RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1757
(348 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 = 213 bits (546), Expect = 2e-69
Identities = 56/162 (34%), Positives = 96/162 (59%), Gaps = 2/162 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
+ K+F+GGL+ +T E + +YF +YG V + I DP TG+SRGF F+++ +VD++
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
+ H + K IDPKR R K KIFVGG+ ++ ++ ++FSQ+G+I + Q
Sbjct: 62 VKT-QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Query: 134 FDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
DK +GF F+++D + D+V +N +++++KR
Sbjct: 121 LDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKR 162
Score = 102 bits (258), Expect = 1e-26
Identities = 31/83 (37%), Positives = 46/83 (55%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
++ K+FVGG+ + KE ++FSQ+G + + D TGQSRGF FVTY + 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 = 212 bits (541), Expect = 2e-68
Identities = 63/186 (33%), Positives = 97/186 (52%), Gaps = 8/186 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGS 126
+ A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG
Sbjct: 71 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSV 186
I + D+ K+GF F++FDD + D+++ + G +V++ E M S
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE-MASA 189
Query: 187 SGAVRG 192
S + RG
Sbjct: 190 SSSQRG 195
Score = 102 bits (257), Expect = 2e-26
Identities = 29/92 (31%), Positives = 48/92 (52%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
R + +K+FVGG+ +T E + DYF QYG++E I I D +G+ RGFAFV
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 64 TYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
T+ +VD ++ H + + ++ +
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183
Score = 88.9 bits (221), Expect = 3e-21
Identities = 22/87 (25%), Positives = 44/87 (50%)
Query: 89 PKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
K + + K+F+GGL+ E T++ +R +F Q+G++T+ D + +GF F++
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 149 FDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D + + 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 = 147 bits (374), Expect = 9e-44
Identities = 33/166 (19%), Positives = 69/166 (41%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPYTGQSRGFAFVTYTTQKAV 71
R+L+VG + E+ + D+F+ + ++ Q + FAF+ + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEITEQDVRDYFSQYGSITEF 130
+A + + +R K+F+GGL + + V++ + +G + F
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVADQVLKNPK-QVICGKEVDVKR 175
D + + KG+ F + D NV DQ + + K++ V+R
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 137 bits (348), Expect = 2e-39
Identities = 37/194 (19%), Positives = 75/194 (38%), Gaps = 16/194 (8%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV Y +A
Sbjct: 23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82
Query: 71 VDDLLAA-GDHYIGNKKIDPKRVTKRVNPLKC------------KIFVGGLTTEITEQDV 117
L +G + I R + +I+V + ++++ D+
Sbjct: 83 AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 118 RDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPK-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 = 68.9 bits (169), Expect = 7e-14
Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 1/89 (1%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ + +++VG + E+ E +R F+ +G I +D KGF F+
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 148 SFDDQNVADQVLKNPKQV-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 = 135 bits (341), Expect = 8e-39
Identities = 46/176 (26%), Positives = 80/176 (45%), Gaps = 19/176 (10%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG--QSRGFAFVTYTT---- 67
+D K+FVG + R EK++ + F QYG V I++ D QS+G FVT+ T
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-----CKIFVGGLTTEITEQDVRDYFS 122
+A + L + + P ++ + K+F+G ++ + TE D+R FS
Sbjct: 61 LEAQNAL---HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFS 117
Query: 123 QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK--NPKQVI--CGKEVDVK 174
+G I E + +G F++F + +A +K + 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 = 125 bits (316), Expect = 3e-35
Identities = 42/151 (27%), Positives = 70/151 (46%), Gaps = 8/151 (5%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAV 71
+ L V L +N ++E F GE+ES + D TGQS G+ FV Y +KA+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEF 130
+ L + K I ++ ++V GL +T++++ FSQYG I
Sbjct: 62 NTL---NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS 118
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+ D+ + +G FI FD + A++ +K
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Score = 71.5 bits (176), Expect = 4e-15
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+ L+V GL + +KE+ FSQYG + + I D TG SRG F+ + + +
Sbjct: 85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 73 D 73
+
Sbjct: 145 E 145
>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 = 122 bits (309), Expect = 4e-34
Identities = 30/169 (17%), Positives = 64/169 (37%), Gaps = 10/169 (5%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
LF+G L+ N E+ S+ +++ + TG +R F +V + + + ++
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLE 68
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLK---CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
L + +I ++ R + + L+ ITE ++++ F I
Sbjct: 69 KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR- 127
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPK-QVICGKEVDVKRVK 177
KG +I F + A++ L+ + I G+ V +
Sbjct: 128 ----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172
Score = 66.9 bits (164), Expect = 2e-13
Identities = 15/93 (16%), Positives = 31/93 (33%), Gaps = 6/93 (6%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ G R L L N E E+ + F E+ G+S+G A++
Sbjct: 87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYI 141
Query: 64 TYTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
+ ++ + L I + + ++
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 118 bits (297), Expect = 3e-33
Identities = 39/94 (41%), Positives = 52/94 (55%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G G ++ KLFVGGL +T ++ + YFSQYGEV I D T QSRGF
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 62 FVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
FV + V +LA+ H + + IDPK T R
Sbjct: 62 FVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPR 95
Score = 88.4 bits (220), Expect = 4e-22
Identities = 28/75 (37%), Positives = 41/75 (54%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+FVGGL T++ +R YFSQYG + + DK+ N +GF F+ F D N VL
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 161 NPKQVICGKEVDVKR 175
+ + G+ +D K
Sbjct: 77 SRPHTLDGRNIDPKP 91
>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 = 119 bits (302), Expect = 3e-33
Identities = 36/150 (24%), Positives = 65/150 (43%), Gaps = 8/150 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
L V L ++ ++E+ F G + + I D TG S G+AFV +T+ Q+A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQ 131
L + NK++ +K ++V L IT+ + F +YGSI +
Sbjct: 64 VL---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 132 QPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
DK +G F+ ++ + A + +
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Score = 68.0 bits (167), Expect = 7e-14
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+ L+V L R + +++ F +YG + +I D TG+ RG AFV Y ++
Sbjct: 86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 145
Query: 73 D 73
+
Sbjct: 146 E 146
>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 = 120 bits (303), Expect = 5e-33
Identities = 34/187 (18%), Positives = 70/187 (37%), Gaps = 29/187 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPYTGQSRGFAFVTYTTQKAV 71
R+L+VG + E+ + D+F+ + ++ Q + FAF+ + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC---------------------KIFVGGLTT 110
+A + + +R K+F+GGL
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 111 EITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK--NPKQVICG 168
+ + V++ + +G + F D + + KG+ F + D NV DQ + N +
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-GMQLGD 183
Query: 169 KEVDVKR 175
K++ V+R
Sbjct: 184 KKLLVQR 190
Score = 75.5 bits (186), Expect = 2e-16
Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 1/95 (1%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
Y + + KLF+GGL + ++ + + +G +++ ++ D TG S+G+A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159
Query: 62 FVTYTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
F Y D +A + +G+KK+ +R +
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194
Score = 60.4 bits (147), Expect = 4e-11
Identities = 19/105 (18%), Positives = 37/105 (35%), Gaps = 5/105 (4%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVA 155
+++VG + ITE+ + D+F+ + Q N K F F+ F +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 156 DQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSA 200
Q + + G+ + ++R G VS+
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTV 109
>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 = 116 bits (292), Expect = 1e-32
Identities = 34/83 (40%), Positives = 53/83 (63%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
A D K+FVGGL +T +K++ DYF+++GEV +IK DP TG+SRGF F+ +
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63
Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
+V+ +L +H + + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86
Score = 87.6 bits (218), Expect = 6e-22
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+FVGGL+ + +++D++DYF+++G + + D + +GF FI F D ++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 = 116 bits (292), Expect = 1e-32
Identities = 30/89 (33%), Positives = 50/89 (56%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G + K+FVGG+ N GE E+ +YF ++G V + + D + RGF F+T+
Sbjct: 1 GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
Query: 67 TQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+++VD + H I KK++ KR R
Sbjct: 61 DEQSVDQAVNMHFHDIMGKKVEVKRAEPR 89
Score = 100 bits (252), Expect = 9e-27
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
KIFVGG+ E ++R+YF ++G +TE +D K +GF FI+F+D+ DQ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 PKQVICGKEVDVKR 175
I GK+V+VKR
Sbjct: 72 HFHDIMGKKVEVKR 85
>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 = 115 bits (290), Expect = 4e-32
Identities = 34/85 (40%), Positives = 49/85 (57%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
+ K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVT+ Q
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
VD +LA H + +K IDPK R
Sbjct: 80 VDKVLAQSRHELDSKTIDPKVAFPR 104
Score = 104 bits (262), Expect = 4e-28
Identities = 28/100 (28%), Positives = 52/100 (52%), Gaps = 2/100 (2%)
Query: 76 AAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFD 135
++ H+ + + P+ + CK+F+GGL+ + T++ +R+YF Q+G + E D
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGSSG--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60
Query: 136 KSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+GF F++F DQ D+VL + + K +D K
Sbjct: 61 PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV 100
>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 = 113 bits (284), Expect = 3e-31
Identities = 31/85 (36%), Positives = 50/85 (58%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
+ RKLF+GGL T E+ + +Y+ Q+G++ + DP + +SRGF FVT+++
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
VD +AA H I + ++PKR R
Sbjct: 82 VDAAMAARPHSIDGRVVEPKRAVAR 106
Score = 92.0 bits (229), Expect = 3e-23
Identities = 27/91 (29%), Positives = 45/91 (49%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
+ P KR K+F+GGL+ E TE+ +R+Y+ Q+G +T+ D + +GF
Sbjct: 12 LETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGF 71
Query: 145 CFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
F++F D + I G+ V+ KR
Sbjct: 72 GFVTFSSMAEVDAAMAARPHSIDGRVVEPKR 102
>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 = 113 bits (284), Expect = 3e-31
Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 4/113 (3%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S + K+FVGGL +T + + YF +G++E + D TG+SRG+
Sbjct: 3 SGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62
Query: 62 FVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKC----KIFVGGLTT 110
FVT + A + + I +K + P I V G ++
Sbjct: 63 FVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115
Score = 84.3 bits (209), Expect = 2e-20
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
KIFVGGL T+ +R YF +G I E D+ +G+ F++ D+ A++ K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 161 NPKQVICGKEVDVKR--VKFNPETMGSVSGAVRGA 193
+P +I G++ +V + P ++ +
Sbjct: 78 DPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSG 112
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 111 bits (280), Expect = 5e-31
Identities = 27/74 (36%), Positives = 44/74 (59%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+FVGGL NT +++ YF Q+G+V+ + D T + RGF FVT+ ++ V+ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 GDHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 104 bits (261), Expect = 2e-28
Identities = 27/74 (36%), Positives = 46/74 (62%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
KIFVGGL+ T +DV+ YF Q+G + + FDK+ N +GF F++F+ +++ ++V +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 162 PKQVICGKEVDVKR 175
I K V+ K+
Sbjct: 61 HFHEINNKMVECKK 74
>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 = 116 bits (293), Expect = 8e-31
Identities = 32/169 (18%), Positives = 62/169 (36%), Gaps = 15/169 (8%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+LFVG L + E++ F +YGE + I D RGF F+ ++ +
Sbjct: 19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE 72
Query: 73 DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQ 131
A D + ++ + + T + V L+ ++ + + FSQ+G + +
Sbjct: 73 IAKAELDGTILKSRPLRIRFATHGAA-----LTVKNLSPVVSNELLEQAFSQFGPVEKAV 127
Query: 132 QPFDKSKNMKKGFCFISFDDQNVADQVLK--NPKQVICGKEVDVKRVKF 178
D G F+ F + A + L+ + V+
Sbjct: 128 VVVDDR-GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175
>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 = 110 bits (277), Expect = 1e-30
Identities = 29/74 (39%), Positives = 45/74 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+FVGGL +T E++I +YF +GEVESI + D T + RGF F+T+ ++ V ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 GDHYIGNKKIDPKR 91
H +G K + K
Sbjct: 61 KYHNVGLSKCEIKV 74
Score = 107 bits (271), Expect = 1e-29
Identities = 22/74 (29%), Positives = 43/74 (58%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 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 = 111 bits (280), Expect = 1e-30
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 1/91 (1%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
+ L V GL T E+++ +YFS +GEV + +K D TG S+GF FV
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 65 YTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+T + +++ H I + D K +
Sbjct: 64 FTEYETQVKVMSQ-RHMIDGRWCDCKLPNSK 93
Score = 89.6 bits (223), Expect = 2e-22
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ V GL + TEQD+++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
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 109 bits (276), Expect = 2e-30
Identities = 33/74 (44%), Positives = 47/74 (63%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVT+ Q VD +LA
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPKR 91
H + +K IDPK
Sbjct: 62 SRHELDSKTIDPKV 75
Score = 94.5 bits (236), Expect = 1e-24
Identities = 26/75 (34%), Positives = 43/75 (57%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
CK+F+GGL+ + T++ +R+YF Q+G + E D +GF F++F DQ D+VL
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVKR 175
+ + K +D K
Sbjct: 61 QSRHELDSKTIDPKV 75
>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 = 113 bits (286), Expect = 1e-29
