RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6490
(398 letters)
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 275 bits (706), Expect = 1e-92
Identities = 70/185 (37%), Positives = 111/185 (60%), Gaps = 3/185 (1%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+S + KLF+GGLS++T+ E LR +F +G +TD ++M+DP T+RSRGFGF+T+
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPK---NRPKIGNRTKKIFVGGVSQDTSAEEVK 267
A E V+ + H +DG+ ++PK A + RP KKIFVGG+ +DT ++
Sbjct: 63 ATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 122
Query: 268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQP 327
YF Q+GK+E ++ D+ + + RGF FVTF++ + VD I +H + E +KA
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS 182
Query: 328 KEAVQ 332
K+ +
Sbjct: 183 KQEMA 187
Score = 125 bits (317), Expect = 1e-34
Identities = 32/111 (28%), Positives = 56/111 (50%)
Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
V K + S G T K+FVGG+ T LR+YF +G + + IM D +
Sbjct: 84 VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSG 143
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
+ RGF F+TF + ++V+K++ HT++G + + A K + +++
Sbjct: 144 KKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQR 194
>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 = 271 bits (695), Expect = 3e-91
Identities = 79/168 (47%), Positives = 121/168 (72%), Gaps = 4/168 (2%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S K+F+GGL+W T+ + LREYFG +G VTD+ IMKDP T RSRGFGF++F +P +V++V+
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
K H LDGK IDPK A P++ ++T KIFVGG+ D +E + +FSQ+G + +
Sbjct: 63 KTQ-HILDGKVIDPKRAIPRDEQ---DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 281 MLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
+++D+ T + RGFGFVT+++ + VD +C+ F K++K+E K+A+P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 132 bits (334), Expect = 2e-37
Identities = 35/112 (31%), Positives = 59/112 (52%), Gaps = 4/112 (3%)
Query: 130 NVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT 189
VV+ H L +GK D R+ P + + K+FVGG+ ++ E+F +G +
Sbjct: 60 EVVKTQHIL---DGKVI-DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTII 115
Query: 190 DVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN 241
D +M D T +SRGFGF+T+ + V++V + +KI+ K A P++
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 167
Score = 113 bits (286), Expect = 2e-30
Identities = 27/82 (32%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+ K+F+GG++ DT+ + ++ YF ++G V + ++ D T R RGFGF++FE VD +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+ H++ K ++ K+A P++
Sbjct: 62 VK-TQHILDGKVIDPKRAIPRD 82
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 198 bits (506), Expect = 3e-62
Identities = 40/199 (20%), Positives = 89/199 (44%), Gaps = 10/199 (5%)
Query: 140 LVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT 199
+ G+ G + G ++++VG + ++ + +R+ F FG + + + D +T
Sbjct: 7 MTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 66
Query: 200 QRSRGFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNR--------PKIGNRTK 250
+ +GF F+ + PE + L+ + L G+ I + + +
Sbjct: 67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 126
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
+I+V V QD S +++K+ F FGK++ + D T +H+G+GF+ +E + +
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 310 IHFHMIKNKKVECKKAQPK 328
++ + + + KA
Sbjct: 187 MNLFDLGGQYLRVGKAVTP 205
>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 = 174 bits (443), Expect = 2e-53
Identities = 26/173 (15%), Positives = 70/173 (40%), Gaps = 9/173 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-----IMKDPITQRSRGFGFITFAEP 213
++ +L+VG + + + E + ++F + + + + + F F+ F
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 214 ETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQF 273
+ + + G+ + + K+F+GG+ + ++VK + F
Sbjct: 62 DETTQAMAFDGIIFQGQSLKIRRPHDYQPL---PGAHKLFIGGLPNYLNDDQVKELLTSF 118
Query: 274 GKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKA 325
G ++ ++ D T +G+ F + + V D ++ + +KK+ ++A
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 96.5 bits (241), Expect = 5e-24
Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
R P + KLF+GGL + ++++E FG + ++KD T S+G+ F
Sbjct: 83 RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142
Query: 210 FAEPETVEKVL-KVPIHTLDGKKIDPKHAT 238
+ + ++ + + L KK+ + A+
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
Score = 81.1 bits (201), Expect = 2e-18
Identities = 10/96 (10%), Positives = 37/96 (38%), Gaps = 7/96 (7%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML-----MDQQTKRHRGFGFVTFENEEVV 304
++++VG + + E + +F+ ++ + Q + + F F+ F + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 305 DHICEIHFHMIKNKKVECKKAQPKEAVQ--ANLLVG 338
+ + + ++ ++ + + L +G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIG 100
>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 = 165 bits (421), Expect = 5e-51
Identities = 41/114 (35%), Positives = 60/114 (52%), Gaps = 1/114 (0%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG D T K+FVGGL + T+ LR+YF FG + + +++ D T +SRG
Sbjct: 2 SSGSSGMHGSQKD-TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVS 258
+GF+T A+ E+ K P +DG+K + A +P+ I V G S
Sbjct: 61 YGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPS 114
Score = 121 bits (305), Expect = 8e-34
Identities = 29/109 (26%), Positives = 51/109 (46%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
++ + + KIFVGG+ T+ ++ YF FG +EE V++ D+QT + RG+GFV
Sbjct: 5 SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
Query: 297 TFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
T + + C+ +I +K A ++ + GP
Sbjct: 65 TMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
>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 = 157 bits (399), Expect = 7e-47
Identities = 42/180 (23%), Positives = 76/180 (42%), Gaps = 19/180 (10%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT--QRSRGFGFITFAEPET 215
D K+FVG + S + LRE F +GAV ++ +++D +S+G F+TF +
Sbjct: 2 DAI--KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 216 VEKVLKVPIHTLDGKKIDPKHATP------KNRPKIGNRTKKIFVGGVSQDTSAEEVKAY 269
+ + L K+ P P + +K+F+G +S+ + +++
Sbjct: 60 ALEA----QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVM 115
Query: 270 FSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKNKKVECKKA 325
FS FG++EE +L RG FVTF + + + + + K A
Sbjct: 116 FSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>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 = 156 bits (396), Expect = 1e-46
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 9/171 (5%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
+ L V L + E+ R FG G + +++D IT +S G+GF+ + +P+ EK
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 220 LKVPIH--TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE 277
+ ++ L K I +A P + R ++V G+ + + +E++ FSQ+G++
