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
+ E E QY I F+ F + FD ++V + PK ++
Sbjct: 7 MDFETGEHQY-----QYKDILSVFEDAFVDN-----------FDCKDVQDM----PKSIL 46
Query: 167 CGKEVD 172
+E+D
Sbjct: 47 SKEEID 52
Score = 33.3 bits (75), Expect = 0.11
Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 16/90 (17%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFS----QYGSITEFQQPFDKSKNMKKGFC 145
+ N L CKI + TT + V D+ S + S+ + K
Sbjct: 256 AKAWNAFN-LSCKILL---TT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEV--KSLL 307
Query: 146 --FISFDDQNVAEQVLA-NPKQV-ICGKEV 171
++ Q++ +VL NP+++ I + +
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESI 337
>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 = 49.1 bits (117), Expect = 1e-07
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 9/67 (13%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTT---- 67
+++V L ++ EK++ F +Y + S + + G+ +G AF+
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 68 QKAVDDL 74
KA+ +
Sbjct: 106 AKALKEA 112
Score = 44.4 bits (105), Expect = 5e-06
Identities = 19/111 (17%), Positives = 41/111 (36%), Gaps = 20/111 (18%)
Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTK---RVNPLK---------CKIFVGGLTTEIS 113
D++ I ++++ R+++ + C+I+V L +
Sbjct: 2 PLGSDSDEM---PSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQ 58
Query: 114 EQDVRDYFSQYGSITEFQQP----FDKSKNMK-KGFCFISFDDQNVAEQVL 159
E+D++ F +Y + Q K + KG FI ++ A + L
Sbjct: 59 EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 11/70 (15%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
P R E ++ V GL + +++ D+ + G+V + D G V F
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61
Query: 68 ---QKAVDDL 74
AV L
Sbjct: 62 EDMTYAVRKL 71
Score = 41.7 bits (98), Expect = 3e-05
Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 8/83 (9%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ ++ V GL S QD++D+ + G + + + G + F + +
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 68
Query: 160 AN-PKQVICGKEVDVKRVKFNPE 181
E + ++ +
Sbjct: 69 RKLDNTKFRSHEGETAYIRVKVD 91
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 47.9 bits (114), Expect = 2e-07
Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
I + L +++E +V +G +T K FI + + A ++
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLL------MLKGKNQAFIEMNTEEAANTMVNYY 72
Query: 161 -NPKQVICGKEVDV 173
+ V+ G+ + +
Sbjct: 73 TSVTPVLRGQPIYI 86
Score = 40.6 bits (95), Expect = 5e-05
Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R + + L + E E+ +G+V ++ + + AF+ T++A +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAAN---T 67
Query: 77 AGDHYIGNKK-IDPKRV 92
++Y + + +
Sbjct: 68 MVNYYTSVTPVLRGQPI 84
>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 = 49.4 bits (117), Expect = 2e-07
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+++ G T+ + D++++ G + Q K K G F+ FD A++ +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK-GSIFVVFDSIESAKKFVE 168
Query: 161 NPKQVICGKEVDVK 174
P Q ++ +
Sbjct: 169 TPGQKYKETDLLIL 182
Score = 48.7 bits (115), Expect = 3e-07
Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 1/75 (1%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
R +++ G + +I ++ G+V +I ++ +G FV F + ++
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAK 164
Query: 73 DLLAAGDHYIGNKKI 87
+ +
Sbjct: 165 KFVETPGQKYKETDL 179
>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 = 47.1 bits (112), Expect = 3e-07
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G++G + + L T EI + FS++G + + + A V F
Sbjct: 1 GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL 54
Query: 67 T----QKAVDDL 74
+KA L
Sbjct: 55 EPLEARKAFRHL 66
Score = 42.1 bits (99), Expect = 1e-05
Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 6/58 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K I L ++++ FS++GS+ P + F + A +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARK 61
>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 = 46.8 bits (111), Expect = 3e-07
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPHTGQSR---GFAFVTFTT----Q 68
+FV GL + + E+ +YF ++G++ + I N S+ A+VT+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 69 KAVDDL 74
+A+ +
Sbjct: 78 RAIQCV 83
Score = 41.8 bits (98), Expect = 2e-05
Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 100 KCKIFVGGLTTEISEQDV---RDYFSQYGSITE---FQQPFDKSKNMKKGFCFISFDDQN 153
K +FV GL+ +++ +V +YF ++G I + ++++
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 154 VAEQ 157
A +
Sbjct: 75 DALR 78
>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 = 46.4 bits (110), Expect = 4e-07
Identities = 9/74 (12%), Positives = 25/74 (33%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
+ + L E++E +V +G +T K F+ + A ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71
Query: 160 ANPKQVICGKEVDV 173
+ + + + +
Sbjct: 72 SAVTPHLRNQPIYI 85
Score = 37.9 bits (88), Expect = 4e-04
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R L + L E E+ +G+V +I + + + AF+ T++A
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAI---T 66
Query: 77 AGDHYIGNKK-IDPKRV 92
++Y + + +
Sbjct: 67 MVNYYSAVTPHLRNQPI 83
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 46.0 bits (109), Expect = 7e-07
Identities = 8/77 (10%), Positives = 22/77 (28%), Gaps = 7/77 (9%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
++ + L +++ D + + S +T G
Sbjct: 14 LVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTG 70
Query: 62 FVTFTT----QKAVDDL 74
+ F + +A++ L
Sbjct: 71 ALEFPSEEILVEALERL 87
Score = 41.7 bits (98), Expect = 2e-05
Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 3/82 (3%)
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS 137
H+ + + ++ + +I + L S QD++D + T F +
Sbjct: 6 HHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD 65
Query: 138 KNMKKGFCFISFDDQNVAEQVL 159
G + F + + + L
Sbjct: 66 ---FDGTGALEFPSEEILVEAL 84
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 45.5 bits (108), Expect = 9e-07
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
+ + GL + E D+ + ++G I+ K + F+D A +
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77
Query: 160 ANPKQVICGKEVDV 173
A+ + I G V
Sbjct: 78 ADNQIYIAGHPAFV 91
Score = 44.0 bits (104), Expect = 3e-06
Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ + GL E ++ + ++G + + + + A V F V
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVV------MPKKRQALVEFED---VLGACN 72
Query: 77 AGDHYIGNK-KIDPKRV 92
A ++ N+ I
Sbjct: 73 AVNYAADNQIYIAGHPA 89
>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 = 44.8 bits (106), Expect = 2e-06
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 15/94 (15%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+ V GL + E D+ + ++G+I K + F++ + A++ +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71
Query: 163 KQV---ICGKEVDV-----KRVKFNPETMGSVSG 188
V I G++ KR+ P G SG
Sbjct: 72 ADVPVYIAGQQAFFNYSTSKRIT-RPGNSGPSSG 104
Score = 42.5 bits (100), Expect = 1e-05
Identities = 13/89 (14%), Positives = 32/89 (35%), Gaps = 13/89 (14%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++G + V GL + E ++ + ++G + + + + A
Sbjct: 2 SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55
Query: 63 VTFTT----QKAVDDLLAAGDHYIGNKKI 87
V F ++ V YI ++
Sbjct: 56 VEFENIDSAKECVTFAADVP-VYIAGQQA 83
>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 = 44.9 bits (106), Expect = 2e-06
Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 6/57 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ GGL +S + + G + P + K + F + +++