Identities = 35/177 (19%), Positives = 75/177 (42%), Gaps = 19/177 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFVTYTT--- 67
E L++ + ++ I D V SI + + SR FA++ T+
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKED 171
Query: 68 -QKAVDDLLAAGDHYIGNKKI-----DPKRVTKRVNPLKC---KIFVGGLTTEIT-EQDV 117
+ V+ L I + +P +KR + +I + L+TE+ E +
Sbjct: 172 ARYCVEKL---NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLL 228
Query: 118 RDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVADQVLKNPKQVICGKEVDV 173
R+ F +GSI + P + ++ F+ F++++ A++ L+ + ++ +E+ V
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISV 285
Score = 112 bits (281), Expect = 7e-29
Identities = 24/176 (13%), Positives = 61/176 (34%), Gaps = 13/176 (7%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+ + A + + V L ++ + ++ YF G + + + + ++ FA
Sbjct: 27 TSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFA 84
Query: 62 FVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDY 120
+ + + +G +I V+ L C +++ T++++RD
Sbjct: 85 RIEFARYDGALAAITKTHKVVGQNEI-------IVSHLTECTLWMTNFPPSYTQRNIRDL 137
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK--NPKQVICGKEVDVK 174
+ + N + F +I + A ++ N + I G + K
Sbjct: 138 LQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK-IEGYTLVTK 192
Score = 71.6 bits (176), Expect = 2e-14
Identities = 22/124 (17%), Positives = 36/124 (29%), Gaps = 7/124 (5%)
Query: 57 SRGFAFVTYT-TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQ 115
S + +++ +D+ A G R N + V L +
Sbjct: 1 SMEYGHHARPDSKRPLDEGSPAA---AGLTSKKANEALTR-NRELTTVLVKNLPKSYNQN 56
Query: 116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 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 = 110 bits (276), Expect = 4e-28
Identities = 33/175 (18%), Positives = 64/175 (36%), Gaps = 16/175 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDD 73
L V L + +++ + +G +E + TGQS+G+ F Y +A D
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 74 LLAAGDHYIGNKKI-----DPKRVTKRVNPLKCKIFVGGLTTEITEQD-VRDYFSQYGSI 127
L +G + + D ++T + +C + V L + D + S S
Sbjct: 157 L---LGKPLGPRTLYVHWTDAGQLTPALLHSRC-LCVDRLPPGFNDVDALCRALSAVHSP 212
Query: 128 TEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP-KQVICGKEVDVKRVKFNPE 181
T Q + KGF + ++ +A++ + + G + V P
Sbjct: 213 TFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266
Score = 105 bits (263), Expect = 2e-26
Identities = 27/167 (16%), Positives = 62/167 (37%), Gaps = 26/167 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
RK+ + GL + +E++D S Y ++ + + +G AFVT + A++
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-LKYC------FVDKYKGTAFVTLLNGEQAEAAIN 75
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVN--PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEF 130
+ +++ V P + V L +T+Q + +GS+
Sbjct: 76 AF---HQSRLREREL-------SVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERC 125
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVADQVLK--NPKQVICGKEVDVKR 175
+ + KG+ F + ++ A + + + + + V
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL-GKPLGPRTLYVHW 171
Score = 55.8 bits (135), Expect = 5e-09
Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 80 HYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSK 138
H + ++I + T+R + KI + GL ++T Q+V D S Y F
Sbjct: 1 HMLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCF-------V 53
Query: 139 NMKKGFCFISFDDQNVADQVLK--NPKQVICGKEVDVKR 175
+ KG F++ + A+ + + + + +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 = 105 bits (264), Expect = 4e-27
Identities = 45/185 (24%), Positives = 77/185 (41%), Gaps = 15/185 (8%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
L+VG LH + E + + FS G + SI + D T +S G+A+V + +
Sbjct: 12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 73 DLLAAGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQY 124
L + I K + DP V IF+ L I + + D FS +
Sbjct: 72 RALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAF 127
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN-PKQVICGKEVDVKRVKFNPETM 183
G+I + D +N KG+ F+ F+ Q A++ ++ ++ ++V V R K E
Sbjct: 128 GNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185
Query: 184 GSVSG 188
+
Sbjct: 186 AELGA 190
Score = 68.1 bits (167), Expect = 1e-13
Identities = 26/117 (22%), Positives = 52/117 (44%), Gaps = 6/117 (5%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
++ +F+ L ++ K + D FS +G + S + D S+G+ FV + TQ+A +
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157
Query: 73 DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSIT 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 = 101 bits (255), Expect = 3e-26
Identities = 35/166 (21%), Positives = 66/166 (39%), Gaps = 14/166 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R L+VG L + E + YF G + +I I D ++ +AFV Y + L
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 77 AGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSIT 128
+ I N + + + +FVG L + ++ +R+ F + S
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTF----NLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN-PKQVICGKEVDV 173
+D +G+ F+SF Q+ A + + Q + G+ + +
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Score = 64.5 bits (158), Expect = 9e-13
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
A + +D LFVG L+ N ++ + + F + S + D TG SRG+ FV
Sbjct: 75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134
Query: 64 TYTTQKAVDDLLAAGD-HYIGNKKI 87
++T+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 = 97.3 bits (243), Expect = 2e-25
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
G + +FVG + E E+ ++FSQYG+V + I R FAFVT+ +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
L D I + +
Sbjct: 56 QSLCGE-DLIIKGISVHISNAEPK 78
Score = 94.2 bits (235), Expect = 2e-24
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FVG T ++TE ++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 = 96.5 bits (241), Expect = 3e-25
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+FVG T ++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
Score = 95.0 bits (237), Expect = 1e-24
Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT 67
+ + K+FVG + +E+ +F QYGEV + I R FAFVT+
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
K L D I + +
Sbjct: 58 DKVAQSLC-GEDLIIKGISVHISNAEPK 84
>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 = 4e-22
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 2/84 (2%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
G+ +FVGG+ E EI +F++YG V+ + I D TG S+G+ FV++ V
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
++ + KK+ ++
Sbjct: 64 QKIVESQ-INFHGKKLKLGPAIRK 86
Score = 83.0 bits (206), Expect = 4e-20
Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 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 = 88.1 bits (219), Expect = 5e-22
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 5/87 (5%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 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 = 86.6 bits (215), Expect = 2e-21
Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 6/91 (6%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FV G + + +YF +G + D K F + D + 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 = 86.6 bits (215), Expect = 2e-21
Identities = 26/103 (25%), Positives = 51/103 (49%), Gaps = 3/103 (2%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
++G++G +D KLF+G + RN EK++ F ++G++ +++ D +TG +G AF+T
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 65 YTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGG 107
Y +++ A K + +V P + G
Sbjct: 62 YCERESAL---KAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101
Score = 69.7 bits (171), Expect = 3e-15
Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ K+F+G + + E+D++ F ++G I E D+ M KG F+++ ++ A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 157 QVLK--NPKQVI--CGKEVDVK 174
+ + ++ + + + VK
Sbjct: 70 KAQSALHEQKTLPGMNRPIQVK 91
>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 = 83.4 bits (207), Expect = 3e-20
Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 1/92 (1%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
+ + +DE KLFVGGL +T E+ + FS+YG++ + + D T +SRGF FVT
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 65 YTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
+ D + A + + ++I + K
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92
Score = 63.0 bits (154), Expect = 8e-13
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+FVGGL+ + EQ + FS+YG I+E D+ +GF F++F++ + A +
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 161 --NPKQVICGKEVDVKR 175
N K + G+++ V +
Sbjct: 73 AMNGKS-VDGRQIRVDQ 88
>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 = 83.5 bits (207), Expect = 3e-20
Identities = 18/84 (21%), Positives = 36/84 (42%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
D R +F L +++ D+FS G+V + I +D + +S+G A+V + ++V
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVN 97
+ + I + N
Sbjct: 83 AIGLTGQRLLGVPIIVQASQAEKN 106
Score = 73.1 bits (180), Expect = 3e-16
Identities = 17/106 (16%), Positives = 37/106 (34%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
+ +P +F L I +D+ D+FS G + + + D++ KG
Sbjct: 9 SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
Query: 144 FCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGA 189
++ F + + Q + G + V+ + + S
Sbjct: 69 IAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114
>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 = 83.0 bits (206), Expect = 4e-20
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++GP + L V L T + F +YG V + I +P+T RGFAFV +
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 67 T----QKAVDDL 74
Q A +
Sbjct: 64 DRRDAQDAEAAM 75
Score = 58.8 bits (143), Expect = 2e-11
Identities = 14/56 (25%), Positives = 24/56 (42%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ V LT + +R F +YG + + P + +GF F+ F D+ A
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 82.3 bits (203), Expect = 1e-19
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEV--ESISIKNDPYTGQSRGFAFVTYT 66
G + RK+FVGGL + E EI F ++G + + +G+AF+ +
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 67 TQKAVDDLLAAGDHYIGN-------KKIDPKRV 92
+ +V L+ A G I K V
Sbjct: 61 EESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
Score = 70.8 bits (173), Expect = 2e-15
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK--KGFCFISFDDQNVADQV 158
K+FVGGL +I E ++ F ++G + +SK+ KG+ F+ F +++ +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 159 LKNPKQV-------ICGKEVDVKRVKFNP 180
+ + + + K V+ P
Sbjct: 69 IDACLEEDGKLYLCVSSPTIKDKPVQIRP 97
>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 = 80.7 bits (200), Expect = 2e-19
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G +G + ++V L + ++ FS+YG+V ++I D T +S+G A
Sbjct: 2 SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61
Query: 62 FVTYTT----QKAVDDL 74
F+ + Q +
Sbjct: 62 FILFLDKDSAQNCTRAI 78
Score = 63.4 bits (155), Expect = 4e-13
Identities = 19/64 (29%), Positives = 29/64 (45%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P K ++V L +T D+ FS+YG + + DK KG FI F D++ A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 158 VLKN 161
+
Sbjct: 74 CTRA 77
>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 = 80.3 bits (199), Expect = 4e-19
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ + L V GL T E+++ + FS+YG + +SI D + +SRGFAFV
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 64 TYTT----QKAVDDL 74
+ ++A +
Sbjct: 63 YFENVDDAKEAKERA 77
Score = 61.1 bits (149), Expect = 3e-12
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
C + V GL+ TE+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
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 81.0 bits (200), Expect = 6e-19
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+G +G +R L+VGGL +K ++ F +G++ I I D T + RGFA
Sbjct: 49 GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108
Query: 62 FVTYTT----QKAVDDL 74
FV + A+D++
Sbjct: 109 FVEFELAEDAAAAIDNM 125
Score = 63.6 bits (155), Expect = 1e-12
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A +
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 160 KN 161
N
Sbjct: 123 DN 124
>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 = 79.1 bits (196), Expect = 6e-19
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT-- 67
G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV +
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 68 --QKAVDDL 74
A+D++
Sbjct: 61 DAAAAIDNM 69
Score = 64.5 bits (158), Expect = 2e-13
Identities = 19/64 (29%), Positives = 31/64 (48%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 158 VLKN 161
+ N
Sbjct: 65 AIDN 68
>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 = 80.5 bits (199), Expect = 8e-19
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
+ GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+
Sbjct: 9 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68
Query: 63 VTYTT----QKAVDDL 74
V Y T Q A++ L
Sbjct: 69 VEYETYKEAQAAMEGL 84
Score = 61.6 bits (150), Expect = 4e-12
Identities = 16/60 (26%), Positives = 29/60 (48%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++ A ++
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
>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 = 79.2 bits (196), Expect = 9e-19
Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY----TTQKAVD 72
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ + ++ AV
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 73 DL 74
+L
Sbjct: 63 NL 64
Score = 66.1 bits (162), Expect = 5e-14
Identities = 15/61 (24%), Positives = 28/61 (45%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+++G + + TE+ + D S G + + FD KG+ FI F D + ++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 161 N 161
N
Sbjct: 63 N 63
>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 = 79.8 bits (197), Expect = 1e-18
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+ + L V GL T E+++ + FS+YG + +SI D + +SRGFA
Sbjct: 32 RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91
Query: 62 FVTYTT----QKAVDDL 74
FV + ++A +
Sbjct: 92 FVYFENVDDAKEAKERA 108
Score = 61.3 bits (149), Expect = 7e-12
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
C + V GL+ TE+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
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 80.2 bits (198), Expect = 1e-18
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ G P L V L T + F +YG V + I D YT +SRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 64 TYTT----QKAVDDL 74
+ + A+D +
Sbjct: 95 RFHDKRDAEDAMDAM 109
Score = 58.2 bits (141), Expect = 8e-11
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
+ V LT + +R F +YG + + P D+ +GF F+ F D+ A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 20/67 (29%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT---- 67
G + L+VG LH N E + F +G++++I + D TG+S+G+ F+T++
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 68 QKAVDDL 74
++A++ L
Sbjct: 61 RRALEQL 67
Score = 59.9 bits (146), Expect = 8e-12
Identities = 19/60 (31%), Positives = 27/60 (45%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++VG L ITE +R F +G I D KG+ FI+F D A + L+
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 78.5 bits (194), Expect = 2e-18
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
+ GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+
Sbjct: 10 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 63 VTYTT----QKAVDDL 74
V Y T Q A++ L
Sbjct: 70 VEYETYKEAQAAMEGL 85
Score = 61.9 bits (151), Expect = 2e-12
Identities = 16/61 (26%), Positives = 29/61 (47%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++ A ++
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 161 N 161
Sbjct: 84 G 84
>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 = 78.5 bits (194), Expect = 2e-18
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 7 GTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