Sbjct: 61 INT-LNGLRLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 278 ETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI---HFHMIKNKKVECKKA 325
+ +L+DQ T RG GF+ F+ + + + + K A
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 86.1 bits (214), Expect = 3e-20
Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 12/117 (10%)
Query: 117 DDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSE 176
DP A+ + LN +R + + V+ + P+ A L+V GL + +
Sbjct: 52 IDPKDAEKAINTLNGLRLQTKTIKVS--------YARPSSASIRDANLYVSGLPKTMTQK 103
Query: 177 KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
+L + F +G + I+ D +T SRG GFI F + E+ I L+G+K
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA----IKGLNGQKPS 156
>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 = 155 bits (395), Expect = 3e-46
Identities = 34/179 (18%), Positives = 71/179 (39%), Gaps = 8/179 (4%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+ T LF+G L+ S +L+ A D+ ++ D T +R FG++ F
Sbjct: 3 HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDF 61
Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYF 270
E +EK L++ + G +I + + K + + +S + + +E+K F
Sbjct: 62 ESAEDLEKALELTGLKVFGNEIKLEKPKGR-DSKKVRAARTLLAKNLSFNITEDELKEVF 120
Query: 271 SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
++ + Q + +G ++ F++E + + E I + V K
Sbjct: 121 EDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 83.8 bits (208), Expect = 2e-19
Identities = 20/107 (18%), Positives = 48/107 (44%), Gaps = 8/107 (7%)
Query: 236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
H + +F+G ++ + S E+K S+ + + +D +T +R FG+
Sbjct: 3 HMVEGSES---TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGY 58
Query: 296 VTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA----NLLVG 338
V FE+ E ++ E+ + +++ +K + +++ + LL
Sbjct: 59 VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAK 105
>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 = 151 bits (384), Expect = 1e-45
Identities = 51/105 (48%), Positives = 62/105 (59%), Gaps = 2/105 (1%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG + D+ KLFVGGL W T+ E LR YF +G V D +IMKD T +SRG
Sbjct: 2 SSGSSGMNNSGADEIG--KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG 59
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
FGF+ F +P V VL HTLDG+ IDPK TP+ G +
Sbjct: 60 FGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104
Score = 124 bits (314), Expect = 3e-35
Identities = 27/94 (28%), Positives = 50/94 (53%)
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ K+FVGG+ T+ E +++YFSQ+G+V + V++ D+ T + RGFGFV F++
Sbjct: 8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
V + H + + ++ K P+ +
Sbjct: 68 PNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSG 101
>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 = 148 bits (377), Expect = 1e-44
Identities = 52/100 (52%), Positives = 66/100 (66%), Gaps = 3/100 (3%)
Query: 148 DSGRSTPTGD--DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
S P G + K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGF
Sbjct: 10 HSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69
Query: 206 GFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK-NRPK 244
GF+TF + V+KVL H LD K IDPK A P+ +PK
Sbjct: 70 GFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 135 bits (342), Expect = 2e-39
Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 6/106 (5%)
Query: 225 HTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD 284
H + P+ +G+ K+F+GG+S T+ E ++ YF QFG+V+E +++ D
Sbjct: 7 HHHHSSGLVPR------GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60
Query: 285 QQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEA 330
TKR RGFGFVTF ++ VD + H + +K ++ K A P+ A
Sbjct: 61 PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106
>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 = 148 bits (375), Expect = 3e-44
Identities = 38/98 (38%), Positives = 50/98 (51%), Gaps = 1/98 (1%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S ++ L V GL W+T+ + L+EYF FG V V + KD T S+GFG
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPK 244
F+ F E ET KV+ H +DG+ D K K
Sbjct: 61 FVRFTEYETQVKVMSQR-HMIDGRWCDCKLPNSKQSQD 97
Score = 125 bits (315), Expect = 2e-35
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 1/94 (1%)
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ +T + V G+ T+ +++K YFS FG+V + D +T +GFGFV F
Sbjct: 7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
E + HMI + +CK K++ +
Sbjct: 67 YETQVKVMS-QRHMIDGRWCDCKLPNSKQSQDSG 99
>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 = 151 bits (384), Expect = 3e-43
Identities = 27/184 (14%), Positives = 61/184 (33%), Gaps = 12/184 (6%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
PT A L V L + ++ E FG++ ++ T +S+G+GF + + ++ +
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 219 VLKVPIHTLDGKKIDPKH-----ATPKNRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQ 272
L GK + P+ ++ + V + + + S
Sbjct: 153 A----KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSA 208
Query: 273 FGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
+ Q + +GF + +E E + + + + P
Sbjct: 209 VHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267
Query: 332 QANL 335
++ L
Sbjct: 268 RSML 271
Score = 123 bits (311), Expect = 9e-33
Identities = 20/180 (11%), Positives = 63/180 (35%), Gaps = 16/180 (8%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
K+ + GL +++++ + + +K + +G F+T E
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQA 70
Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
E + ++ + + + +P + V + + ++ + FG +
Sbjct: 71 EAAIN----AFHQSRLRERELSVQLQPTDAL----LCVANLPPSLTQQQFEELVRPFGSL 122
Query: 277 EETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
E ++ ++T + +G+GF + ++ ++ + + + + A L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
Score = 69.2 bits (170), Expect = 2e-13
Identities = 17/113 (15%), Positives = 28/113 (24%), Gaps = 18/113 (15%)
Query: 142 NGKSSGDS----GRSTPTGDDPTSAK---LFVGGLSWQ-TSSEKLREYFGMFGAVTDVLI 193
GK G + P L V L + L + T +
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL 217
Query: 194 MKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH-----ATPKN 241
+ +GF + + E E+ + DG + H P
Sbjct: 218 ACGQ-DGQLKGFAVLEYETAEMAEEAQQ----QADGLSLGGSHLRVSFCAPGP 265
>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 = 144 bits (366), Expect = 7e-43
Identities = 35/99 (35%), Positives = 59/99 (59%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+ KLF+GGLS++T+ E LR Y+ +G +TD ++M+DP ++RSRGFGF+TF
Sbjct: 17 LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
Query: 211 AEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
+ V+ + H++DG+ ++PK A + G +
Sbjct: 77 SSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSGPSS 115
Score = 128 bits (323), Expect = 1e-36
Identities = 34/97 (35%), Positives = 55/97 (56%), Gaps = 1/97 (1%)
Query: 234 PKHATPKNR-PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