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80
Score = 44.5 bits (105), Expect = 2e-06
Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
+ GGL ++ + G V+++ + + + ++F + T ++A L
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 45.9 bits (108), Expect = 3e-06
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 15/74 (20%)
Query: 6 NGTAGPGRNDERKLFVGGLHRN---------TGEKEINDYFSQYGEVESISIKNDPHTGQ 56
G G R + L+VGG+ E I FS+ G+++ I +
Sbjct: 124 MGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------E 177
Query: 57 SRGFAFVTFTTQKA 70
S+ FV F Q
Sbjct: 178 SKNCGFVKFKYQAN 191
Score = 37.5 bits (86), Expect = 0.002
Identities = 17/102 (16%), Positives = 26/102 (25%), Gaps = 6/102 (5%)
Query: 56 QSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQ 115
+ + + G K T V + + L E
Sbjct: 99 IGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIES 158
Query: 116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+R FS+ G I + K F+ F Q AE
Sbjct: 159 RIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEF 194
>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 = 47.4 bits (112), Expect = 4e-06
Identities = 45/255 (17%), Positives = 78/255 (30%), Gaps = 95/255 (37%)
Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPH----TG--QS-RGFAFVTFTTQ 68
L + L + + + N + +V IS+ N +G QS G +T
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQV-EISLVNGAKNLVVSGPPQSLYGLN-LTLRKA 396
Query: 69 KAVDDLLAAGDHYIGNKKIDPKRV--TKRVNPLKCKIFVGGL-------------TTEIS 113
KA L D R+ ++R K K L +++
Sbjct: 397 KAPSGL-------------DQSRIPFSER----KLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 114 EQDV-RDYFSQYGSITEFQQP-FD--KSKNMKKGFCFISFDDQNVAEQVLANPKQVICGK 169
+D+ ++ S + Q P +D +++ +++E+++ I
Sbjct: 440 NKDLVKNNVSFNAK--DIQIPVYDTFDGSDLRVL-------SGSISERIV----DCIIRL 486
Query: 170 EVDVKR---------VKFNPETMGSVSG-------AVRGAGARVASAGTAYAAAPGRVVA 213
V + + F P G SG G G RV AGT P
Sbjct: 487 PVKWETTTQFKATHILDFGP---GGASGLGVLTHRNKDGTGVRVIVAGT-LDINP----- 537
Query: 214 YPSTYAGYAATDYGY 228
DYG+
Sbjct: 538 ---------DDDYGF 543
Score = 37.3 bits (86), Expect = 0.005
Identities = 35/233 (15%), Positives = 65/233 (27%), Gaps = 85/233 (36%)
Query: 38 SQYGEVESISIK---------NDPHTGQSRGFAFVTF-----TTQKAVDDLLAAGDHYIG 83
Q+ +V ++ + ND H A TT +L+ YI
Sbjct: 78 GQFDQVLNLCLTEFENCYLEGNDIHA-----LA-AKLLQENDTTLVKTKELIKN---YIT 128
Query: 84 NKKIDPKRVTKRVNPL--------KCKIFV--GGLTTEISEQ-DVRDYFSQ-------YG 125
+ + + K+ N ++ GG Q + DYF + Y
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG-------QGNTDDYFEELRDLYQTYH 181
Query: 126 S-ITEF------------QQPFDKSKNMKKGFCFISF-DDQNVA--EQVLAN-----P-- 162
+ + + D K +G + + ++ + + L + P
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
Query: 163 --KQ-----VICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAP 208
Q V K + F P + S G + +A A A
Sbjct: 242 GVIQLAHYVVTA------KLLGFTPGELRSYLKGATGHSQGLVTA-VAIAETD 287
Score = 37.0 bits (85), Expect = 0.006
Identities = 41/257 (15%), Positives = 74/257 (28%), Gaps = 112/257 (43%)
Query: 1 MA---YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESIS--IKNDP-- 52
M Y+ + A + ++ +++F YG SI + N+P
Sbjct: 1631 MGMDLYKTSKAA-------QDVW----------NRADNHFKDTYGF--SILDIVINNPVN 1671
Query: 53 ---HTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCK-IFVGGL 108
H G +G ++ ++ A I + K+ +++ K +N F
Sbjct: 1672 LTIHFGGEKG--------KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS-- 1721
Query: 109 TTEISEQDVRDYFSQYGSITEFQQP---------FD--KSKNMKKGFCF----------- 146
E+ + T+F QP F+ KSK +
Sbjct: 1722 -----EKGLLS-------ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA 1769
Query: 147 -------ISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVAS 199