G++G + + +F+ L ++ E+ + + Q+G+++ + + P T S+G AF
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63
Query: 65 YTTQKAVDDLLAAGDH 80
+ TQ+A LAA
Sbjct: 64 FMTQEAAQKCLAAASL 79
Score = 64.7 bits (158), Expect = 2e-13
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+F+ L+ + E+ + + Q+G + + KG F F Q A + L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 161 --NPKQVICGKEVDVKRVKFNP 180
+ + 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 = 78.4 bits (194), Expect = 2e-18
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++GP +D + V L +T E ++ + F +G + I + D TGQS+GFAF
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 63 VTYTT----QKAVDDL 74
+++ +A+ +
Sbjct: 62 ISFHRREDAARAIAGV 77
Score = 59.5 bits (145), Expect = 1e-11
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
I V L+ + E D+++ F +GSI+ DK+ KGF FISF + A +
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
>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 = 78.0 bits (193), Expect = 3e-18
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 7 GTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
G++G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 65 YTT----QKAVDDL 74
+ A+D++
Sbjct: 61 FELAEDAAAAIDNM 74
Score = 63.0 bits (154), Expect = 7e-13
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+ A +
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 160 KN 161
N
Sbjct: 72 DN 73
>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 = 79.9 bits (197), Expect = 3e-18
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 4/75 (5%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ L V L T + F +YG V + I D YT +SRGFAFV
Sbjct: 58 SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117
Query: 64 TYTT----QKAVDDL 74
+ + A+D +
Sbjct: 118 RFHDKRDAEDAMDAM 132
Score = 60.2 bits (146), Expect = 2e-11
Identities = 24/119 (20%), Positives = 39/119 (32%), Gaps = 20/119 (16%)
Query: 58 RGFAFVTYTTQKAVDDLLA--AGDHYIGNKKIDPKRVTKRVNPLK--------------- 100
G TT +AVD A Y + +D +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 101 ---CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ V LT + +R F +YG + + P D+ +GF F+ F D+ A+
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
>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 = 77.2 bits (191), Expect = 3e-18
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT---- 67
G + L++ GL T ++++ YG++ S D T + +G+ FV + +
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 68 QKAVDDL 74
QKAV L
Sbjct: 61 QKAVTAL 67
Score = 58.7 bits (143), Expect = 2e-11
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK- 160
+++ GL T+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 = 8e-18
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
+++ L+ N E + D +YGEVE + I P T + G A V +T+ ++ V
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 73 DL 74
+L
Sbjct: 67 NL 68
Score = 62.4 bits (152), Expect = 1e-12
Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 1/74 (1%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++ L + E ++D +YG + E + G + F A + +KN
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 162 P-KQVICGKEVDVK 174
+ G + +
Sbjct: 68 LHLTSVMGNIIHAQ 81
>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 = 77.5 bits (191), Expect = 9e-18
Identities = 20/79 (25%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D+R ++VG + + +++ +FS G + I+I D ++G +G+A++ + + +VD
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 75 LAAGDHYIGNK--KIDPKR 91
+A + + K+ PKR
Sbjct: 95 VAMDETVFRGRTIKVLPKR 113
Score = 62.4 bits (152), Expect = 2e-12
Identities = 24/86 (27%), Positives = 39/86 (45%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K ++VG + T QD+ +FS GSI DK KG+ +I F ++N D +
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 160 KNPKQVICGKEVDVKRVKFNPETMGS 185
+ 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 = 76.5 bits (189), Expect = 1e-17
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++GP RN + ++VGGL E + + F Q G V + + D TGQ +G+ F
Sbjct: 2 SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61
Query: 63 VTYTT----QKAVDDL 74
V + + A+ +
Sbjct: 62 VEFLSEEDADYAIKIM 77
Score = 57.3 bits (139), Expect = 9e-11
Identities = 16/62 (25%), Positives = 30/62 (48%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
++VGGL +++E + + F Q G + P D+ +G+ F+ F + AD +
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 160 KN 161
K
Sbjct: 75 KI 76
>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 = 76.6 bits (189), Expect = 1e-17
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A V Y T
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 68 ---QKAVDDL 74
A + L
Sbjct: 79 KQALAAKEAL 88
Score = 62.3 bits (152), Expect = 2e-12
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FV + E E ++++ F YG I D+ KG+ + ++ A +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
>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 = 2e-17
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D ++G +GFA++ ++ +++V
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 75 LA 76
LA
Sbjct: 65 LA 66
Score = 58.7 bits (143), Expect = 2e-11
Identities = 16/59 (27%), Positives = 25/59 (42%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
I+VG + T +++ +F GS+ DK KGF +I F D+ L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
>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 = 77.6 bits (191), Expect = 2e-17
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 63 VTYTT----QKAVDDL 74
V Y T A + L
Sbjct: 119 VEYETHKQALAAKEAL 134
Score = 61.8 bits (150), Expect = 9e-12
Identities = 12/61 (19%), Positives = 24/61 (39%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FV + E E ++++ F YG I D+ KG+ + ++ A +
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 161 N 161
Sbjct: 133 A 133
>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 = 2e-17
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ KLF+GGL+R T EK + F ++G + + + D T +SRGFAF+T+ +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63
Query: 74 LLAAGD-HYIGNKKIDPKRVTKR 95
+ + K I ++ K
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAKKP 86
Score = 66.2 bits (162), Expect = 9e-14
Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 2/105 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+F+GGL E E+ ++ F ++G I+E D++ + +GF FI+F++ A K
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKNAAK 66
Query: 161 NP-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAGAAY 204
+ + + GK + V++ K G + R S +
Sbjct: 67 DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111
>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 = 75.3 bits (186), Expect = 2e-17
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT--- 67
G + +LFV L + E+++ FS YG + + D T + +GFAFVT+
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 68 -QKAVDDL 74
KA ++
Sbjct: 63 AVKAYAEV 70
Score = 59.2 bits (144), Expect = 2e-11
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
++FV L+ +E+D+ FS YG ++E P D KGF F++F A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
>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 = 75.8 bits (187), Expect = 2e-17
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT-- 67
G +L+VG LH N E + F +G +ESI + D TG+S+G+ F+T++
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 68 --QKAVDDL 74
+KA++ L
Sbjct: 80 CAKKALEQL 88
Score = 57.7 bits (140), Expect = 7e-11
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
+++VG L ITE +R F +G I Q D KG+ FI+F D A +
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 75.1 bits (185), Expect = 3e-17
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 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 = 63.9 bits (156), Expect = 3e-13
Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 7/79 (8%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
I + + + S Y ++ + DK +GF F+ A Q+L
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 160 KN-----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 = 74.1 bits (183), Expect = 5e-17
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKND-PYTGQSRGFAFVTYTT----QKAVD 72
K+ +G L RN + I + FS YG+++ I + + + S+G+A+V + +KA+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 73 DL 74
+
Sbjct: 66 HM 67
Score = 61.0 bits (149), Expect = 2e-12
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVADQVL 159
K+ +G LT +T+ + + FS YG I P ++ KG+ ++ F++ + A++ L
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 160 K--NPKQVICGKEVDVKRVK 177
K + Q I G+E+ V
Sbjct: 65 KHMDGGQ-IDGQEITATAVL 83
>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 = 74.2 bits (183), Expect = 8e-17
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY----TTQK 69
R +FVG + E+++ D FS+ G V S + D TG+ +G+ F Y T
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 70 AVDDL 74
A+ +L
Sbjct: 66 AMRNL 70
Score = 62.7 bits (153), Expect = 1e-12
Identities = 19/60 (31%), Positives = 33/60 (55%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FVG + E TE+ ++D FS+ G + F+ +D+ KG+ F + DQ A ++N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
>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 = 74.8 bits (184), Expect = 1e-16
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
P + R L V + E ++ F +YG +ES+ I D T QSRG+ FV + +
Sbjct: 35 MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSG 94
Query: 68 ---QKAVDDL 74
Q+A+ L
Sbjct: 95 SSAQQAIAGL 104
Score = 56.7 bits (137), Expect = 3e-10
Identities = 20/98 (20%), Positives = 37/98 (37%), Gaps = 8/98 (8%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
++ P + + V + T + E +R F +YG I + D+ +G
Sbjct: 26 QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85
Query: 144 FCFISFDDQNVADQVLK--NPKQVICGKEVDVKRVKFN 179
+ F+ F + A Q + 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 = 73.9 bits (182), Expect = 1e-16
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPYTGQSRGFAF 62
+ P + K+ V + ++EI + FS +GE++++ + K TG RGF F
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 63 VTYTT----QKAVDDL 74
V + T +KA + L
Sbjct: 63 VDFITKQDAKKAFNAL 78
Score = 58.5 bits (142), Expect = 3e-11
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 4/81 (4%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVADQV 158
KI V + + ++++R+ FS +G + + P + +GF F+ F + A +
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 159 LKNPKQVICGKEVDVKRVKFN 179
+ +R+
Sbjct: 75 FNALCH---STHLYGRRLVLE 92
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dnk_A 2dno_A
Length = 105
Score = 73.9 bits (182), Expect = 1e-16
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G+ G +RKLFVG L++ E+++ F +G ++ ++ P G S+G A
Sbjct: 2 SSGSSGSESRGG-RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59
Query: 62 FVTYTT----QKAVDDL 74
FV +++ Q A+ L
Sbjct: 60 FVKFSSHTEAQAAIHAL 76
Score = 59.2 bits (144), Expect = 2e-11
Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 5/86 (5%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
++ K+FVG L + +E+DV F +G I E + KG F+ F
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSH 66
Query: 153 NVADQVLK--NPKQVI--CGKEVDVK 174
A + + Q + + VK
Sbjct: 67 TEAQAAIHALHGSQTMPGASSSLVVK 92
>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 = 73.0 bits (180), Expect = 2e-16
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT---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 = 55.3 bits (134), Expect = 3e-10
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
I+VG L T + V++ FSQ+G + + +D+ KGF F+ ++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE 53
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 75.0 bits (184), Expect = 2e-16
Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 3/98 (3%)
Query: 1 MSYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIK--NDPYTGQSR 58
+ T RN ++VG T ++++ G + + +K + GQS+
Sbjct: 40 KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99
Query: 59 GFAFVTYTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
G+A V ++ +V LL + +K+D + T++
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
Score = 58.8 bits (142), Expect = 9e-11
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGS--ITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
++VG + T+Q + G + E + +++ KG+ + +N ++L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 160 KN-PKQVICGKEVDVK 174
+ P +V+ G++VDV+
Sbjct: 117 ELLPGKVLNGEKVDVR 132
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 71.9 bits (177), Expect = 4e-16
Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S + ++ KLF+ GL + ++E+ + +G V+ + + + G+ +G A
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 62 FVTYTT----QKAVDDL 74
+V Y +AV +
Sbjct: 62 YVEYENESQASQAVMKM 78
Score = 61.1 bits (149), Expect = 4e-12
Identities = 11/62 (17%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K K+F+ GL T++++ + +G++ + + +++ KG ++ +++++ A Q +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQAV 75
Query: 160 KN 161
Sbjct: 76 MK 77
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 72.1 bits (177), Expect = 5e-16
Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
R +++ G + +I ++ G+V +I ++ +G FV + + ++
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF 68
Query: 75 LAAGDHYIGNKKI 87
+ +
Sbjct: 69 VETPGQKYKETDL 81
Score = 70.5 bits (173), Expect = 1e-15
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+++ G T+ T D++++ G + Q K KG F+ FD A + ++
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVET 71
Query: 162 PKQVICGKEVDVKR 175
P Q ++ +
Sbjct: 72 PGQKYKETDLLILF 85
>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 = 71.0 bits (174), Expect = 1e-15
Identities = 17/102 (16%), Positives = 40/102 (39%), Gaps = 9/102 (8%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQ--PFDKSKNMKKGFCFISFDDQNVAD- 156
C++F+GG+ +++ + ++ K +GF F+ ++ A
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 157 --QVLKNPKQVICGKEVDVK----RVKFNPETMGSVSGAVRG 192
+ L + + G ++ V + + + M +VSG G
Sbjct: 68 ARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSSG 109
Score = 66.7 bits (163), Expect = 5e-14
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 10/87 (11%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDP-YTGQSRGFAFVTYTTQKAVD 72
+LF+GG+ + +EI + ++ E V + + ++RGFAFV Y + +A
Sbjct: 7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66
Query: 73 D---LLAAGDHYIGNKKI-----DPKR 91
L G + +I +P+
Sbjct: 67 MARRKLMPGRIQLWGHQIAVDWAEPEI 93
>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 = 70.7 bits (174), Expect = 1e-15
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 1/88 (1%)
Query: 8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT 67
G LF+G L+ N E+ S+ +++ D TG +R F +V + +
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFES 67
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ ++ L + +I ++ R
Sbjct: 68 AEDLEKALELTGLKVFGNEIKLEKPKGR 95
Score = 51.9 bits (125), Expect = 6e-09
Identities = 11/77 (14%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+F+G L + +++ S+ + + D + F ++ F+ ++ L+
Sbjct: 18 FNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE 76
Query: 161 NPKQVICGKEVDVKRVK 177
+ G E+ +++ K
Sbjct: 77 LTGLKVFGNEIKLEKPK 93
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 69.9 bits (172), Expect = 2e-15
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
G + ++FV L + K + D F++ G V IK + G+S+G V + +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 68 ---QKAVDDL 74
++A +
Sbjct: 59 EVAERACRMM 68
Score = 50.3 bits (121), Expect = 2e-08
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
C+IFV L + T + ++D F++ G + + K+ KG + F+ VA++ +
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKS--KGCGVVKFESPEVAERACR 66
Query: 161 --NPKQVICGKEVDVKRVKFNP 180
N + + G+E+DV+ +
Sbjct: 67 MMNGMK-LSGREIDVRIDRNAS 87
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 70.0 bits (172), Expect = 3e-15
Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 16 FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTAD 74
Query: 63 VTYTT----QKAVDDL 74
V + KA+
Sbjct: 75 VHFERKADALKAMKQY 90
Score = 46.9 bits (112), Expect = 4e-07
Identities = 12/59 (20%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+ V L +++ D+++ F+++G++ + +D+S G + F+ + A + +K
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMK 88
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G +R +FVG L E+ + + F Q G + ++I D G+ + F
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFG 60
Query: 62 FVTYTT----QKAVDDL 74
FV + A+ L
Sbjct: 61 FVCFKHPESVSYAIALL 77
Score = 53.8 bits (130), Expect = 1e-09
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 9/81 (11%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FVG L + E+ + + F Q G +T+ D+ K F F+ F +
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 161 --NPKQVICGKEVDVKRVKFN 179
N G + + + +
Sbjct: 76 LLN------GIRLYGRPINVS 90
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 69.7 bits (171), Expect = 4e-15
Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
R + ++ ++L V + + ++ F Q+G++ + I + S+GF FV
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFV 74
Query: 64 TYTT----QKAVDDL 74
T+ +A + L
Sbjct: 75 TFENSADADRAREKL 89
Score = 54.6 bits (132), Expect = 8e-10
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++ V + + D+R F Q+G I + + F++ KGF F++F++ AD+ +
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 162 PKQVICGKEVDVKRVKFN 179
+ G V+ ++++ N
Sbjct: 89 ----LHGTVVEGRKIEVN 102
>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 = 5e-15
Identities = 26/185 (14%), Positives = 51/185 (27%), Gaps = 45/185 (24%)
Query: 15 DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 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 RVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
R+ + E+TE++ + + G K+ + + +D ++
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177
Query: 155 ADQVL 159
A + L
Sbjct: 178 ALETL 182
Score = 54.3 bits (130), Expect = 7e-09
Identities = 9/77 (11%), Positives = 22/77 (28%), Gaps = 1/77 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK-AVDDLLAA 77
L E+ + + G S+K + + + ++ A++ L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 78 GDHYIGNKKIDPKRVTK 94
+ + N K
Sbjct: 186 NHYQMKNPNGPYPYTLK 202
Score = 43.5 bits (102), Expect = 3e-05
Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 7/82 (8%)
Query: 101 CKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+ V GL + V + F YG++ + + K G + D D+ +
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAI 59
Query: 160 KN-PKQVICGKEVDVKRVKFNP 180
+ + G++++V K
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPA 81
>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 = 69.2 bits (170), Expect = 5e-15
Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT--- 67
++ ++L V + + ++ F Q+G++ + I + S+GF FVT+
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSAD 67
Query: 68 -QKAVDDL 74
+A + L
Sbjct: 68 ADRAREKL 75
Score = 56.5 bits (137), Expect = 1e-10
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
++ V + + D+R F Q+G I + + F++ + KGF F++F++ AD+ +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRARE 73
Query: 161 NPKQVICGKEVDVKRVKFN 179
+ G V+ ++++ N
Sbjct: 74 K----LHGTVVEGRKIEVN 88
>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 = 68.4 bits (168), Expect = 7e-15
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
L++G L T ++++ + G ++ I + GQS+GFA V ++ + L+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 76 AA 77
Sbjct: 63 DL 64
Score = 52.6 bits (127), Expect = 3e-09
Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+++G LT T++D+ + G I E + +++ KGF + + + +++
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 160 K 160
Sbjct: 63 D 63
>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 = 68.5 bits (168), Expect = 9e-15
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
GP N++ +++VG L + K+I D F +YG + I +KN FAFV
Sbjct: 10 GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFV 66
Query: 64 TYTT----QKAVDDL 74
+ + AV
Sbjct: 67 EFEDPRDAEDAVYGR 81
Score = 59.6 bits (145), Expect = 1e-11
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
C+I+VG L +I +D+ D F +YG+I + + F F+ F+D A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAE 75
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 68.1 bits (167), Expect = 1e-14
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQ---SRGFAFVTYTT- 67
G + LF+ L+ +T E+ + FS+ G ++S +I S GF FV Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 68 ---QKAVDDL 74
QKA+ L
Sbjct: 61 EQAQKALKQL 70
Score = 53.0 bits (128), Expect = 3e-09
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK---KGFCFISFDDQNVADQ 157
+F+ L TE+ ++ FS+ G+I K+K GF F+ + A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 158 VLK--NPKQVICGKEVDVKR 175
LK + G +++V+
Sbjct: 66 ALKQLQ-GHTVDGHKLEVRI 84
>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 = 68.9 bits (169), Expect = 1e-14
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 21 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTA 79
Query: 62 FVTYTT----QKAVDDL 74
V + KA+
Sbjct: 80 DVHFERRADALKAMKQY 96
Score = 47.4 bits (113), Expect = 5e-07
Identities = 12/59 (20%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+ V L +++ D+++ F+++G++ + +D+S G + F+ + A + +K
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALKAMK 94
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 70.3 bits (172), Expect = 1e-14
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+ + G G KL V L + +I + F+++G ++ ++ D +G+S G A
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTA 132
Query: 62 FVTYTT----QKAVDDL 74
V + KA+
Sbjct: 133 DVHFERRADALKAMKQY 149
Score = 48.3 bits (115), Expect = 5e-07
Identities = 14/80 (17%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK- 160
K+ V L +++ D+++ F+++G++ + +D+S G + F+ + A + +K
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQ 148
Query: 161 -NPKQVICGKEVDVKRVKFN 179
G +D + +
Sbjct: 149 YK------GVPLDGRPMDIQ 162
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPYTGQSRGFAFVTYTTQKA 70
G + +F+G L EK + D FS +G + ++ I DP TG S+G+AF+ + + A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 71 VDDLLAAGD-HYIGNKKIDPKRVTKRVNP 98
D + A + Y+ N+ I V+
Sbjct: 61 SDAAIEAMNGQYLCNRPI-------TVSY 82
Score = 55.3 bits (134), Expect = 4e-10
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKGFCFISFDDQNVADQVLK 160
IF+G L EI E+ + D FS +G I + + D KG+ FI+F + +D ++
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 161 NPK-QVICGKEVDV 173
Q +C + + V
Sbjct: 67 AMNGQYLCNRPITV 80
>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 = 1e-14
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
LFVG L+ N ++ + + F + S + D TG SRG+ FV++T+Q + + +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 78 GD-HYIGNKKIDPKRVTKRVN 97
+ + + R+N
Sbjct: 63 MQGQDLNGRPL-------RIN 76
Score = 55.2 bits (134), Expect = 3e-10
Identities = 14/56 (25%), Positives = 26/56 (46%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
+FVG L + ++ +R+ F + S +D +G+ F+SF Q+ A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58
>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 = 68.0 bits (167), Expect = 2e-14
Identities = 22/118 (18%), Positives = 48/118 (40%), Gaps = 17/118 (14%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G G G +F+ L ++ K + D FS +G + S + D S+G+ FV +
Sbjct: 1 GPLGSG-----NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFE 53
Query: 67 TQKAVDDLLAAGD-HYIGNKKI-----DPKRVTKRVNPLKCK----IFVGGLTTEITE 114
TQ+A + + + + ++K+ ++ + + K +++ T
Sbjct: 54 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111
Score = 58.4 bits (142), Expect = 5e-11
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
IF+ L I + + D FS +G+I + D++ + KG+ F+ F+ Q A++ ++
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIE 63
Query: 161 --NPKQVICGKEVDVKRVKFNPETMGSVSG 188
N ++ ++V V R K E +
Sbjct: 64 KMN-GMLLNDRKVFVGRFKSRKEREAELGA 92
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 101
Score = 67.3 bits (165), Expect = 2e-14
Identities = 12/95 (12%), Positives = 39/95 (41%), Gaps = 10/95 (10%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
+ + + L + L + E+ + + F + ++ G+S+G+AF
Sbjct: 2 SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAF 57
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
+ + + + + L + + ++I+ + + R+
Sbjct: 58 IEFASFEDAKEALNSCN----KREIEGRAI--RLE 86
Score = 53.8 bits (130), Expect = 2e-09
Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ + L+ TE+ +++ F + I Q KS KG+ FI F A + L
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS----KGYAFIEFASFEDAKEALN 71
Query: 161 NPKQVICGKEVDVKRVKFNPET 182
+ +E++ + ++ +
Sbjct: 72 S----CNKREIEGRAIRLELQG 89
>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 = 66.8 bits (164), Expect = 2e-14
Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
GP + +FVG L I F+ +G + + D TG+S+G+ FV++ +
Sbjct: 1 GPLGSHFH-VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59
Query: 70 AVDDLLAA-GDHYIGNKKIDPKRVTKRVN 97
++ + G ++G ++I R N
Sbjct: 60 DAENAIQQMGGQWLGGRQI-------RTN 81
Score = 52.9 bits (128), Expect = 2e-09
Identities = 17/59 (28%), Positives = 33/59 (55%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FVG L+ EIT + F+ +G I++ + D + KG+ F+SF ++ A+ ++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>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 = 66.9 bits (164), Expect = 2e-14
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKA 70
R L L N E E+ + F E+ + G+S+G A++ + + +K
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKN 69
Query: 71 VDDL 74
+++
Sbjct: 70 LEEK 73
Score = 52.3 bits (126), Expect = 5e-09
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+ L+ ITE ++++ F I KG +I F + A++ L+
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 162 PKQVICGKEVD 172
+ G E+D
Sbjct: 73 KQ----GAEID 79
>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 = 68.3 bits (167), Expect = 4e-14
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QK 69
L+VG L T E++I + FS+ G+++ I + D + GF FV Y + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 70 AVDDL 74
A+ +
Sbjct: 97 AMRYI 101
Score = 62.5 bits (152), Expect = 4e-12
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 7/113 (6%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
C ++VG L+ TE+ + + FS+ G I + DK K GFCF+ + + A+ ++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 161 NPKQVICGKEVDVKRVKFN---PETMGSVSGAVRGAGARVSSAGAAYAAAPGR 210
I G +D + ++ + G G R G Y A G
Sbjct: 100 Y----INGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGG 148
>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 = 69.2 bits (169), Expect = 4e-14
Identities = 30/200 (15%), Positives = 59/200 (29%), Gaps = 52/200 (26%)
Query: 19 LFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----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 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ + + ++E+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 = 43.7 bits (103), Expect = 2e-05
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 101 CKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+ V L E +T Q + F YG + + F+ KK + D N A +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAM 58
Query: 160 KNPK-QVICGKEVDVKRVK 177
+ + GK + + K
Sbjct: 59 SHLNGHKLHGKPIRITLSK 77
>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 = 66.6 bits (163), Expect = 6e-14
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 7 GTAGPGRN-----DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
G++G + +FVG L ++I F+ +G + + D TG+S+G+
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 62 FVTYTT----QKAVDDL 74
FV++ + A+ +
Sbjct: 61 FVSFFNKWDAENAIQQM 77
Score = 54.3 bits (131), Expect = 1e-09
Identities = 18/56 (32%), Positives = 34/56 (60%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
+FVG L+ EIT +D++ F+ +G I++ + D + KG+ F+SF ++ A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
>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 = 65.8 bits (161), Expect = 6e-14
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPYTGQ 56
+ +D +FV GL N + + DYF Q G +++ I++ D TG+
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
Query: 57 SRGFAFVTYTTQKAVD 72
+G A V++ +
Sbjct: 62 LKGEATVSFDDPPSAK 77
Score = 57.7 bits (140), Expect = 5e-11
Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
IFV GL +T + V DYF Q G I ++ D+ KG +SFDD
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 154 VAD 156
A
Sbjct: 75 SAK 77
>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 = 66.2 bits (162), Expect = 7e-14
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 9/93 (9%)
Query: 1 MSYRANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSR 58
++ ++ G AG + + LF+ L + G++++ F +G V S + D T S+
Sbjct: 8 LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
Query: 59 GFAFVTYTT----QKAVDDLLAAGDHYIGNKKI 87
F FV+Y Q A+ + IG K++
Sbjct: 68 CFGFVSYDNPVSAQAAIQSM---NGFQIGMKRL 97
Score = 51.2 bits (123), Expect = 2e-08
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 94 KRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
++ P +F+ L E +QD+ F +G++ + DK N+ K F F+S+D+
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 154 VADQVLK--NPKQVICGKEVDVKRVKFN 179
A ++ N G ++ +KR+K
Sbjct: 79 SAQAAIQSMN------GFQIGMKRLKVQ 100
>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 = 65.7 bits (161), Expect = 1e-13
Identities = 21/101 (20%), Positives = 34/101 (33%), Gaps = 18/101 (17%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
A D L++ L + E+E+ + +G+V S I D +G SRG F +
Sbjct: 18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMEST 76
Query: 68 ---QKAVDDLLAAGDHYIGNKKIDPKRVTKRVN---PLKCK 102
+ + +I PL CK
Sbjct: 77 EKCEAVIGHF---NGKFIKTPPG-------VSAPTEPLLCK 107
Score = 51.5 bits (124), Expect = 1e-08
Identities = 15/101 (14%), Positives = 32/101 (31%), Gaps = 9/101 (8%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
++ K+ +++ L + EQ++ + +G + + D S +G
Sbjct: 10 ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGV 68
Query: 145 CFISFDDQNVADQVLK--NPKQVICGKEVDV-----KRVKF 178
F + + V+ N K I KF
Sbjct: 69 GFARMESTEKCEAVIGHFNGKF-IKTPPGVSAPTEPLLCKF 108
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 15/77 (19%)
Query: 7 GTAGPGRNDER-----KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
G++G ++ +LFVG L + E+E+ F +YG+ + I D +GF
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54
Query: 62 FVTYTT----QKAVDDL 74
F+ T + A +L
Sbjct: 55 FIRLETRTLAEIAKVEL 71
Score = 60.3 bits (147), Expect = 5e-12
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
++FVG L +ITE+++R F +YG E D KGF FI + + +A+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 66
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 64.6 bits (158), Expect = 3e-13
Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
+ L++ L E+++ F+++ E + I+ TG+ RG AF+T+ +A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 73 DL 74
+
Sbjct: 86 LV 87
Score = 56.1 bits (136), Expect = 3e-10
Identities = 13/60 (21%), Positives = 28/60 (46%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+++ L+ +TE+D+ F+++ F +G FI+F ++ +A Q L
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 64.3 bits (157), Expect = 3e-13
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDD 73
LF+ L + + ++ F +G V S + D T S+ F FV++ Q A+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 74 LLAAGDHYIGNKKI 87
+ +G K++
Sbjct: 102 M---NGFQVGTKRL 112
Score = 49.7 bits (119), Expect = 6e-08
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P C +F+ L E T+ D+ F +G++ + DK ++ K F F+SFD+ + A
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 158 VLK--NPKQVICGKEVDVKRVK 177
+K N G +V KR+K
Sbjct: 98 AIKAMN------GFQVGTKRLK 113
>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 = 64.3 bits (157), Expect = 4e-13
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