P R + + +K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D +KR RG
Sbjct: 11 TLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
Query: 293 FGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
FGFVTF + VD H I + VE K+A +E
Sbjct: 71 FGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVARE 107
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 142 bits (361), Expect = 2e-42
Identities = 46/75 (61%), Positives = 57/75 (76%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF + V+KVL
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 223 PIHTLDGKKIDPKHA 237
H LD K IDPK A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 118 bits (298), Expect = 3e-33
Identities = 32/75 (42%), Positives = 50/75 (66%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+F+GG+S T+ E ++ YF QFG+V+E +++ D TKR RGFGFVTF ++ VD +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 311 HFHMIKNKKVECKKA 325
H + +K ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 142 bits (361), Expect = 2e-42
Identities = 44/84 (52%), Positives = 55/84 (65%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
+ ++ + K+FVGGLSW TS + L++YF FG V D I DP T RSRGFGFI F +
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63
Query: 214 ETVEKVLKVPIHTLDGKKIDPKHA 237
+VEKVL H LDG+ IDPK A
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKKA 87
Score = 120 bits (304), Expect = 5e-34
Identities = 32/85 (37%), Positives = 52/85 (61%)
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
N K K+FVGG+S DTS +++K YF++FG+V + + MD T R RGFGF+ F++
Sbjct: 3 NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62
Query: 301 EEVVDHICEIHFHMIKNKKVECKKA 325
V+ + + H + + ++ KKA
Sbjct: 63 AASVEKVLDQKEHRLDGRVIDPKKA 87
>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 = 143 bits (362), Expect = 2e-42
Identities = 40/94 (42%), Positives = 62/94 (65%)
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ G+++ KIFVGG+ + E++ YF +FG V E VM+ D + +R RGFGF+TFE+
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
E+ VD +HFH I KKVE K+A+P+++ +
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSG 95
Score = 135 bits (342), Expect = 2e-39
Identities = 35/85 (41%), Positives = 53/85 (62%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
S K+FVGG+ +LREYF FG VT+V+++ D QR RGFGFITF + ++
Sbjct: 5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64
Query: 216 VEKVLKVPIHTLDGKKIDPKHATPK 240
V++ + + H + GKK++ K A P+
Sbjct: 65 VDQAVNMHFHDIMGKKVEVKRAEPR 89
>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 = 147 bits (374), Expect = 3e-42
Identities = 52/235 (22%), Positives = 79/235 (33%), Gaps = 21/235 (8%)
Query: 143 GKSSGDSGRSTPTGDDPTS-AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
G + P T +LFVG L + E + F +G ++V I +D
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT 261
RGFGFI E LDG + + R + + V +S
Sbjct: 58 -RGFGFIRLESRTLAEIA----KAELDGTILKSRPL----RIRFATHGAALTVKNLSPVV 108
Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-----IHFHMIK 316
S E ++ FSQFG VE+ V+++D R G GFV F + E
Sbjct: 109 SNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT 167
Query: 317 NKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQA 371
+ V + + + + R P P T S+ +A
Sbjct: 168 PRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKA 222
>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 = 145 bits (367), Expect = 7e-42
Identities = 27/192 (14%), Positives = 71/192 (36%), Gaps = 23/192 (11%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-----IMKDPITQRSRGFGFITFAEPET 215
+ +L+VG + + + E + ++F + + + + + F F+ F +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 216 VEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK-----------------KIFVGGVS 258
+ + G+ + + + K+F+GG+
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123
Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKN 317
+ ++VK + FG ++ ++ D T +G+ F + + V D I ++ + +
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 318 KKVECKKAQPKE 329
KK+ ++A
Sbjct: 184 KKLLVQRASVGA 195
Score = 89.3 bits (222), Expect = 4e-21
Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
+ S T ++ KLF+GGL + ++++E FG + ++KD T
Sbjct: 95 SENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 154
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDG-----KKIDPKHATPKNR 242
S+G+ F + + ++ I L+G KK+ + A+ +
Sbjct: 155 SKGYAFCEYVDINVTDQA----IAGLNGMQLGDKKLLVQRASVGAK 196
Score = 68.1 bits (167), Expect = 1e-13
Identities = 9/94 (9%), Positives = 36/94 (38%), Gaps = 5/94 (5%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFEN 300
G ++++VG + + E + +F+ ++ ++ Q + + F F+ F +
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
+ + + + ++ ++ + +
Sbjct: 61 VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGM 94
>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 = 140 bits (356), Expect = 1e-40
Identities = 34/173 (19%), Positives = 70/173 (40%), Gaps = 15/173 (8%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ L V L + +L F G + IM+D T S G+ F+ F ++ +
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 221 KVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGK 275
K L+G + K +A P ++V + + + +++ F ++G
Sbjct: 63 K----VLNGITVRNKRLKVSYARPGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 276 VEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIK--NKKVECKKA 325
+ + +L D+ T R RG FV + E I ++ + + ++ + + A
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 87.6 bits (218), Expect = 9e-21
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
+ P G+ L+V L + ++L FG +G++ I++D +T R RG F+
Sbjct: 78 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 210 FAEPETVEKVLKVPIHTLDGKKID 233
+ + E ++ I L+ +
Sbjct: 138 YNKREEAQEA----ISALNNVIPE 157
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 136 bits (344), Expect = 4e-40
Identities = 34/75 (45%), Positives = 48/75 (64%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T+ E ++ YF FG V D ++M D T R RGFGF+TF + VEKV ++
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 223 PIHTLDGKKIDPKHA 237
H ++ K ++ K A
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 131 bits (333), Expect = 2e-38
Identities = 48/75 (64%), Positives = 63/75 (84%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEI
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 311 HFHMIKNKKVECKKA 325
HFH I NK VECKKA
Sbjct: 61 HFHEINNKMVECKKA 75
>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 = 133 bits (336), Expect = 7e-39
Identities = 35/75 (46%), Positives = 46/75 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T EK+REYFG FG V + + D T + RGF FITF E E V+K+++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 223 PIHTLDGKKIDPKHA 237
H + K + K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 132 bits (334), Expect = 1e-38
Identities = 35/75 (46%), Positives = 47/75 (62%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S DT E+++ YF FG+VE + MD +T + RGF F+TF+ EE V I E