+S + +V+ R G ++ A R
Sbjct: 1770 LASLADVMSIES---LVEVVF-------------YR--------GM---TMQVAVPRDEL 1802
Query: 200 AGTAY---AAAPGRVVA 213
+ Y A PGRV A
Sbjct: 1803 GRSNYGMIAINPGRVAA 1819
>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 = 39.9 bits (93), Expect = 1e-04
Identities = 19/94 (20%), Positives = 30/94 (31%), Gaps = 16/94 (17%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKK 142
++K D K+ RV I + L S+ V YG I + K
Sbjct: 15 DQKFDQKQELGRV------IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMK 62
Query: 143 GFCFISFDDQNVAEQVL---ANPKQVICGKEVDV 173
FI + + A ++ G+ V V
Sbjct: 63 SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 37.1 bits (85), Expect = 0.004
Identities = 8/54 (14%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 106 GGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
GGL +S + + G + P +K + F + +++
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAY 73
Score = 29.4 bits (65), Expect = 1.2
Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 17 RKLFV--GGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
+ L V GGL ++ + G V+++ ++ ++F + T
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRT 65
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.2 bits (78), Expect = 0.014
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
G A G++ ++ V L ++ FS++G V I + Q A + +
Sbjct: 18 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQY 73
Query: 66 TT 67
Sbjct: 74 AD 75
Score = 33.1 bits (75), Expect = 0.035
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
I V L ++ + FS++G++ F K+ + + + D A+ +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTV-LKIITFTKNNQFQ---ALLQYADPVSAQHAKLS 85
>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 = 34.3 bits (78), Expect = 0.018
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 4/66 (6%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
A G A G++ ++ V L ++ FS++G V I + Q A
Sbjct: 32 AAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----A 87
Query: 62 FVTFTT 67
+ +
Sbjct: 88 LLQYAD 93
Score = 32.4 bits (73), Expect = 0.090
Identities = 8/59 (13%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
I V L ++ + FS++G++ + + + + D A+ +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS 103
>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 = 33.3 bits (76), Expect = 0.019
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
E+ + +YGEVE +++ D G +V F +KAV DL
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDL 88
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 121
Score = 31.9 bits (72), Expect = 0.071
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
F G L T ++++ FS +GE++ I G G ++A+ A +
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVR----GAKEGIILFKEKAKEALGKAKDANN 78
Query: 80 HYIGNKKIDPKRVTKRV 96
GN ++ K VT V
Sbjct: 79 ---GNLQLRNKEVTWEV 92
>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 = 32.1 bits (72), Expect = 0.16
Identities = 16/112 (14%), Positives = 35/112 (31%), Gaps = 7/112 (6%)
Query: 53 HTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEI 112
H S G ++ + + I ++ + +R + + + +I
Sbjct: 7 HHHHSSGLVPRGSHMEQPSGSVETGFEDKIPKRRFS-EMQNERREQAQRTVLIH-CPEKI 64
Query: 113 SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
SE Y SQ+G I F +S + + + F + +
Sbjct: 65 SENKFLKYLSQFGPINNHF--FYESFGL---YAVVEFCQKESIGSLQNGTHT 111
Score = 31.7 bits (71), Expect = 0.26
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+R + + E + Y SQ+G + + ++ +A V F ++++ L
Sbjct: 53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGL------YAVVEFCQKESIGSL 105
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 30.5 bits (68), Expect = 0.26