R L++ L +E+ D F +YG + I + N T ++RG A+V Y + AVD
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65
Query: 73 DL 74
L
Sbjct: 66 HL 67
Score = 55.1 bits (133), Expect = 8e-10
Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+++ L +IT +++ D F +YG I + + +G ++ ++D A + +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE---TRGTAYVVYEDIFDAKNAVDH 66
>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 = 63.5 bits (155), Expect = 5e-13
Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 91 RVTKRVNPLKCKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+ R + +K ++F+G L + ++++D+ FS YG I + N+K F FI F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQF 64
Query: 150 DDQNVADQVLKNP-KQVICGKEVDV 173
D+ ++ +++ GK++ +
Sbjct: 65 DNPQSVRDAIEXESQEMNFGKKLIL 89
Score = 57.3 bits (139), Expect = 8e-11
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 2 SYRANGTAGPGRNDERKLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGF 60
+ ++G G + + +LF+G L +N ++++ FS YG + I+IK F
Sbjct: 8 HHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAF 59
Query: 61 AFVTYTTQKAVDD 73
F+ + ++V D
Sbjct: 60 GFIQFDNPQSVRD 72
>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 = 63.0 bits (154), Expect = 5e-13
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK- 160
K+++G L+ +T 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
Score = 60.7 bits (148), Expect = 4e-12
Identities = 14/72 (19%), Positives = 24/72 (33%), Gaps = 12/72 (16%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G KL++G L ++ F G+AFV Y
Sbjct: 1 GSSGSSGM--NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYP 52
Query: 67 T----QKAVDDL 74
+A++ L
Sbjct: 53 DQNWAIRAIETL 64
>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 = 63.1 bits (154), Expect = 6e-13
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPYTGQSRGFAFV 63
++G++G + L++G L E I+ F+ GE V S+ I + TG G+ FV
Sbjct: 2 SSGSSGMAAS----LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57
Query: 64 TYTTQKAVDDLLAA 77
+ + L
Sbjct: 58 EFADLATAEKCLHK 71
Score = 55.0 bits (133), Expect = 4e-10
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ + +++G L + E + F+ G ++ + ++ + G+CF+ F D A
Sbjct: 6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65
Query: 156 DQVLKNPK-QVICGKEVDVKRVKFN 179
++ L + + G KR K N
Sbjct: 66 EKCLHKINGKPLPGATP-AKRFKLN 89
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 68.3 bits (166), Expect = 6e-13
Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 4/95 (4%)
Query: 3 YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
+ + + + LFV ++ +T E ++ F YG ++ I + +G+ RG+AF
Sbjct: 89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
+ Y ++ D+ +A H KKID +RV V
Sbjct: 149 IEYEHER---DMHSAYKH-ADGKKIDGRRVLVDVE 179
Score = 58.7 bits (141), Expect = 1e-09
Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 1/88 (1%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
K DP +FV + + TE +R F YG I + K +G+
Sbjct: 87 KMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Query: 145 CFISFDDQNVADQVLKNPKQV-ICGKEV 171
FI ++ + K+ I G+ V
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRV 174
>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 = 66.3 bits (161), Expect = 8e-13
Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPYTGQSRGFA 61
A L++G L T ++++ + G ++ I + GQS+GFA
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115
Query: 62 FVTYTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
V ++ + L+ + + V K+
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150
Score = 62.8 bits (152), Expect = 1e-11
Identities = 25/157 (15%), Positives = 50/157 (31%), Gaps = 8/157 (5%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+++G LT T++D+ + G I E + +++ KGF + + + +++
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 160 KN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAGAAYAAAPGRVVAYPSTY 218
PK+ + G+ V N + + R +G A PG
Sbjct: 130 DLLPKRELHGQNPVVT--PVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGG---SSRAA 184
Query: 219 AGYAAADYGYTAGSYDAYATAYPGYDYSAMGYAYPAP 255
G G+ +PA
Sbjct: 185 FPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAG 221
>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 = 63.2 bits (154), Expect = 8e-13
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPYTGQSRGFAFVTYT 66
D ++V GL+ + ++ D+F Q G V+ I I D TG+ +G A V+Y
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 67 TQKAVD 72
Sbjct: 74 DPPTAK 79
Score = 56.6 bits (137), Expect = 2e-10
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
I+V GL +T D+ D+F Q G + ++ DK KG +S++D
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 154 VAD 156
A
Sbjct: 77 TAK 79
>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 = 62.3 bits (152), Expect = 9e-13
Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 7 GTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
G++G D+ L+VGGL E ++ ++F Q+GE+ +I++ + AF+
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54
Query: 65 YTT----QKAVDDLLAAGDHYIGNKKI 87
+ T + A + + +++
Sbjct: 55 FATRQAAEVAAEKSF--NKLIVNGRRL 79
Score = 61.9 bits (151), Expect = 1e-12
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ ++VGGL ITE D+R++F Q+G I + FI F + A+
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAE 62
Query: 157 QVLKNP--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 = 62.5 bits (152), Expect = 9e-13
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT-- 67
P R RKL + + + + ++ QYG VES N VTY++
Sbjct: 9 VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKD 65
Query: 68 --QKAVDDLLAAGDHYIGNKKI 87
++A+D L + N +
Sbjct: 66 QARQALDKL---NGFQLENFTL 84
Score = 47.4 bits (113), Expect = 2e-07
Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K+ + + + + + QYG + +Q S + +++ ++ A Q L
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQAL 71
Query: 160 KN 161
Sbjct: 72 DK 73
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 62.7 bits (153), Expect = 9e-13
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K++VG L G+ E+ FS YG + ++ I +P GFAFV + + +D +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 78 GDHYIGNKKIDPKRVTKRVN 97
D K I RV RV
Sbjct: 57 LD----GKVICGSRV--RVE 70
Score = 58.5 bits (142), Expect = 3e-11
Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 6/101 (5%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K++VG L T + ++ FS YG + + GF F+ F+D A+ ++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 162 P-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAG 201
+VICG V V+ P R V G
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNG 97
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 63.2 bits (154), Expect = 1e-12
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPYTGQSRGFAFVTYT 66
D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V++
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 67 TQKAVD 72
+
Sbjct: 66 DPPSAK 71
Score = 56.3 bits (136), Expect = 2e-10
Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
IFV GL +T + V DYF Q G I ++ D+ KG +SFDD
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 154 VAD 156
A
Sbjct: 69 SAK 71
>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 = 63.1 bits (154), Expect = 1e-12
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G GR +FV L G K++ + FS G V I D G+SRG
Sbjct: 2 SSGSSGALQAGRLG-STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59
Query: 62 FVTYTT----QKAVDDL 74
VT+ +A+
Sbjct: 60 TVTFEQSIEAVQAISMF 76
Score = 48.5 bits (116), Expect = 1e-07
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 4/87 (4%)
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
L +FV L ++ + +++ FS G + DK +G ++F+ A
Sbjct: 12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAV 70
Query: 157 QVLK--NPKQVICGKEVDVKRVKFNPE 181
Q + N Q++ + + VK +
Sbjct: 71 QAISMFN-GQLLFDRPMHVKMDERALP 96
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+F+G L E TEQ++R F QYG + E + K + F+ +D+ A+ ++
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIR 60
Query: 161 N-PKQVICGKEVDV 173
N + G ++V
Sbjct: 61 NLHHYKLHGVNINV 74
Score = 60.3 bits (147), Expect = 5e-12
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 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
>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 = 62.7 bits (153), Expect = 1e-12
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 5 ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G R L+VG L R+ E I FSQ G +S + + + + F
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCF 59
Query: 63 VTYTT----QKAVDDL 74
V + A+ +
Sbjct: 60 VEFYEHRDAAAALAAM 75
Score = 54.6 bits (132), Expect = 7e-10
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++VG L+ ++TE + FSQ G + + + N +CF+ F + A L
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 = 62.3 bits (152), Expect = 1e-12
Identities = 20/91 (21%), Positives = 33/91 (36%), Gaps = 14/91 (15%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G KL VG + +E+ F +YG V I + +AFV
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHME 52
Query: 67 TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
+ + + D N + KR+ V
Sbjct: 53 RAEDAVEAIRGLD----NTEFQGKRM--HVQ 77
Score = 58.8 bits (143), Expect = 2e-11
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+ VG ++ T Q++R F +YG + E + K + F+ + A + ++
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECD--------IVKDYAFVHMERAEDAVEAIR 62
Query: 161 N-PKQVICGKEVDV 173
GK + V
Sbjct: 63 GLDNTEFQGKRMHV 76
>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 = 61.8 bits (151), Expect = 1e-12
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
KIFVG ++ T Q++R F + G + E + K + F+ + + A +
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECD--------VVKDYAFVHMEKEADAKAAIA 61
Query: 161 N-PKQVICGKEVDVKRVKFNPETMGSVSG 188
+ + GK ++V+ + G SG
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKKSGPSSG 90
Score = 59.5 bits (145), Expect = 9e-12
Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G N K+FVG + +E+ F + G V + + +AFV
Sbjct: 1 GSSGSSGN-TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHME 51
Query: 67 T----QKAVDDL 74
+ A+ L
Sbjct: 52 KEADAKAAIAQL 63
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 62.3 bits (151), Expect = 2e-12
Identities = 18/110 (16%), Positives = 36/110 (32%), Gaps = 16/110 (14%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYF-----SQYGEVESISIKNDPYTGQSRGFAFV 63
G + + V GL ++ + YF S G V S + +
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVL 52
Query: 64 TYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEIT 113
T+ + +LA DH + ++ + R ++ + GL +
Sbjct: 53 TFREPADAERVLAQADHELHGAQLSLRPAPPRAP---ARLLLQGLPPGTS 99
Score = 61.5 bits (149), Expect = 3e-12
Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 24/104 (23%)
Query: 101 CKIFVGGLTTEITEQDVRDYF-----SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ V GL + ++ + YF S G + +Q+ ++F + A
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL--------GCGGVLTFREPADA 60
Query: 156 DQVLKNPKQVICGKEVDVKRVK-----------FNPETMGSVSG 188
++VL + G ++ ++ P T G SG
Sbjct: 61 ERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPSSG 104
>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 = 63.4 bits (154), Expect = 2e-12
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
+ K++VG L N + E+ F YG + S+ + +P GFAFV + +
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDA 123
Query: 72 DD 73
D
Sbjct: 124 AD 125
Score = 61.0 bits (148), Expect = 1e-11
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
PL CK++VG L + ++ F YG + + GF F+ F+D A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAAD 125
Query: 158 VLKNP-KQVICGKEVDV 173
++ + +CG V V
Sbjct: 126 AVRELDGRTLCGCRVRV 142
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 61.6 bits (150), Expect = 3e-12
Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 7/81 (8%)
Query: 92 VTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+ + P ++G + TE D+ F +G I +F+ + KG CFI +D
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDT 72
Query: 152 QNVADQVLKN-PKQVICGKEV 171
A + G+ +
Sbjct: 73 HEQAAVCIVALANFPFQGRNL 93
Score = 56.9 bits (138), Expect = 1e-10
Identities = 9/60 (15%), Positives = 20/60 (33%), Gaps = 10/60 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
++G + E ++ F +G + + +G F+ Y T + L
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 60.7 bits (148), Expect = 4e-12
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 10/78 (12%)
Query: 98 PLKCKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
P K ++F+G L + ++++D+ FS YG I + N+K F FI FD+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQFDNPQSVR 59
Query: 157 QVLKNP-KQVICGKEVDV 173
++ +++ GK++ +
Sbjct: 60 DAIECESQEMNFGKKLIL 77
Score = 54.5 bits (132), Expect = 6e-10
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 15 DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ +LF+G L +N ++++ FS YG + I+IK F F+ + ++V D
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRD 60
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 61.2 bits (149), Expect = 4e-12
Identities = 28/106 (26%), Positives = 49/106 (46%), Gaps = 8/106 (7%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
K++ + V + +P C ++ GG+ + +T+Q +R FS +G I E + + KG+
Sbjct: 10 KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGY 63
Query: 145 CFISFDDQNVADQVLKN-PKQVICGKEVDVKRVKFNPE-TMGSVSG 188
F+ F A + + I G V K +P+ T G SG
Sbjct: 64 SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSSG 109
Score = 55.4 bits (134), Expect = 5e-10
Identities = 11/60 (18%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
++ GG+ ++ + FS +G++ I + + +G++FV ++T A+ +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
>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 = 60.7 bits (148), Expect = 5e-12
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++GP + + LFV GL +T E+ + + F I D TG S+GF F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGF 58
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
V + +++ A + + +ID +V ++
Sbjct: 59 VDFNSEEDAKAAKEAME----DGEIDGNKV--TLD 87
Score = 46.5 bits (111), Expect = 5e-07
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FV GL+ + TE+ +++ F + D+ KGF F+ F+ + A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 161 NPKQVICGKEVDVKRVKFN 179
+ E+D +V +
Sbjct: 73 A----MEDGEIDGNKVTLD 87
>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 = 5e-12
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFV 63
+ A G+ + V + EI D+F Y + S+ +K + G G A V
Sbjct: 4 GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62
Query: 64 TYTT----QKAVDDLLAAGDHYIGNKKI 87
+ + AV DL D IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87
Score = 48.8 bits (117), Expect = 6e-08
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 1/81 (1%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P I V + ++ ++ D+F Y I K M G ++F+ ++ A
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 158 VLKN-PKQVICGKEVDVKRVK 177
+ + + I ++V +
Sbjct: 73 AVIDLNDRPIGSRKVKLVLGS 93
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 15/77 (19%)
Query: 7 GTAGPGRNDE-----RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
G++G +++ + L+V L +T E+ I F+ +K + R +A
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYA 54
Query: 62 FVTYTT----QKAVDDL 74
FV ++ +A+ L
Sbjct: 55 FVHFSNREDAVEAMKAL 71
Score = 52.7 bits (127), Expect = 3e-09
Identities = 11/76 (14%), Positives = 29/76 (38%), Gaps = 10/76 (13%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++V L +E+ + F+ + + + F+ F ++ A + +K
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70
Query: 162 PKQVICGKEVDVKRVK 177
+ GK +D ++
Sbjct: 71 ----LNGKVLDGSPIE 82
>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 = 60.1 bits (146), Expect = 1e-11
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 97 NPLKCKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+ ++F+G L T + + DV FS+YG + ++ KG+ F+ + ++ A