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 311 HFHMIKNKKVECKKA 325
+H + K E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 132 bits (334), Expect = 7e-37
Identities = 46/197 (23%), Positives = 85/197 (43%), Gaps = 17/197 (8%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G G P+ A L+VG L + L E F G + + + +D IT+RS G+
Sbjct: 1 GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-------HATPKNRPKIGNRTKKIFVGGVSQ 259
++ F +P E+ L T++ I K P R IF+ + +
Sbjct: 61 YVNFQQPADAERALD----TMNFDVIKGKPVRIMWSQRDPSLRKSGVGN---IFIKNLDK 113
Query: 260 DTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNK 318
+ + FS FG + ++ D +G+GFV FE +E + I +++ ++ ++
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Query: 319 KVECKKAQPKEAVQANL 335
KV + + ++ +A L
Sbjct: 172 KVFVGRFKSRKEREAEL 188
>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 = 130 bits (330), Expect = 2e-35
Identities = 24/182 (13%), Positives = 58/182 (31%), Gaps = 13/182 (7%)
Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
+ + + V L + K+ +YF G + V + +++ F I FA
Sbjct: 32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFA 89
Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFS 271
+ + + +I H T +++ + ++
Sbjct: 90 RYDGALAAITKTHKVVGQNEIIVSHLTECT----------LWMTNFPPSYTQRNIRDLLQ 139
Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI-HFHMIKNKKVECKKAQPKEA 330
V ++ L + R F ++ ++E + E + I+ + K + P E
Sbjct: 140 DINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199
Query: 331 VQ 332
+
Sbjct: 200 SK 201
Score = 128 bits (324), Expect = 1e-34
Identities = 27/177 (15%), Positives = 69/177 (38%), Gaps = 9/177 (5%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
T L++ + +R+ V + + SR F +I E
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175
Query: 220 LKVPIH--TLDGKKIDPKHATPKNRPKIGNRTK----KIFVGGVSQDTSAEE-VKAYFSQ 272
++ ++ ++G + K + P + K + +I + +S + E ++ F
Sbjct: 176 VEK-LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG 234
Query: 273 FGKVEET-VMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPK 328
FG +E+ + ++ + F+ FEN++ + +++ ++ N+++ A K
Sbjct: 235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK 291
Score = 71.2 bits (175), Expect = 5e-14
Identities = 13/137 (9%), Positives = 33/137 (24%), Gaps = 14/137 (10%)
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDT 261
S +G + K P+ + V + +
Sbjct: 1 SMEYGHHARPDS-------KRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSY 53
Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVE 321
+ +V YF G + + K++ F + F + ++ ++
Sbjct: 54 NQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKTHKVVGQNEII 111
Query: 322 CKKAQPKEAVQANLLVG 338
+ L +
Sbjct: 112 VSHLT-----ECTLWMT 123
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 120 bits (303), Expect = 6e-34
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+K+FVG + ++E+L+++F +G V DV I K R F F+TFA+ +
Sbjct: 7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVA 61
Query: 217 EKVLKVPIHTLDGKKIDPKHATPKN 241
+ + + G + +A PK+
Sbjct: 62 QSLCGED-LIIKGISVHISNAEPKH 85
Score = 120 bits (302), Expect = 8e-34
Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
+ + K+FVG ++D +AEE++ +F Q+G+V + + K R F FVTF
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFA 56
Query: 300 NEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
+++V +C +IK V A+PK
Sbjct: 57 DDKVAQSLCGED-LIIKGISVHISNAEPKH 85
>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 = 119 bits (301), Expect = 1e-33
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
S+ +FVG + + ++LRE+F +G V DV I K R F F+TFA+ + +
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQ 56
Query: 218 KVLKVPIHTLDGKKIDPKHATPKN 241
+ + G + +A PK+
Sbjct: 57 SLCGED-LIIKGISVHISNAEPKH 79
Score = 118 bits (299), Expect = 2e-33
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+ + +FVG + D + +E++ +FSQ+G V + + K R F FVTF ++++
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQS 57
Query: 307 ICEIHFHMIKNKKVECKKAQPKE 329
+C +IK V A+PK
Sbjct: 58 LCGED-LIIKGISVHISNAEPKH 79
>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 = 121 bits (306), Expect = 2e-33
Identities = 36/169 (21%), Positives = 76/169 (44%), Gaps = 12/169 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+VG L + + L++YF + G + ++ IM D ++ + F+ + + L+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ-- 59
Query: 224 IHTLDGKKIDPKH-----ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
TL+GK+I+ A + + T +FVG ++ + E ++ F F
Sbjct: 60 --TLNGKQIENNIVKINWAFQSQQSSSDD-TFNLFVGDLNVNVDDETLRNAFKDFPSYLS 116
Query: 279 TVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQ 326
++ D QT RG+GFV+F +++ + + + + + + A
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 76.4 bits (189), Expect = 7e-17
Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 10/93 (10%)
Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
+N + + LFVG L+ E LR F F + +M D T
Sbjct: 73 IN-WAFQS-----QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG 126
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
SRG+GF++F + + + ++ G+ ++
Sbjct: 127 SSRGYGFVSFTSQDDAQNA----MDSMQGQDLN 155
Score = 66.0 bits (162), Expect = 4e-13
Identities = 17/94 (18%), Positives = 39/94 (41%), Gaps = 6/94 (6%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+ ++VG + + + + +K YF G + +++D + ++ + FV + + +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59
Query: 310 I-HFHMIKNKKVECKKAQPK----EAVQANLLVG 338
+ I+N V+ A NL VG
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVG 93
>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 = 110 bits (277), Expect = 5e-30
Identities = 34/101 (33%), Positives = 57/101 (56%), Gaps = 1/101 (0%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G S +G KLFVGGLS+ T+ + L + F +G +++V+++KD TQRSRGFGF+T
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 210 FAEPETVEKVLKVPI-HTLDGKKIDPKHATPKNRPKIGNRT 249
F + + + ++DG++I A + + G +
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
Score = 90.4 bits (225), Expect = 2e-22
Identities = 27/82 (32%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
K+FVGG+S DT+ + ++ FS++G++ E V++ D++T+R RGFGFVTFEN + +
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
++ + +++ +A
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSS 93
>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 = 108 bits (273), Expect = 2e-29
Identities = 28/103 (27%), Positives = 50/103 (48%), Gaps = 4/103 (3%)
Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
S P G +FVGG+ + ++R +F +G+V +V I+ D T S+G+GF++F
Sbjct: 1 SLPEGK-IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58
Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPK-NRPKIGNRTKKIF 253
V+K+++ GKK+ A K N + + +
Sbjct: 59 NDVDVQKIVESQ-INFHGKKLKLGPAIRKQNLSTYHVQPRPLI 100
Score = 108 bits (273), Expect = 2e-29
Identities = 25/94 (26%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ P+ +FVGG+ E++++F+++G V+E ++ D +T +G+GFV+F N