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 27 NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
N + I +YF +YGE+ NDP++ + +
Sbjct: 17 NIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYA 56
Score = 27.0 bits (59), Expect = 3.6
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 99 LKCKIFVGGL----TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+ C+I V TT I + +++YF +YG I+ F+ D + + I + +
Sbjct: 1 MSCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSD 59
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 29.8 bits (67), Expect = 0.26
Identities = 12/94 (12%), Positives = 26/94 (27%), Gaps = 20/94 (21%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEIS-EQDVRDYFSQYGSITEFQQPFDKSKNMKK 142
+++ +RV + + + + +G I+ K
Sbjct: 9 KGRVETRRV----------VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKI 52
Query: 143 GFCFISFDDQNVAEQVL---ANPKQVICGKEVDV 173
FI A+ + ++ GK V V
Sbjct: 53 NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV 86
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.7 bits (66), Expect = 0.29
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+ + +YGEV ++ + + G A V F T KA +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAEL 69
Score = 26.7 bits (58), Expect = 3.5
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 5/50 (10%)
Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
S+ + +YG + + K G + F AE + N
Sbjct: 29 YSKDVLLRLLQKYGEVLNL-----VLSSKKPGTAVVEFATVKAAELAVQN 73
>3q62_A 3-hydroxydecanoyl-[acyl-carrier-protein] dehydrat; structural
genomics, center for structural genomics of infec
diseases, csgid; HET: MES; 1.40A {Yersinia
pseudotuberculosis} PDB: 1mka_A* 1mkb_A
Length = 175
Score = 29.6 bits (66), Expect = 0.85
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 140 MKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVAS 199
+ + + QVL + K+V ++ KRV MG G V G + +
Sbjct: 103 GEGKGRALGVGEVKFTGQVLPDAKKVT--YRINFKRVIMRKLIMGVADGEVLVDGKVIYT 160
Query: 200 A 200
A
Sbjct: 161 A 161
>3ksr_A Putative serine hydrolase; catalytic triad, structural genomics,
JOIN for structural genomics, JCSG; 2.69A {Xanthomonas
campestris PV}
Length = 290
Score = 29.8 bits (67), Expect = 0.95
Identities = 7/34 (20%), Positives = 13/34 (38%)
Query: 59 GFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV 92
+ T + +DD+ AA D +D +
Sbjct: 70 ASMRQSVTRAQNLDDIKAAYDQLASLPYVDAHSI 103
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 28.5 bits (64), Expect = 0.96
Identities = 8/49 (16%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
+ ++ + +++G V I + ++G +V + AV+ L
Sbjct: 31 KDDVIEECNKHGGVIHIYV----DKNSAQGNVYVKCPSIAAAIAAVNAL 75
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.6 bits (63), Expect = 1.6
Identities = 4/26 (15%), Positives = 12/26 (46%)
Query: 26 RNTGEKEINDYFSQYGEVESISIKND 51
R +K++ ++ + E + N+
Sbjct: 113 REKAKKDLEEWNQRQSEQVEKNKINN 138
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif,
RRM, RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 30 EKEINDYFSQYGEVESISI----KNDPHTGQSRGFAFVTFTT----QKAVDDL 74
E E+ + ++G V + I + + + FV F+ KA+ L
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 28.9 bits (64), Expect = 2.2
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 6/88 (6%)
Query: 178 FNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYA 237
F+P + A+ G A A +P T G+ + G++ S Y+
Sbjct: 1492 FSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTS-PTYS 1550
Query: 238 TAYPGY-----DYSAMGYAYPAAATSYG 260
P Y YS +Y + SY
Sbjct: 1551 PTSPAYSPTSPSYSPTSPSYSPTSPSYS 1578
>3d3a_A Beta-galactosidase; protein structure initiative II, PSI II,
NYSGXRC, 11092F, structural genomics; 2.15A {Bacteroides
thetaiotaomicron vpi-5482}