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC--------SVHKGYAFVQYSNERHA 75
Query: 156 DQVLKNP-KQVICGKEVDV 173
+ +V+ G+ +D+
Sbjct: 76 RAAVLGENGRVLAGQTLDI 94
Score = 54.3 bits (131), Expect = 1e-09
Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 14/94 (14%)
Query: 1 MSYRANGTAGPGRND----ERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPYTG 55
MS + + +ND ++F+G L+ + ++ FS+YG V S+
Sbjct: 8 MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH------ 61
Query: 56 QSRGFAFVTYTTQKAVDDLLAAGDHY-IGNKKID 88
+G+AFV Y+ ++ + + + + +D
Sbjct: 62 --KGYAFVQYSNERHARAAVLGENGRVLAGQTLD 93
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 59.7 bits (145), Expect = 1e-11
Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAGD 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 = 50.1 bits (120), Expect = 3e-08
Identities = 12/58 (20%), Positives = 27/58 (46%)
Query: 104 FVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+ + ++ + FS+ G + + P D++ KGF F+ N A +++K+
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
>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 = 59.5 bits (145), Expect = 1e-11
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDD 73
L+V L ++ + FS +G + S + + G+S+GF FV +++ KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 74 LLAAGDHYIGNKKI 87
+ + K +
Sbjct: 75 M---NGRIVATKPL 85
Score = 48.7 bits (117), Expect = 8e-08
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
++V L I ++ +R FS +G+IT + + ++ KGF F+ F A +
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATK 70
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFV 63
+ + G+ + V + EI D+F Y + S+ +K + G G A V
Sbjct: 4 GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62
Query: 64 TYTT----QKAVDDLLAAGDHYIGNKKI 87
+ + AV DL D IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87
Score = 48.5 bits (116), Expect = 9e-08
Identities = 12/64 (18%), Positives = 25/64 (39%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P I V + ++ ++ D+F Y I K M G ++F+ ++ A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 158 VLKN 161
+ +
Sbjct: 73 AVID 76
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 59.6 bits (145), Expect = 1e-11
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT---- 67
G +LFV + E E+N+ F +G ++ + I GFAFV +
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESA 78
Query: 68 QKAVDDL 74
KA++++
Sbjct: 79 AKAIEEV 85
Score = 56.2 bits (136), Expect = 3e-10
Identities = 13/90 (14%), Positives = 35/90 (38%), Gaps = 11/90 (12%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ ++FV ++ E ++ + F +G + E + + GF F+
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFV 70
Query: 148 SFDDQNVADQVLK--NPKQVICGKEVDVKR 175
F++ A + ++ + K + ++V
Sbjct: 71 EFEEAESAAKAIEEVHGKS-FANQPLEVVY 99
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 59.2 bits (144), Expect = 2e-11
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
+VG L NT + +I+ F + S+ + D T + +GF +V + ++ + L
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 77 AGDHYIGNKKIDPKRVTKRVN 97
+G++ + RV+
Sbjct: 75 YDGALLGDRSL-------RVD 88
Score = 53.0 bits (128), Expect = 3e-09
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+VG L + D+ F I + DK + KGFC++ FD+ + + L
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 162 PKQVICGKEVDV 173
++ + + V
Sbjct: 76 DGALLGDRSLRV 87
>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 = 61.9 bits (150), Expect = 2e-11
Identities = 31/213 (14%), Positives = 59/213 (27%), Gaps = 52/213 (24%)
Query: 6 NGTAGPGRNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
G L V L+ + + F YG+V+ + I + + A V
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQ 78
Query: 65 YTT----QKAVDDL-----------------------------LAAGDHYIGNK----KI 87
Q A+ L Y + K
Sbjct: 79 MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
+ + + P + + + ++E+D++ FS G + + + F K + I
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALI 194
Query: 148 SFDDQNVADQVLK--NPKQVICGKEVDVKRVKF 178
A Q L + + + RV F
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHL---RVSF 224
>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 = 13/75 (17%), Positives = 33/75 (44%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+ + GL +++++ +FS + + G F+ F Q +A++ LK
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 163 KQVICGKEVDVKRVK 177
K+ I + +++ +
Sbjct: 78 KERIGHRYIEIFKSS 92
Score = 57.8 bits (140), Expect = 6e-11
Identities = 20/91 (21%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFVT 64
+ P ++ + + GL ++EI +FS V +++ D G+S G AFV
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF-QGRSTGEAFVQ 63
Query: 65 YTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ +Q+ + L IG++ I+ + ++
Sbjct: 64 FASQEIAEKALKKHKERIGHRYIEIFKSSRA 94
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 19/93 (20%)
Query: 10 GPGRND-ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
G G+ + +L+VGGL NT + F ++G + +I FA++ Y +
Sbjct: 10 GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESL 63
Query: 68 ---QKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
Q A + + RV+
Sbjct: 64 DAAQAACAKM--------RGFPLGGPDRRLRVD 88
Score = 51.1 bits (123), Expect = 1e-08
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 95 RVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
+ NP ++VGGL + + F ++GSI F +I ++ +
Sbjct: 13 KANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDA 65
Query: 155 ADQVLKNPK-QVICGKEVDVKRVKF 178
A + + G + + RV F
Sbjct: 66 AQAACAKMRGFPLGGPDRRL-RVDF 89
>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 = 58.6 bits (142), Expect = 4e-11
Identities = 10/88 (11%), Positives = 27/88 (30%), Gaps = 2/88 (2%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFVTYTT 67
G + + + + + + ++ + E ++ + D GQ G A V +
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKN 66
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ + ++ VT
Sbjct: 67 EDDARKSERLHRKKLNGREAFVHVVTLE 94
Score = 56.7 bits (137), Expect = 2e-10
Identities = 19/113 (16%), Positives = 36/113 (31%), Gaps = 2/113 (1%)
Query: 89 PKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
VN K + + IT+ DV + + G +
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 149 FDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAG 201
F +++ A + + ++ + G+E V V E M + G S+G
Sbjct: 64 FKNEDDARKSERLHRKKLNGREAFVHVV--TLEDMREIEKNPPAQGKSGPSSG 114
>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 = 57.5 bits (139), Expect = 8e-11
Identities = 17/94 (18%), Positives = 41/94 (43%), Gaps = 2/94 (2%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
S ++G P D+ + V G+ + E ++ D+F V+++ + D G++ G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNG 59
Query: 62 FVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
V + + + + L + + ++ T+R
Sbjct: 60 LVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER 93
Score = 52.1 bits (125), Expect = 8e-09
Identities = 18/98 (18%), Positives = 32/98 (32%), Gaps = 4/98 (4%)
Query: 96 VNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+NP + V G+ E DVRD+F + D G + F
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR-NNGNGLVKFLSPQDT 69
Query: 156 DQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
+ LK + ++ + V+V + G +
Sbjct: 70 FEALKRNRMLMIQRYVEVSPA--TERQWVAAGGHITSG 105
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FV L +TE+ + FSQ+G + + K + FI FD+++ A + ++
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 64
Query: 162 -PKQVICGKEVDVKRVK 177
+ + G+ +++ K
Sbjct: 65 MNGKDLEGENIEIVFAK 81
Score = 55.7 bits (135), Expect = 3e-10
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
+ LFV L E+ + FSQ+G++E + + +AF+ + KA++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAME 63
Query: 73 DL 74
++
Sbjct: 64 EM 65
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 56.8 bits (137), Expect = 1e-10
Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 6/91 (6%)
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
P PL ++VG L + D++ + GS+ P + + F+
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFL 61
Query: 148 SFDDQNVADQVLKNPKQV-ICGKEVDVKRVK 177
+ D A Q + + + + + V +
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 47.1 bits (112), Expect = 3e-07
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 2 SYRANGTAGPGRND--ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRG 59
S + + PG ++VG L R+ ++ + G V P R
Sbjct: 3 SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RR 57
Query: 60 FAFVTYTTQKAVDDLLAA 77
AF+ Y A ++
Sbjct: 58 RAFLHYPDSAAAQQAVSC 75
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 57.5 bits (139), Expect = 1e-10
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 2/88 (2%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFVTYTT 67
+ +++ GL K + D+F + VE SI I P G++ G FV +
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRN 76
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
+ L Y+GN+ I +TK+
Sbjct: 77 EADYKAALCRHKQYMGNRFIQVHPITKK 104
Score = 57.2 bits (138), Expect = 2e-10
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 2/99 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+++ GL E + V D+F + + + G F+ F ++ L
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 163 KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAG 201
KQ + + + V + + M +R S+G
Sbjct: 88 KQYMGNRFIQVHPI--TKKGMLEKIDMIRKRLQSGPSSG 124
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 15/82 (18%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYT-GQSRGFAFVTYTTQKAVDDLL 75
F+G L + E+ I ++F + ++ + +P + +GF + + ++ L
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
Query: 76 AAGDHYIGNKKIDPKRVTKRVN 97
+ + +GN++I RV+
Sbjct: 79 SLNEESLGNRRI-------RVD 93
Score = 51.5 bits (124), Expect = 8e-09
Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVADQVLK 160
F+G L ++TE+ ++++F I+ + P + S + KGF + F+D + L
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 161 NPKQVICGKEVDV 173
++ + + + V
Sbjct: 80 LNEESLGNRRIRV 92
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 56.8 bits (137), Expect = 2e-10
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 2/95 (2%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGF 60
G+ ++ + + GL ++EI +FS V I++ DP G+ G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP-EGKITGE 86
Query: 61 AFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
AFV + +Q+ + L IG++ I+ + ++
Sbjct: 87 AFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE 121
Score = 54.9 bits (132), Expect = 1e-09
Identities = 14/75 (18%), Positives = 32/75 (42%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ + GL T++++ +FS + + G F+ F Q +A++ L
Sbjct: 43 GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102
Query: 161 NPKQVICGKEVDVKR 175
K+ I + ++V +
Sbjct: 103 KHKERIGHRYIEVFK 117
>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 = 55.9 bits (135), Expect = 4e-10
Identities = 16/107 (14%), Positives = 39/107 (36%), Gaps = 9/107 (8%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKN 139
++G + +R ++V G ++T +R FS +G+I +
Sbjct: 19 SHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP---- 72
Query: 140 MKKGFCFISFDDQNVADQVLKN-PKQVICGKEVDVKRVKFNPETMGS 185
+ F++++ ADQ + + ++ V + P +
Sbjct: 73 --RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAA 117
Score = 52.1 bits (125), Expect = 9e-09
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 12/62 (19%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVD 72
L+V G + + FS +G + +S+ R AFVTY +AV
Sbjct: 40 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVA 91
Query: 73 DL 74
+L
Sbjct: 92 EL 93
>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 = 58.3 bits (140), Expect = 6e-10
Identities = 26/203 (12%), Positives = 55/203 (27%), Gaps = 8/203 (3%)
Query: 103 IFVGGLTTEITEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQV 158
I++ L +I + +++ FSQ+G I + +S M+ G F+ F + + A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMR-GQAFVIFKEVSSATNA 68
Query: 159 LKN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAGAAYAAAPGRVVAYPST 217
L++ K + ++ K + + + + G + P A
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128
Query: 218 YAGYAAADYGYTAGSYDAYATAYPGYDYSAMGYAYPAPAVQTMDTPLVVMMHMLQHTLVM 277
A A + Y P L
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188
Query: 278 TIVQWVTHTLHQLLHMEEANYGY 300
++ L + +
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILF 211
Score = 50.6 bits (120), Expect = 2e-07
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
A P +++ L+ + E+ FSQ+G++ I + + + RG AFV
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVI 58
Query: 65 YTT----QKAVDDL 74
+ A+ +
Sbjct: 59 FKEVSSATNALRSM 72
Score = 42.6 bits (99), Expect = 9e-05
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 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 = 32.9 bits (74), Expect = 0.13
Identities = 14/72 (19%), Positives = 24/72 (33%), Gaps = 11/72 (15%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDLL 75
F+ L T E ++ F+Q+ + + + AFV + A D L
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDAL- 264
Query: 76 AAGDHYIGNKKI 87
G N +
Sbjct: 265 -QGFKITQNNAM 275
>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 = 54.6 bits (132), Expect = 6e-10
Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
++V G ++T +R FS +G+I + + F++++ ADQ
Sbjct: 13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQ 64
Query: 158 VLKN-PKQVICGKEVDVKRVKFNPE 181
+ + ++ V + P
Sbjct: 65 AVAELNGTQVESVQLKVNIARKQPM 89
Score = 52.7 bits (127), Expect = 3e-09
Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT--- 67
L+V G + + FS +G + +S+ R AFVTY
Sbjct: 10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMES 61
Query: 68 -QKAVDDL 74
+AV +L
Sbjct: 62 ADQAVAEL 69
>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 = 54.2 bits (131), Expect = 7e-10
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G + + G N EK + ++ + V +I I + G G+ FV ++
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNA-HGNKTGYIFVDFS 58
Query: 67 TQKAVDDLLAAGDHYIGNKKI 87
++ V L Y+G + I
Sbjct: 59 NEEEVKQALKCNREYMGGRYI 79
Score = 48.5 bits (116), Expect = 9e-08
Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+ + G +TE++V ++ + + + K G+ F+ F ++ Q LK
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALKC 69
Query: 162 PKQVICGKEVDVKRVKFNPETMG 184
++ + G+ ++V R K + + G
Sbjct: 70 NREYMGGRYIEVFREK-SGPSSG 91
>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 = 54.6 bits (132), Expect = 8e-10
Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 16/97 (16%)
Query: 9 AGPGRNDER-------KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPY-TGQSRGF 60
G + R F+G L + E+ I ++F + ++ + +P + +GF
Sbjct: 1 GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59
Query: 61 AFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
+ + ++ L+ + +GNK+I RV+
Sbjct: 60 GYAEFEDLDSLLSALSLNEESLGNKRI-------RVD 89
Score = 52.3 bits (126), Expect = 6e-09
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVADQVLK 160
F+G L ++TE+ ++++F I+ + P + S + KGF + F+D + L
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 161 NPKQVICGKEVDV 173
++ + K + V
Sbjct: 76 LNEESLGNKRIRV 88
>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 = 53.6 bits (129), Expect = 1e-09
Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 7/62 (11%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
I V L + Q+V D Y + + K F++ + A +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCY-------VDRNKRTAFVTLLNGEQAQNAI 57
Query: 160 KN 161
+
Sbjct: 58 QM 59
Score = 49.7 bits (119), Expect = 3e-08
Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
G + + V L +++ +E++D Y Y +++ AFVT +
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYC-------YVDRNKRTAFVTLLNGEQA 53
Query: 72 DDLLAAGDHY 81
+ + Y
Sbjct: 54 QNAIQMFHQY 63
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 54.2 bits (131), Expect = 1e-09
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 9/94 (9%)