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 59
Query: 301 EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQAN 334
+ V I E KK++ A K+ +
Sbjct: 60 DVDVQKIVE-SQINFHGKKLKLGPAIRKQNLSTY 92
>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 = 106 bits (266), Expect = 3e-28
Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+ KLF+GGL+ +T+ + L+ FG G +++VL++KD T +SRGF FITF P
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 217 EKVLKVPI-HTLDGKKIDPKHATPKNRPKIGNR 248
+ K +L GK I + A + G R
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94
Score = 84.7 bits (210), Expect = 3e-20
Identities = 22/85 (25%), Positives = 50/85 (58%), Gaps = 2/85 (2%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+ K+F+GG++++T+ + +KA F + G + E +++ D +T + RGF F+TFEN
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62
Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
+ +++ + K ++ ++A+
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPS 87
>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 = 104 bits (261), Expect = 1e-27
Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 7/103 (6%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S D +F+ LS+ + E L E FG + V ++ P T+ S+G
Sbjct: 1 GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
Query: 207 FITFAEPETVEKVLK-------VPIHTLDGKKIDPKHATPKNR 242
F F E +K L LDG+++ A ++
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 83.2 bits (206), Expect = 9e-20
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 7/98 (7%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
P K +F+ +S D+ E + QFG ++ +++ T+ +G F F
Sbjct: 5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64
Query: 299 ENEEVVD-------HICEIHFHMIKNKKVECKKAQPKE 329
+E E + ++++ A ++
Sbjct: 65 MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 102
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 103 bits (259), Expect = 1e-27
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 5/89 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+FV G S +L EYF FG V V++ KD F + + E VL
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGAREAVLSQ 64
Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
H+L G ++ + K +++ K
Sbjct: 65 SQHSLGGHRLRVRPREQKEFQSPASKSPK 93
Score = 100 bits (252), Expect = 2e-26
Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+ + +FV G + + ++ YF FG V V++ K F V + +
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVAS-VVMD----KDKGVFAIVEMGDVGARE 59
Query: 306 HICEIHFHMIKNKKVECKKAQPKE 329
+ H + ++ + + KE
Sbjct: 60 AVLSQSQHSLGGHRLRVRPREQKE 83
>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 = 100 bits (251), Expect = 2e-26
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + + L V GLS T+ LRE F +G + DV I+ D ++RSRGF
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
F+ F + ++ +G ++D
Sbjct: 61 FVYFENVDDAKEA----KERANGMELD 83
Score = 81.5 bits (202), Expect = 2e-19
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
+ + + V G+S T+ +++ FS++G + + ++ DQQ++R RGF FV
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 297 TFENEE 302
FEN +
Sbjct: 63 YFENVD 68
>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 = 101 bits (253), Expect = 2e-26
Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 1/102 (0%)
Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
GKS + ++ + +F L+ + L ++F G V DV I+ D ++RS
Sbjct: 7 GKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRS 66
Query: 203 RGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATP-KNRP 243
+G ++ F E ++V + + L G I + + KNR
Sbjct: 67 KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRL 108
Score = 93.5 bits (233), Expect = 1e-23
Identities = 17/102 (16%), Positives = 43/102 (42%), Gaps = 2/102 (1%)
Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT 287
GK + + + RT +F ++ +++ +FS GKV + ++ D+ +
Sbjct: 6 SGKSPVREPVDNLSPEERDART--VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63
Query: 288 KRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
+R +G +V F + V + + + + +Q ++
Sbjct: 64 RRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 105
>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 = 99.2 bits (248), Expect = 7e-26
Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S P D + L V L+++TS + LR F +G V DV I ++P T+ RGF
Sbjct: 1 GSSGSSGPDVDGMIT--LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
F+ F + + +DG ++D
Sbjct: 59 FVRFHDRRDAQDA----EAAMDGAELD 81
Score = 77.7 bits (192), Expect = 7e-18
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+ + V ++ TS + ++ F ++G+V + + + TK RGF FV F +
Sbjct: 6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDR 65
Query: 302 E 302
Sbjct: 66 R 66
>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 = 96.5 bits (241), Expect = 9e-25
Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 9/104 (8%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G S +G T L+VGGL+ + + L F FG +TD+ I D T++ RGF F+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
F E I ++ ++ + A P + G
Sbjct: 61 FELAEDAAAA----IDNMNESELFGRTIRVNLAKPMRIKESGPS 100
Score = 82.3 bits (204), Expect = 1e-19
Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 1/84 (1%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+ ++VGG++++ + + A F FG + + + +D +T++HRGF FV FE E
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
I ++ + + + A+P
Sbjct: 70 AIDNMNESELFGRTIRVNLAKPMR 93
>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 = 96.7 bits (241), Expect = 1e-24
Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 11/108 (10%)
Query: 142 NGKSSGDSGRSTPTGDDP-TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
G+ G R +P + L V GLS T+ LRE F +G + DV I+ D ++
Sbjct: 26 GGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR 85
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
RSRGF F+ F + ++ +G ++D + + K RP
Sbjct: 86 RSRGFAFVYFENVDDAKEA----KERANGMELDGRRIRVDFSITK-RP 128
Score = 78.6 bits (194), Expect = 6e-18
Identities = 19/69 (27%), Positives = 37/69 (53%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
+ + + + V G+S T+ +++ FS++G + + ++ DQQ++R RGF
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90
Query: 294 GFVTFENEE 302
FV FEN +
Sbjct: 91 AFVYFENVD 99
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 95.4 bits (238), Expect = 2e-24
Identities = 31/107 (28%), Positives = 48/107 (44%), Gaps = 9/107 (8%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S P + A ++VGGL + S L E F G V + + KD +T + +G+G
Sbjct: 1 GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
F+ F E + +K +D K+ K A+ N+ G
Sbjct: 61 FVEFLSEEDADYAIK----IMDMIKLYGKPIRVNKASAHNKNLSGPS 103
Score = 77.3 bits (191), Expect = 9e-18
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
N+ ++VGG+ + S + F Q G V T M D+ T +H+G+GFV F +EE D+
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 307 ICEI-HFHMIKNKKVECKKAQPKE 329
+I + K + KA
Sbjct: 73 AIKIMDMIKLYGKPIRVNKASAHN 96