Length = 612
Score = 28.5 bits (63), Expect = 2.9
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 216 STYAGYAATDYGYTAG-SYDAYATAYPGYDYSA 247
S Y + T +G+ G ++ ++ YDY A
Sbjct: 275 SLYMTHGGTSFGHWGGANFPNFSPTCTSYDYDA 307
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 27.0 bits (59), Expect = 3.6
Identities = 6/59 (10%), Positives = 19/59 (32%), Gaps = 5/59 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ + I+ + + G + + K ++ + F+ A++ A
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQ--RIVIFKRNGIQ---AMVEFESVLCAQKAKAA 81
>3thd_A Beta-galactosidase; TIM-barrel domain, glycosyl hydrolase,
glycosylation, hydrolase; HET: NAG DGJ; 1.79A {Homo
sapiens} PDB: 3thc_A*
Length = 654
Score = 27.9 bits (61), Expect = 4.2
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 218 YAGYAATDYGYTAGSYDAYATAYPGYDYSA 247
Y T++ Y G+ YA YDY A
Sbjct: 283 YMFIGGTNFAYWNGANSPYAAQPTSYDYDA 312
>2g38_A PE family protein; protein-protein complex, structural genomics,
PSI, protein S initiative, TB structural genomics
consortium, TBSGC; 2.20A {Mycobacterium tuberculosis}
SCOP: a.25.4.1
Length = 99
Score = 25.9 bits (57), Expect = 6.0
Identities = 16/88 (18%), Positives = 21/88 (23%), Gaps = 12/88 (13%)
Query: 180 PETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATA 239
PE + + VR R + A V P+ A YA
Sbjct: 8 PEALTVAATEVRRIRDRAIQSDAQ-VAPMTTAVRPPAADLVSEK-----AATFLVEYARK 61
Query: 240 YPGYDYSAMGY------AYPAAATSYGG 261
Y +A A A Y
Sbjct: 62 YRQTIAAAAVVLEEFAHALTTGADKYAT 89
>2rr7_A Dynein heavy chain 9; microtubule-binding, stalk head, MTBD,
antiparallel coil, motor protein, DSH; NMR
{Chlamydomonas reinhardtii}
Length = 155
Score = 26.5 bits (59), Expect = 7.5
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 178 FNPETMGSVSGAVRG 192
F P+ + S A G
Sbjct: 113 FQPKVIEKQSVACAG 127
>2cf2_C Fatty acid synthase, DH domain; transferase, fatty acid metabolism,
fatty acid biosynthesis, multienzyme; 4.30A {Sus scrofa}
SCOP: d.38.1.2
Length = 342
Score = 26.8 bits (58), Expect = 7.8
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 146 FISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASA 200
+ + QVL K+V + KR+ MG G V G + +A
Sbjct: 276 ALGVGEVKFTGQVLPTAKKVTY--RIHFKRIVNRRLIMGLADGEVLVDGRLIYTA 328
>2wtm_A EST1E; hydrolase; 1.60A {Clostridium proteoclasticum} PDB: 2wtn_A*
Length = 251
Score = 26.5 bits (59), Expect = 9.3
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 55 GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP 89
G+S G F T K + ++LA D+ +
Sbjct: 68 GKSDG-KFEDHTLFKWLTNILAVVDYAKKLDFVTD 101
>3vte_A Tetrahydrocannabinolic acid synthase; BI-covalent flavinylation,
oxidoreductase; HET: NAG FAD; 2.75A {Cannabis sativa}
Length = 518
Score = 26.9 bits (59), Expect = 9.5
Identities = 12/90 (13%), Positives = 27/90 (30%), Gaps = 12/90 (13%)
Query: 192 GAGARVASAGTAYA--AAPGRVVAYPSTY--AGYAATDYGYTAGSYDA---YAT-----A 239
G ++ + + A + Y +++ + Y+ Y + A
Sbjct: 394 GIMEEISESAIPFPHRAGIMYELWYTASWEKQEDNEKHINWVRSVYNFTTPYVSQNPRLA 453
Query: 240 YPGYDYSAMGYAYPAAATSYGGGKYREAAY 269
Y Y +G A+ +Y + Y
Sbjct: 454 YLNYRDLDLGKTNHASPNNYTQARIWGEKY 483
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
0.316 0.133 0.392
Gapped
Lambda K H
0.267 0.0480 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,330,990
Number of extensions: 263999
Number of successful extensions: 1281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1017
Number of HSP's successfully gapped: 402
Length of query: 275
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 183
Effective length of database: 4,133,061
Effective search space: 756350163
Effective search space used: 756350163
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.0 bits)