Query: 103 IFVGGLTTEITEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK- 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 = 46.1 bits (110), Expect = 7e-07
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPYTGQSRGFAFVTYTT-- 67
E LFVG L + + + ++F + Y + D TG S+G+ FV +T
Sbjct: 4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL 62
Query: 68 --QKAVDDLLAAGDHYIGNKKI 87
++A+ + G +G+K +
Sbjct: 63 EQKRALTEC--QGAVGLGSKPV 82
>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 = 53.8 bits (130), Expect = 1e-09
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
A P +++ L+ + E ++ FS++G++ I + + + RG AFV
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVI 57
Query: 65 YTT----QKAVDDL 74
+ A+ +
Sbjct: 58 FKEVSSATNALRSM 71
Score = 47.6 bits (114), Expect = 2e-07
Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 100 KCKIFVGGLTTEITEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
I++ L +I + +++ FS++G I + +S M+ G F+ F + + A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMR-GQAFVIFKEVSSA 64
Query: 156 DQVLKNPK-QVICGKEVDV 173
L++ + K + +
Sbjct: 65 TNALRSMQGFPFYDKPMRI 83
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 53.6 bits (129), Expect = 2e-09
Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 13/91 (14%)
Query: 16 ERKLFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
+ + V + + I+ FS++G++ + + G+++G+ F+ Y +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72
Query: 70 AVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK 100
D + D K+D K+ T RVN
Sbjct: 73 HAVDAVKNAD----GYKLD-KQHTFRVNLFT 98
Score = 44.7 bits (106), Expect = 2e-06
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 101 CKIFVGGL------TTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
I V + E + + FS++G IT P + K KG+ F+ +
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAH 73
Query: 155 ADQVLKN 161
A +KN
Sbjct: 74 AVDAVKN 80
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 52.9 bits (127), Expect = 3e-09
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 11/75 (14%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ P R E ++ V GL + +++ D+ + G+V + D G V
Sbjct: 3 SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 55
Query: 64 TYTT----QKAVDDL 74
+ AV L
Sbjct: 56 EFVRKEDMTYAVRKL 70
Score = 46.7 bits (111), Expect = 5e-07
Identities = 10/83 (12%), Positives = 29/83 (34%), Gaps = 8/83 (9%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+ ++ V GL + QD++D+ + G + + + G + F + +
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 67
Query: 160 KN-PKQVICGKEVDVKRVKFNPE 181
+ E + ++ +
Sbjct: 68 RKLDNTKFRSHEGETAYIRVKVD 90
>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 = 51.7 bits (124), Expect = 6e-09
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPYTGQSRGFAFVT 64
GP + R+L+VG + E+ + D+F+ + ++ Q + FAF+
Sbjct: 1 GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59
Query: 65 YTTQKAVDDLLA 76
+ + +A
Sbjct: 60 FRSVDETTQAMA 71
Score = 51.7 bits (124), Expect = 6e-09
Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 5/79 (6%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVAD 156
+++VG + ITE+ + D+F+ + Q N K F F+ F +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 157 QVLKNPKQVICGKEVDVKR 175
Q + + G+ + ++R
Sbjct: 68 QAMAFDGIIFQGQSLKIRR 86
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 52.2 bits (125), Expect = 9e-09
Identities = 22/105 (20%), 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 DPYTGQSRGFAFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
P G+ G AFV + ++ + L +G + I+ R T
Sbjct: 62 YP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105
Score = 49.9 bits (119), Expect = 5e-08
Identities = 18/99 (18%), Positives = 36/99 (36%), Gaps = 5/99 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQP---FDKSKNMKKGFCFISFDDQNVADQVL 159
+ + GL T ++V +F Q+ IT ++ G F+ F + A L
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 160 KNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVS 198
+ K ++ + +++ R + V A S
Sbjct: 86 RKHKDLLGKRYIELFRS--TAAEVQQVLNRFSSASGPSS 122
>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 = 51.8 bits (124), Expect = 9e-09
Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
+D + GL + +++ ++FS I + G+ RG A + +++
Sbjct: 9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESEQD 67
Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
V L Y+G + ++ +
Sbjct: 68 VQKALEKHRMYMGQRYVEVYEINNE 92
Score = 46.0 bits (109), Expect = 9e-07
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 2/79 (2%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVADQV 158
I GL T +DV ++FS ++G I + + +
Sbjct: 12 FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKA 71
Query: 159 LKNPKQVICGKEVDVKRVK 177
L+ + + + V+V +
Sbjct: 72 LEKHRMYMGQRYVEVYEIN 90
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 50.5 bits (121), Expect = 1e-08
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 19 LFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+ V + + I+ FS++G++ + + G+++G+ F+ Y +
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVN 97
D + D K+D K+ T RVN
Sbjct: 62 DAVKNAD----GYKLD-KQHTFRVN 81
Score = 45.8 bits (109), Expect = 6e-07
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 103 IFVGGL------TTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
I V + E + + FS++G IT P + K KG+ F+ + A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAHAV 61
Query: 157 QVLKN 161
+KN
Sbjct: 62 DAVKN 66
>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 = 51.5 bits (123), Expect = 2e-08
Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 4/97 (4%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPYTGQSR 58
S + GP + + + GL + +++ ++ S V + G+
Sbjct: 3 SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQS 61
Query: 59 GFAFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
G AFV ++ V L +G++ I+ + +
Sbjct: 62 GEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRT 98
Score = 48.0 bits (114), Expect = 2e-07
Identities = 15/102 (14%), Positives = 40/102 (39%), Gaps = 6/102 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQY---GSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+ + GL + +DV+++ S + + + + + G F+ + ++ L
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78
Query: 160 KNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAG 201
K ++ + + ++V + + M V A S+G
Sbjct: 79 KKDRESMGHRYIEVFKS--HRTEMDWVLKHSGPNSASGPSSG 118
>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 = 3e-08
Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 1 MSYRANGTAGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPYTGQ 56
M G+ P + + + ++ +++ + S G++ I + +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70
Query: 57 SRGFAFVTYTT----QKAVDDL 74
+ G A++ + T Q V+
Sbjct: 71 NSGKAYIVFATQESAQAFVEAF 92
Score = 48.0 bits (114), Expect = 3e-07
Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 8/78 (10%)
Query: 101 CKIFVGGLTTEITEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ + + E+ ++ ++ S G I + G +I F Q A
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN---SGKAYIVFATQESAQ 86
Query: 157 QVLKNPK-QVICGKEVDV 173
++ + G + +
Sbjct: 87 AFVEAFQGYPFQGNPLVI 104
>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 = 49.8 bits (119), Expect = 5e-08
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 11/70 (15%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT- 67
P R E ++ V GL + +++ D+ + G+V + D G V +
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61
Query: 68 ---QKAVDDL 74
AV L
Sbjct: 62 EDMTYAVRKL 71
Score = 44.4 bits (105), Expect = 4e-06
Identities = 10/83 (12%), Positives = 29/83 (34%), Gaps = 8/83 (9%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+ ++ V GL + QD++D+ + G + + + G + F + +
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 68
Query: 160 KN-PKQVICGKEVDVKRVKFNPE 181
+ E + ++ +
Sbjct: 69 RKLDNTKFRSHEGETAYIRVKVD 91
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 102
Score = 49.3 bits (118), Expect = 5e-08
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
+ + + + GL E +I ++FS + I+ P G+ G A V +
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEF 62
Query: 66 TTQKAVDDLLAAGDHYIGNKKI 87
T + +A + ++ +
Sbjct: 63 ATHEDAVAAMAKDKANMQHRYV 84
Score = 44.3 bits (105), Expect = 4e-06
Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 2/73 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+ + GL TE D+ ++FS G + F A +
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKD 75
Query: 163 KQVICGKEVDVKR 175
K + + V++
Sbjct: 76 KANMQHRYVELFL 88
>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 = 49.1 bits (117), Expect = 8e-08
Identities = 14/106 (13%), Positives = 37/106 (34%), Gaps = 15/106 (14%)
Query: 76 AAGDHYIGNKKIDPKRV----TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQ 131
++ H+ + + P+ ++ I + L ++TE +V +G +T
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL 62
Query: 132 QPFDKSKNMKKGFCFISFDDQNVADQVLK----NPKQVICGKEVDV 173
K FI + + A+ ++ + G+ + +
Sbjct: 63 ------MLKGKNQAFIEMNTEEAANTMVNYYTSVTPV-LRGQPIYI 101
Score = 40.3 bits (94), Expect = 1e-04
Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
R + + L + E E+ +G+V ++ + + + AF+ T++A
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEA 79
>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 = 49.8 bits (119), Expect = 9e-08
Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 2/84 (2%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+ + + GL E +I ++FS V + I+ P G+ G A V
Sbjct: 34 SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGP-DGRVTGEADV 91
Query: 64 TYTTQKAVDDLLAAGDHYIGNKKI 87
+ T + ++ + ++ I
Sbjct: 92 EFATHEEAVAAMSKDRANMQHRYI 115
Score = 46.0 bits (109), Expect = 2e-06
Identities = 16/117 (13%), Positives = 35/117 (29%), Gaps = 4/117 (3%)
Query: 76 AAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFD 135
G +G D + + + + GL + TE D+ ++FS
Sbjct: 24 MTGGQQMGRGSGDSEFTVQSTTG--HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG 80
Query: 136 KSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
G + F A + + + + +++ + G+ S V
Sbjct: 81 P-DGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 48.7 bits (116), Expect = 9e-08
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK-- 160
I + L ++TE +V +G +T K FI + + A+ ++
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLL------MLKGKNQAFIEMNTEEAANTMVNYY 72
Query: 161 -NPKQVICGKEVDV 173
+ V+ G+ + +
Sbjct: 73 TSVTPVLRGQPIYI 86
Score = 41.4 bits (97), Expect = 4e-05
Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 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
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G++G + + L T EI + FS++G + + + A V +
Sbjct: 1 GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL 54
Query: 67 T----QKAVDDL 74
+KA L
Sbjct: 55 EPLEARKAFRHL 66
Score = 44.0 bits (104), Expect = 4e-06
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 6/62 (9%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K I L ++++ FS++GS+ P + F + A +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAF 63
Query: 160 KN 161
++
Sbjct: 64 RH 65
>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 = 50.2 bits (119), Expect = 1e-07
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+++ G T+ T D++++ G + Q K KG F+ FD A + ++
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVE 168
Query: 161 NPKQVICGKEVDVK 174
P Q ++ +
Sbjct: 169 TPGQKYKETDLLIL 182
Score = 47.1 bits (111), Expect = 2e-06
Identities = 9/87 (10%), Positives = 27/87 (31%), Gaps = 1/87 (1%)
Query: 1 MSYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGF 60
R +++ G + +I ++ G+V +I ++ +G
Sbjct: 94 KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGS 152
Query: 61 AFVTYTTQKAVDDLLAAGDHYIGNKKI 87
FV + + ++ + +
Sbjct: 153 IFVVFDSIESAKKFVETPGQKYKETDL 179
>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 = 47.5 bits (113), Expect = 2e-07
Identities = 10/74 (13%), Positives = 24/74 (32%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK-- 160
+ + L E+TE +V +G +T K F+ + A ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71
Query: 161 -NPKQVICGKEVDV 173
+ + + +
Sbjct: 72 SAVTPHLRNQPIYI 85
Score = 39.0 bits (91), Expect = 2e-04
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 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
>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 = 47.9 bits (114), Expect = 2e-07
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPYTGQSR---GFAFVTYTT----Q 68
+FV GL + + E+ +YF ++G++ + I N S+ A+VTY
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 69 KAVDDL 74
+A+ +
Sbjct: 78 RAIQCV 83
Score = 43.7 bits (103), Expect = 6e-06
Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 100 KCKIFVGGLTTEITEQDV---RDYFSQYGSITE---FQQPFDKSKNMKKGFCFISFDDQN 153
K +FV GL+ + + +V +YF ++G I + ++++
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 154 VADQVLKN 161
A + ++
Sbjct: 75 DALRAIQC 82
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 48.3 bits (115), Expect = 3e-07
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 9/67 (13%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPYTGQSRGFAFVTYTT---- 67
+++V L ++ EK++ F +Y + S + + G+ +G AF+
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 68 QKAVDDL 74
KA+ +
Sbjct: 106 AKALKEA 112
Score = 47.1 bits (112), Expect = 7e-07
Identities = 20/112 (17%), Positives = 42/112 (37%), Gaps = 20/112 (17%)
Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTK---RVNPLK---------CKIFVGGLTTEIT 113
D++ I ++++ R+++ + C+I+V L +
Sbjct: 2 PLGSDSDEM---PSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQ 58
Query: 114 EQDVRDYFSQYGSITEFQQP----FDKSKNMK-KGFCFISFDDQNVADQVLK 160
E+D++ F +Y + Q K + KG FI ++ A + LK
Sbjct: 59 EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALK 110
>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 = 48.1 bits (114), Expect = 3e-07
Identities = 18/106 (16%), Positives = 36/106 (33%), Gaps = 12/106 (11%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPYTGQSRGF 60
R + GP + + + GL + +++ ++ S + G+ G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGE 90
Query: 61 AFVTYTTQKAVDDLLAAGDHYIGNKKI--------DPKRVTKRVNP 98
AFV ++ V L +G++ I + V K P
Sbjct: 91 AFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGP 136
Score = 43.8 bits (103), Expect = 1e-05
Identities = 10/80 (12%), Positives = 29/80 (36%), Gaps = 2/80 (2%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVADQ 157
+ + GL + +DV+++ S + + G F+ ++
Sbjct: 44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKM 103
Query: 158 VLKNPKQVICGKEVDVKRVK 177
LK ++ + + ++V +
Sbjct: 104 ALKKDRESMGHRYIEVFKSH 123
>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 = 46.3 bits (110), Expect = 6e-07
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 15/94 (15%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 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 = 43.6 bits (103), Expect = 5e-06
Identities = 12/89 (13%), Positives = 32/89 (35%), Gaps = 13/89 (14%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G + V GL + E ++ + ++G + + + + A
Sbjct: 2 SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55
Query: 63 VTYTT----QKAVDDLLAAGDHYIGNKKI 87
V + ++ V YI ++
Sbjct: 56 VEFENIDSAKECVTFAADVP-VYIAGQQA 83
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 45.9 bits (109), Expect = 8e-07
Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+ + GL + E D+ + ++G I+ K + F+D A +
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77
Query: 163 KQV---ICGKEVDV 173
I G V
Sbjct: 78 ADNQIYIAGHPAFV 91
Score = 44.4 bits (105), Expect = 3e-06
Identities = 11/98 (11%), Positives = 29/98 (29%), Gaps = 15/98 (15%)
Query: 1 MSYRANGTAGPGRNDE-----RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG 55
M + + + + + GL E ++ + ++G + + +
Sbjct: 1 MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV------M 54