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 95.6 bits (238), Expect = 4e-24
Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 10/113 (8%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
G P D L V L+++TS + LR F +G V DV I +D T+
Sbjct: 28 QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
SRGF F+ F + E + +DG +D + A RP + +
Sbjct: 88 SRGFAFVRFHDKRDAEDA----MDAMDGAVLDGRELRVQMARYG-RPPDSHHS 135
Score = 75.2 bits (185), Expect = 1e-16
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK 288
G+++ + P + V ++ TS + ++ F ++G+V + + D+ TK
Sbjct: 27 GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86
Query: 289 RHRGFGFVTFENEE 302
RGF FV F ++
Sbjct: 87 ESRGFAFVRFHDKR 100
>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 = 94.2 bits (235), Expect = 5e-24
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG S G P+ + ++V L + ++ L F +G V V IMKD T++S+G
Sbjct: 2 SSGSSGMSG--GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
FI F + ++ + ++ K++
Sbjct: 60 VAFILFLDKDSAQNC----TRAINNKQLF 84
Score = 73.8 bits (182), Expect = 1e-16
Identities = 11/53 (20%), Positives = 30/53 (56%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++V + + ++ FS++GKV + ++ D+ T++ +G F+ F +++
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 95.6 bits (238), Expect = 6e-24
Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 4/89 (4%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
G G G T L+VGGL+ + + L F FG +TD+ I D T++ RG
Sbjct: 47 DGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 106
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
F F+ F E I ++ ++
Sbjct: 107 FAFVEFELAEDAAAA----IDNMNESELF 131
Score = 80.6 bits (199), Expect = 1e-18
Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 6/95 (6%)
Query: 214 ETVEKVLKVPIHT------LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK 267
E E + +P + +D + ++VGG++++ + +
Sbjct: 22 EMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLH 81
Query: 268 AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
A F FG + + + +D +T++HRGF FV FE E
Sbjct: 82 AAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 93.8 bits (234), Expect = 9e-24
Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 4/87 (4%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S P +A + V LS T L+E F FG+++ + + KD T +S+GF
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
FI+F E + I + G D
Sbjct: 61 FISFHRREDAARA----IAGVSGFGYD 83
Score = 74.6 bits (184), Expect = 9e-17
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 1/88 (1%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ + I V +S+DT +++ F FG + + D+ T + +GF F++F E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 303 VVDH-ICEIHFHMIKNKKVECKKAQPKE 329
I + + + + A+P
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPST 96
>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 = 93.9 bits (234), Expect = 9e-24
Identities = 29/101 (28%), Positives = 51/101 (50%), Gaps = 3/101 (2%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + T +L V + ++ LR+ FG FG + DV I+ + + S+GFG
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFG 58
Query: 207 FITFAEPETVEKVLK-VPIHTLDGKKIDPKHATPKNRPKIG 246
F+TF ++ + + ++G+KI+ +AT + G
Sbjct: 59 FVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99
Score = 72.7 bits (179), Expect = 3e-16
Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 3/92 (3%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ + K++ V + +++ F QFGK+ + ++ +++ +GFGFVTF
Sbjct: 5 SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTF 62
Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
EN D ++H +++ +K+E A +
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARV 94
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 95.4 bits (237), Expect = 9e-24
Identities = 30/141 (21%), Positives = 62/141 (43%), Gaps = 3/141 (2%)
Query: 114 PTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQT 173
+G D + L+ + Q + + T +G A ++VG SW T
Sbjct: 8 SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWT 67
Query: 174 SSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KVPIHTLDGK 230
+ ++L + G V ++ ++ +S+G+ + A +V K+L +P L+G+
Sbjct: 68 TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE 127
Query: 231 KIDPKHATPKNRPKIGNRTKK 251
K+D + AT +N + + +K
Sbjct: 128 KVDVRPATRQNLSQFEAQARK 148
Score = 66.5 bits (162), Expect = 2e-13
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 3/107 (2%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFG 294
A + NR ++VG S T+ +++ G V E ++ + +G+
Sbjct: 43 AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102
Query: 295 FVTFENEEVVDHICE-IHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
V +E V + E + ++ +KV+ + A + Q KR
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149
>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 = 93.5 bits (233), Expect = 1e-23
Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 14/106 (13%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S D + KLF+G + + L+ F FG + ++ ++KD T +G
Sbjct: 1 GSSGSSGMK--DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCA 58
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDP--------KHATPKNRPK 244
F+T+ E E+ K L +K P K A ++R
Sbjct: 59 FLTYCERESALKA----QSALHEQKTLPGMNRPIQVKPADSESRGG 100
Score = 80.4 bits (199), Expect = 7e-19
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
K+F+G + ++ +++K F +FGK+ E +L D+ T H+G F+T+ E
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 309 EIHFHMI---KNKKVECKKAQPKEAVQA 333
+H N+ ++ K A + +
Sbjct: 74 ALHEQKTLPGMNRPIQVKPADSESRGGS 101
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 93.5 bits (232), Expect = 1e-23
Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 9/96 (9%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH--RGFGFVTFENEEVVD 305
++K+FVGG+ D +E+ A F +FG + + +G+ F+ F+ E V
Sbjct: 7 GSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66
Query: 306 -------HICEIHFHMIKNKKVECKKAQPKEAVQAN 334
+ + + ++ K Q + ++
Sbjct: 67 ALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSD 102
Score = 84.6 bits (209), Expect = 3e-20
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 9/95 (9%)
Query: 155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD--PITQRSRGFGFITFAE 212
+ S K+FVGGL +++ F FG + K +G+ F+ F E
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 213 PETVEKVLKVPIH-------TLDGKKIDPKHATPK 240
+V+ ++ + + I K +
Sbjct: 62 ESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIR 96
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 92.7 bits (230), Expect = 2e-23
Identities = 27/116 (23%), Positives = 39/116 (33%), Gaps = 20/116 (17%)
Query: 155 TGDDPTSAKLFVGGLSWQTSSEKLREYFGMF-----GAVTDVLIMKDPITQRSRGFGFIT 209
+ + V GL E L YF G V QR G +T
Sbjct: 2 SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLT 53
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEE 265
F EP E+VL H L G ++ + A P+ ++ + G+ TS
Sbjct: 54 FREPADAERVLAQADHELHGAQLSLRPAPPRA-------PARLLLQGLPPGTSGPS 102
Score = 65.4 bits (159), Expect = 1e-13
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 13/86 (15%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYF-----SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
+ V G+ E + YF S G V +R G +TF
Sbjct: 8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREPAD 59
Query: 304 VDHICEIHFHMIKNKKVECKKAQPKE 329
+ + H + ++ + A P+
Sbjct: 60 AERVLAQADHELHGAQLSLRPAPPRA 85
>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 = 91.8 bits (229), Expect = 3e-23
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
T L+VGGL+ + + L F FG +TD+ I D T++ RGF F+ F E
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 219 VLKVPIHTLDGKKID 233
I ++ ++
Sbjct: 65 A----IDNMNESELF 75
Score = 80.3 bits (199), Expect = 4e-19
Identities = 18/56 (32%), Positives = 34/56 (60%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ ++VGG++++ + + A F FG + + + +D +T++HRGF FV FE E
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 92.0 bits (229), Expect = 3e-23
Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPE 214
+ + ++ T + + + + V ++ ++KD TQ++RGF F+ +
Sbjct: 6 HHHMD-TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 215 TVEKVLKV-----PIHTLDGKKI 232
++L++ P +DGK I
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTI 87
Score = 70.0 bits (172), Expect = 2e-15
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGK--VEETVMLMDQQTKRHRGFGFVTFENEE 302
I + ++ T + + S + V ++ D+QT+++RGF FV +
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
>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 = 91.0 bits (227), Expect = 4e-23
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ LFVG L+ E LR F F + +M D T SRG+GF++F + +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA- 59
Query: 221 KVPIHTLDGKKIDPK-----HATPK 240
+ ++ G+ ++ + A
Sbjct: 60 ---MDSMQGQDLNGRPLRINWAAKL 81
Score = 76.4 bits (189), Expect = 9e-18
Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
T +FVG ++ + E ++ F F ++ D QT RG+GFV+F +++ + +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+ + + + A E
Sbjct: 61 DSMQGQDLNGRPLRINWAAKLE 82
>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 = 91.1 bits (227), Expect = 7e-23
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 14/100 (14%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
S +LFV LS+ +S E L + F +G ++++ D +T++ +GF F+TF PE
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 217 EKVLKVPIHTLDGKKID----------PKHATPKNRPKIG 246
K +DG+ K ++ P G
Sbjct: 64 VKA----YAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
Score = 74.2 bits (183), Expect = 9e-17
Identities = 19/60 (31%), Positives = 33/60 (55%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ + ++FV +S +S E+++ FS +G + E +D TK+ +GF FVTF E
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 90.8 bits (226), Expect = 1e-22
Identities = 33/108 (30%), Positives = 43/108 (39%), Gaps = 12/108 (11%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S P S LFV GLS T+ E L+E F I+ D T S+GFG
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFG 57
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
F+ F E + ++ +ID A PK G +
Sbjct: 58 FVDFNSEEDAKAA----KEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
Score = 67.3 bits (165), Expect = 3e-14
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
+K +FV G+S+DT+ E +K F + ++ D++T +GFGFV F +EE
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+ I KV A+PK
Sbjct: 72 EAMEDGEIDGNKVTLDWAKPKG 93
>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 = 89.9 bits (224), Expect = 1e-22
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
G + +FVG LS + ++ + F FG ++D ++KD T +S+G+GF++F
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 216 VEKVLKVPIHTLDGKKIDPK-----HATPK 240
E I + G+ + + AT K
Sbjct: 61 AENA----IQQMGGQWLGGRQIRTNWATRK 86
Score = 72.6 bits (179), Expect = 2e-16
Identities = 19/79 (24%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
+FVG +S + + + A F+ FG++ + ++ D T + +G+GFV+F N+ ++ I +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 310 IHFHMIKNKKVECKKAQPK 328
+ + +++ A K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
>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 = 90.4 bits (225), Expect = 2e-22
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 1/93 (1%)
Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
+ T LF+G L+ S +L+ A D+ ++ T +R FG++ F
Sbjct: 8 PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFE 66
Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHATPKNRPK 244
E +EK L++ + G +I + ++ +
Sbjct: 67 SAEDLEKALELTGLKVFGNEIKLEKPKGRDGTR 99
Score = 76.9 bits (190), Expect = 1e-17
Identities = 17/83 (20%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+F+G ++ + S E+K S+ + + ++D +T +R FG+V FE+ E ++ E+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALEL 77
Query: 311 HFHMIKNKKVECKKAQPKEAVQA 333
+ +++ +K + ++ +
Sbjct: 78 TGLKVFGNEIKLEKPKGRDGTRG 100
>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 = 90.5 bits (225), Expect = 2e-22
Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 9/103 (8%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S D +FVG LS + ++E ++ F FG ++D ++KD T +S+G+G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
F++F E I + G+ + + AT K
Sbjct: 61 FVSFFNKWDAENA----IQQMGGQWLGGRQIRTNWATRKPPAP 99
Score = 72.0 bits (177), Expect = 9e-16
Identities = 22/99 (22%), Positives = 51/99 (51%), Gaps = 1/99 (1%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
+ + K + +FVG +S + + E++KA F+ FG++ + ++ D T + +G+GFV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 297 TFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQAN 334
+F N+ ++ I ++ + +++ A K +
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101
>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 = 91.8 bits (228), Expect = 2e-22
Identities = 30/113 (26%), Positives = 46/113 (40%), Gaps = 10/113 (8%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
+ S D L V L+++TS + LR F +G V DV I +D T+
Sbjct: 51 TFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 110
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
SRGF F+ F + E + +DG +D + A RP + +
Sbjct: 111 SRGFAFVRFHDKRDAEDA----MDAMDGAVLDGRELRVQMARYG-RPPDSHHS 158
Score = 76.4 bits (188), Expect = 6e-17
Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 16/116 (13%)
Query: 203 RGFGFITFAEPETVEKVLKVPI-------HTLDGKKI----DPKHATPKNRPKIGNR--- 248
G E V+ + + +DG+ + +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 249 --TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ V ++ TS + ++ F ++G+V + + D+ TK RGF FV F ++
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123
>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 = 89.2 bits (222), Expect = 4e-22
Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 4/93 (4%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ---RSRGFGFITFAEPETVE 217