Query: 56 QSRGFAFVTYTTQKAVDDLLAAGDHYIGNK-KIDPKRV 92
+ A V + V A ++ N+ I
Sbjct: 55 PKKRQALVEFED---VLGACNAVNYAADNQIYIAGHPA 89
>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 = 46.1 bits (109), Expect = 1e-06
Identities = 7/58 (12%), Positives = 18/58 (31%), Gaps = 6/58 (10%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ GGL ++ + + G + P + K + F + + +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 81
Score = 45.7 bits (108), Expect = 1e-06
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
+ GGL ++ + G V+++ + + + ++F Y T ++A L
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 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 = 45.6 bits (108), Expect = 1e-06
Identities = 9/75 (12%), Positives = 24/75 (32%), Gaps = 8/75 (10%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
R + + R + + L +++ D + + S T G +
Sbjct: 17 RGSHMSKLPAKRYR-ITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGAL 72
Query: 64 TYTT----QKAVDDL 74
+ + +A++ L
Sbjct: 73 EFPSEEILVEALERL 87
Score = 43.3 bits (102), Expect = 1e-05
Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 4/99 (4%)
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKS 137
H+ + + ++ + +I + L + QD++D + T F +
Sbjct: 6 HHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD 65
Query: 138 KNMKKGFCFISFDDQNVADQVLKN-PKQVICGKEVDVKR 175
G + F + + + L+ G + V+R
Sbjct: 66 ---FDGTGALEFPSEEILVEALERLNNIEFRGSVITVER 101
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 47.1 bits (111), Expect = 3e-06
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 15/74 (20%)
Query: 6 NGTAGPGRNDERKLFVGGLHRN---------TGEKEINDYFSQYGEVESISIKNDPYTGQ 56
G G R + L+VGG+ E I FS+ G+++ I +
Sbjct: 124 MGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------E 177
Query: 57 SRGFAFVTYTTQKA 70
S+ FV + Q
Sbjct: 178 SKNCGFVKFKYQAN 191
Score = 37.5 bits (86), Expect = 0.003
Identities = 16/100 (16%), Positives = 25/100 (25%), Gaps = 6/100 (6%)
Query: 56 QSRGFAFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQ 115
+ + + G K T V + + L E
Sbjct: 99 IGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIES 158
Query: 116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+R FS+ G I + K F+ F Q A
Sbjct: 159 RIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANA 192
>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 = 46.0 bits (108), Expect = 1e-05
Identities = 25/146 (17%), Positives = 43/146 (29%), Gaps = 39/146 (26%)
Query: 28 TGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAGDHYIGNKKI 87
T K++ D+ S IS+ + S T V LL Y+ +
Sbjct: 272 TRFKQVTDFLSAATTTH-ISLDH-----HSMTL------TPDEVKSLLLK---YLDCRPQ 316
Query: 88 DPKRVTKRVNPLKCKIFVGGLTTEITEQDVR-DYFSQYG----------SITEFQQPFDK 136
D R NP + I I + D + S+ +P +
Sbjct: 317 DLPREVLTTNPRRLSIIA----ESIRDGLATWDNWKHVNCDKLTTIIESSL-NVLEPAE- 370
Query: 137 SKNMKKGF--CFISF-DDQNVADQVL 159
+K F + F ++ +L
Sbjct: 371 ---YRKMFDRLSV-FPPSAHIPTILL 392
Score = 36.4 bits (83), Expect = 0.015
Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 21/66 (31%)
Query: 108 LTTEITEQDVRDYFSQYGSITE-FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVI 166
+ E E QY I F+ F + FD ++V D PK ++
Sbjct: 7 MDFETGEHQY-----QYKDILSVFEDAFVDN-----------FDCKDVQDM----PKSIL 46
Query: 167 CGKEVD 172
+E+D
Sbjct: 47 SKEEID 52
Score = 33.3 bits (75), Expect = 0.15
Identities = 41/283 (14%), Positives = 79/283 (27%), Gaps = 109/283 (38%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFS----QYGSITEFQQPFDKSKNMKKGFC 145
+ N L CKI + TT + V D+ S + S+ +
Sbjct: 256 AKAWNAFN-LSCKILL---TT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS---L 306
Query: 146 FISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAGAAYA 205
+ + D D L P++V + NP + + +
Sbjct: 307 LLKYLDCRPQD--L--PREV----------LTTNPRRLSII-------AESIRD------ 339
Query: 206 AAPGRVVAYPSTYAGYAAADYGYTAGSYDAYATA--------YPGYDYSAMGYAYPAPAV 257
+T+ D + + D T P +Y M + +V
Sbjct: 340 --------GLATW------DN-WKHVNCDKLTTIIESSLNVLEP-AEYRKM---FDRLSV 380
Query: 258 ---------QTM---------DTPLVVMMHMLQHTLV------MTIVQWVTHTLHQLLHM 293
+ +VV+ + +++LV TI +++ L +
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI---SIPSIYLELKV 437
Query: 294 EEAN-----------YGYTAGSYDAYATAYP---GYDYSAMGY 322
+ N Y +D+ P Y YS +G+
Sbjct: 438 KLENEYALHRSIVDHYNIPKT-FDSDDLIPPYLDQYFYSHIGH 479
>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 = 40.3 bits (94), Expect = 1e-04
Identities = 18/94 (19%), Positives = 30/94 (31%), Gaps = 16/94 (17%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTE-ITEQDVRDYFSQYGSITEFQQPFDKSKNMKK 142
++K D K+ RV I + L ++ V YG I + K
Sbjct: 15 DQKFDQKQELGRV------IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMK 62
Query: 143 GFCFISFDDQNVADQVL---KNPKQVICGKEVDV 173
FI + + A ++ G+ V V
Sbjct: 63 SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96
>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 = 42.7 bits (100), Expect = 2e-04
Identities = 43/265 (16%), Positives = 69/265 (26%), Gaps = 115/265 (43%)
Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPY----TG---------------- 55
L + L + + + N + +V IS+ N +G
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQV-EISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 56 ------QSRGFAFVTYTTQKAV-------------DDLLAAGDHYIGNKKIDPKRVTKRV 96
QSR + ++ +K LL I NK + V+
Sbjct: 398 APSGLDQSR----IPFSERKLKFSNRFLPVASPFHSHLLVPASDLI-NKDLVKNNVSFNA 452
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
++ ++ T D+R GSI+E + D
Sbjct: 453 KDIQIPVY----DTF-DGSDLRVL---SGSISE-----------------------RIVD 481
Query: 157 QVLKNP----KQVICGKE--VDVKRVKFNPETMGSVSG-------AVRGAGARVSSAGAA 203
+++ P +D F P G SG G G RV AG
Sbjct: 482 CIIRLPVKWETTTQFKATHILD-----FGP---GGASGLGVLTHRNKDGTGVRVIVAG-- 531
Query: 204 YAAAPGRVVAYPSTYAGYAAADYGY 228
T DYG+
Sbjct: 532 -------------TLDINPDDDYGF 543
Score = 41.2 bits (96), Expect = 5e-04
Identities = 40/219 (18%), Positives = 65/219 (29%), Gaps = 87/219 (39%)
Query: 56 QSRGFAFVTYTTQKAVDDLLAAGDHYIGNK---------KIDPKRVT------------K 94
Q +G Y T KA D+ D++ + +P +T +
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRE 1686
Query: 95 RVNPLKCKIFV-GGLTTEITEQDVRDYFSQYG--------SITEFQQP---------FD- 135
+ + + V G L TE +++ ++ + Y S T+F QP F+
Sbjct: 1687 NYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFED 1746
Query: 136 -KSKNMKKGFCF------------------ISFDDQNVADQVLKNPKQVICGKEVDVKRV 176
KSK + +S + +V+ R
Sbjct: 1747 LKSKGLIPADATFAGHSLGEYAALASLADVMSIES---LVEVVF-------------YR- 1789
Query: 177 KFNPETMGS-VSGAV-RGAGARVSSAGAAYAAAPGRVVA 213
G + AV R R S A PGRV A
Sbjct: 1790 -------GMTMQVAVPRDELGR--SNYGMIAINPGRVAA 1819
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 121
Score = 34.2 bits (78), Expect = 0.017
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAGD 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
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 33.5 bits (76), Expect = 0.028
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
I V L +T + FS++G++ F K+ + + + D A +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTV-LKIITFTKNNQFQ---ALLQYADPVSAQHAKLS 85
Score = 33.1 bits (75), Expect = 0.040
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 4/62 (6%)
Query: 6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
G A G++ ++ V L ++ FS++G V I Q A + Y
Sbjct: 18 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQY 73
Query: 66 TT 67
Sbjct: 74 AD 75
>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 = 34.8 bits (79), Expect = 0.034
Identities = 7/54 (12%), Positives = 17/54 (31%), Gaps = 6/54 (11%)
Query: 106 GGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
GGL ++ + + G + P +K + F + + +
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAY 73
Score = 29.4 bits (65), Expect = 2.0
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 17 RKLFV--GGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT 67
+ L V GGL ++ + G V+++ ++ ++F Y T
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRT 65
>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 = 32.9 bits (75), Expect = 0.035
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 30 EKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
E+ + +YGEVE +++ D G +V + +KAV DL
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDL 88
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif,
RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2adb_A
Length = 164
Score = 33.2 bits (75), Expect = 0.055
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 4/66 (6%)
Query: 2 SYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFA 61
+ G A G++ ++ V L ++ FS++G V I Q A
Sbjct: 32 AAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----A 87
Query: 62 FVTYTT 67
+ Y
Sbjct: 88 LLQYAD 93
Score = 33.2 bits (75), Expect = 0.064
Identities = 9/59 (15%), Positives = 20/59 (33%), Gaps = 4/59 (6%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
I V L +T + FS++G++ + + + + D A +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS 103
>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 = 33.9 bits (77), Expect = 0.086
Identities = 29/176 (16%), Positives = 54/176 (30%), Gaps = 8/176 (4%)
Query: 178 FNPETMGSVSGAVRGAGARVSSAGAAYAAAPGRVVAYPSTYAGYAAADYGYTAGSYDAYA 237
F+P + A+ G A A +P T G+ + G++ S Y+
Sbjct: 1492 FSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTS-PTYS 1550
Query: 238 TAYPGYDYSAMGYAYPAPAVQTMDTP-LVVMMHMLQHTLVMTIVQWVTHTLHQLLHMEEA 296
P Y ++ Y+ +P+ + +
Sbjct: 1551 PTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1610
Query: 297 NYGYTAGSY----DAYATAYPGYDYSAMGYAYPAPATSYGGGKYREAAAYPRHAPY 348
+Y T+ SY +Y+ P YS +Y + SY + P ++P
Sbjct: 1611 SYSPTSPSYSPTSPSYSPTSPS--YSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPT 1664
>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 = 31.4 bits (71), Expect = 0.095
Identities = 13/95 (13%), Positives = 24/95 (25%), Gaps = 22/95 (23%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEI-TEQDVRDYFSQYGSITEFQQPFDKSKNMKK 142
+++ +RV + + + +G I+ K
Sbjct: 9 KGRVETRRV----------VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKI 52
Query: 143 GFCFISFDDQNVADQVLK----NPKQVICGKEVDV 173
FI A + P + GK V V
Sbjct: 53 NEAFIEMATTEDAQAAVDYYTTTPAL-VFGKPVRV 86
>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 = 31.7 bits (71), Expect = 0.32
Identities = 14/112 (12%), Positives = 35/112 (31%), Gaps = 7/112 (6%)
Query: 53 YTGQSRGFAFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEI 112
+ S G ++ + + I ++ + +R + + + +I
Sbjct: 7 HHHHSSGLVPRGSHMEQPSGSVETGFEDKIPKRRFS-EMQNERREQAQRTVLIH-CPEKI 64
Query: 113 TEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQ 164
+E Y SQ+G I F +S + + + F + +
Sbjct: 65 SENKFLKYLSQFGPINNHF--FYESFGL---YAVVEFCQKESIGSLQNGTHT 111
Score = 29.8 bits (66), Expect = 1.6
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
+R + + E + Y SQ+G + + +A V + ++++ 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 = 0.37
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 27 NTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
N + I +YF +YGE+ NDP + + Y
Sbjct: 17 NIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYA 56
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.4 bits (65), Expect = 0.53
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 30 EKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ + +YGEV ++ + + G A V + T KA +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAEL 69
Score = 28.2 bits (62), Expect = 1.6
Identities = 7/50 (14%), Positives = 17/50 (34%), Gaps = 5/50 (10%)
Query: 112 ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++ + +YG + + K G + F A+ ++N
Sbjct: 29 YSKDVLLRLLQKYGEVLNL-----VLSSKKPGTAVVEFATVKAAELAVQN 73
>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 = 1.4
Identities = 8/49 (16%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 30 EKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
+ ++ + +++G V I + ++G +V + AV+ L
Sbjct: 31 KDDVIEECNKHGGVIHIYV----DKNSAQGNVYVKCPSIAAAIAAVNAL 75
>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 = 29.2 bits (65), Expect = 1.4
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 140 MKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVSS 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 = 29.4 bits (66), Expect = 1.4
Identities = 7/34 (20%), Positives = 13/34 (38%)
Query: 59 GFAFVTYTTQKAVDDLLAAGDHYIGNKKIDPKRV 92
+ T + +DD+ AA D +D +
Sbjct: 70 ASMRQSVTRAQNLDDIKAAYDQLASLPYVDAHSI 103
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 1.5
Identities = 4/26 (15%), Positives = 12/26 (46%)
Query: 26 RNTGEKEINDYFSQYGEVESISIKND 51
R +K++ ++ + E + N+
Sbjct: 113 REKAKKDLEEWNQRQSEQVEKNKINN 138
>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 = 27.8 bits (62), Expect = 1.6
Identities = 15/64 (23%), Positives = 18/64 (28%), Gaps = 10/64 (15%)
Query: 180 PETMGSVSGAVRGAGARVSSAGAAYAAAPGRVVAYPSTYAGYAAADYGY--TAGSYDAYA 237
PE + + VR R + A A V AAD A YA
Sbjct: 8 PEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRP--------PAADLVSEKAATFLVEYA 59
Query: 238 TAYP 241
Y
Sbjct: 60 RKYR 63
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.1 bits (62), Expect = 2.1
Identities = 6/59 (10%), Positives = 17/59 (28%), Gaps = 5/59 (8%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+ + IT + + G + + K ++ + F+ A +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQ--RIVIFKRNGIQ---AMVEFESVLCAQKAKAA 81
>2rr7_A Dynein heavy chain 9; microtubule-binding, stalk head, MTBD,
antiparallel coil, motor protein, DSH; NMR
{Chlamydomonas reinhardtii}
Length = 155
Score = 28.4 bits (64), Expect = 2.4
Identities = 8/46 (17%), Positives = 17/46 (36%), Gaps = 7/46 (15%)
Query: 147 ISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
FD ++ +V+ + + +F P+ + S A G
Sbjct: 89 RKFDKDHIPPEVIVKIRPFA-------QDPEFQPKVIEKQSVACAG 127
>1l8w_A VLSE1; variable surface protein, VMP-like sequence, immune system;
2.30A {Borrelia burgdorferi} SCOP: a.154.1.1
Length = 348
Score = 28.8 bits (63), Expect = 3.1
Identities = 19/107 (17%), Positives = 35/107 (32%)
Query: 107 GLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVI 166
G ++ + DV+ YF+ + E + S +K + + V + I
Sbjct: 52 GFKSDPKKSDVKTYFTTVAAKLEKTKTDLNSLPKEKSDISSTTGKPDSTGSVGTAVEGAI 111
Query: 167 CGKEVDVKRVKFNPETMGSVSGAVRGAGARVSSAGAAYAAAPGRVVA 213
+ ++ +T S G V+ A AA A V
Sbjct: 112 KEVSELLDKLVKAVKTAEGASSGTAAIGEVVADADAAKVADKASVKG 158
>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 = 26.6 bits (59), Expect = 5.8
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 30 EKEINDYFSQYGEVESISI----KNDPYTGQSRGFAFVTYTT----QKAVDDL 74
E E+ + ++G V + I + + + FV ++ KA+ L
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
>1k7i_A PROC, secreted protease C; metalloprotease, hydrolase; 1.59A
{Erwinia chrysanthemi} SCOP: b.80.7.1 d.92.1.6 PDB:
1k7g_A 1k7q_A 1go8_P 3hbv_P 3hda_P 3hbu_P 1go7_P 3hb2_P
Length = 479
Score = 27.9 bits (61), Expect = 5.9
Identities = 23/117 (19%), Positives = 32/117 (27%), Gaps = 19/117 (16%)
Query: 227 GYTAGSYDAYATAYPGYDYSAMGYAYPAPAVQTMDTPLV------VMMHMLQHTLVMTIV 280
Y A AY +Y G ++ + P H + H L
Sbjct: 140 ASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALG---- 195
Query: 281 QWVTHTLHQLLHMEEANYGYTAGSYDAYATAYPGYDYSAMGYAYPAPATSYGGGKYR 337
L H E N G SY+ A Y +S M + + G Y
Sbjct: 196 ---------LAHPGEYNAGEGDPSYNDAVYAEDSYQFSIMSFWGENETGADYNGHYG 243
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.133 0.398
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: 5,540,531
Number of extensions: 342299
Number of successful extensions: 1605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1339
Number of HSP's successfully gapped: 392
Length of query: 348
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 254
Effective length of database: 4,077,219
Effective search space: 1035613626
Effective search space used: 1035613626
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: 58 (26.7 bits)