S+ LF+ L++ T+ E L+ F GA+ I K S GFGF+ + +PE +
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 218 KVLK-VPIHTLDGKKIDPKHATPKNRPKIGNRT 249
K LK + HT+DG K++ + + +P G +
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKPASGPSS 97
Score = 67.7 bits (166), Expect = 2e-14
Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTK---RHRGFGFVTFENEEVVD 305
+ +F+ ++ T+ E +K FS+ G ++ + + GFGFV ++ E
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
+ ++ H + K+E + ++
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERAT 89
>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 = 87.7 bits (218), Expect = 1e-21
Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 3/103 (2%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP-ITQRSRGF 205
G SG S T++K+ V + +Q + ++RE F FG + V + K T RGF
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 206 GFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPKNRPKIG 246
GF+ F + +K H L G+++ + A + + G
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103
Score = 70.4 bits (173), Expect = 3e-15
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 4/102 (3%)
Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGF 293
+ PK T KI V + + E++ FS FG+++ + T HRGF
Sbjct: 2 SSGSSGQVPK-KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 294 GFVTFENEEVVDHICEIHFHM--IKNKKVECKKAQPKEAVQA 333
GFV F ++ H + +++ + A + VQ+
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102
>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 = 87.2 bits (217), Expect = 2e-21
Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
S+ L+VG L + + + LR F FG + ++++MKD T RS+G+GFITF++ E +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 219 VLKVPIHTLDGKKID 233
+ L+G ++
Sbjct: 63 A----LEQLNGFELA 73
Score = 73.7 bits (182), Expect = 1e-16
Identities = 16/54 (29%), Positives = 33/54 (61%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ ++VG + + + + ++ F FGK++ V++ D T R +G+GF+TF + E
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
>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 = 86.9 bits (216), Expect = 3e-21
Identities = 18/96 (18%), Positives = 44/96 (45%), Gaps = 9/96 (9%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S +++G + + + E++ + G V ++ +M DP T RS+G+ FI F + E+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA- 60
Query: 221 KVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKK 251
+ L+G ++ + +++ + +
Sbjct: 61 ---VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHH 93
Score = 74.6 bits (184), Expect = 6e-17
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++ +++G + D + E++ S G V M+ D QT R +G+ F+ F + E
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55
>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 = 85.4 bits (212), Expect = 7e-21
Identities = 29/89 (32%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG + +FVG L + E L E F G +T V I KD + +
Sbjct: 2 SSGSSGM--FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKS 58
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
FGF+ F PE+V I L+G ++
Sbjct: 59 FGFVCFKHPESVSYA----IALLNGIRLY 83
Score = 65.7 bits (161), Expect = 9e-14
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
+ P + +FVG + E + F Q G + + + D++ + + FGFV
Sbjct: 4 GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFV 62
Query: 297 TFENEE 302
F++ E
Sbjct: 63 CFKHPE 68
>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 = 84.9 bits (211), Expect = 8e-21
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
S+ L++ GL T+ + L + +G + + D T + +G+GF+ F P +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 218 KVLKVPIHTLDGKKID 233
K + L +
Sbjct: 62 KA----VTALKASGVQ 73
Score = 72.2 bits (178), Expect = 3e-16
Identities = 12/54 (22%), Positives = 31/54 (57%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ +++ G+ T+ +++ +GK+ T ++D+ T + +G+GFV F++
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58
>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 = 85.4 bits (212), Expect = 8e-21
Identities = 24/107 (22%), Positives = 43/107 (40%), Gaps = 13/107 (12%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + S L + LS+ + E L+E F + + +S+G+
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYA 56
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
FI FA E ++ L + + ++I+ + P+ P G
Sbjct: 57 FIEFASFEDAKEALN----SCNKREIEGRAIRLELQGPRGSPNSGPS 99
Score = 66.1 bits (162), Expect = 6e-14
Identities = 9/53 (16%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K + + +S + E ++ F + ++ + Q + +G+ F+ F + E
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFE 64
>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 = 84.5 bits (210), Expect = 1e-20
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI-TQRSRGFGFITFAEPETVE 217
K+ +G L+ + + + E F +G + + + + + S+G+ ++ F P+ E
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 218 KVLKVPIHTLDGKKID 233
K LK +DG +ID
Sbjct: 62 KALK----HMDGGQID 73
Score = 68.3 bits (168), Expect = 9e-15
Identities = 12/56 (21%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD-QQTKRHRGFGFVTFENEE 302
+ K+ +G ++++ + + + FS +GK++ M ++ +G+ +V FEN +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPD 58
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 84.5 bits (210), Expect = 1e-20
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
G + + ++VG + + ++E+L +F G+V V I+ D + +GF +I F++ E+
Sbjct: 1 GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 216 VEKVLKVPIHTLDGKKIDPKHATPKNRP 243
V L + G++I NRP
Sbjct: 61 VRTSLALDESLFRGRQIKVIPKRT-NRP 87
Score = 77.2 bits (191), Expect = 5e-18
Identities = 18/81 (22%), Positives = 40/81 (49%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
+ I+VG V +AEE++A+F G V +L D+ + +GF ++ F ++E V
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 309 EIHFHMIKNKKVECKKAQPKE 329
+ + + ++++ +
Sbjct: 66 ALDESLFRGRQIKVIPKRTNR 86
>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 = 86.4 bits (214), Expect = 2e-20
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
S L+VG LS+ T+ E++ E F G + +++ D + + + GF F+ +
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 211 AEPETVEKVLKVPIHTLDGKKID 233
E ++ ++G ++D
Sbjct: 89 YSRADAENAMR----YINGTRLD 107
Score = 76.8 bits (189), Expect = 5e-17
Identities = 20/114 (17%), Positives = 52/114 (45%), Gaps = 2/114 (1%)
Query: 218 KVLKVPIHTLDGKKIDPKH-ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV 276
K L+ + + D + + K+ ++ ++VG +S T+ E++ FS+ G +
Sbjct: 7 KALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66
Query: 277 EETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKE 329
++ +M +D+ K GF FV + + + + + I+ + ++ + +
Sbjct: 67 KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 84.3 bits (209), Expect = 3e-20
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 7/100 (7%)
Query: 145 SSGDSGRSTPTGDDP--TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
SSG R + + +L V + ++ LR+ FG FG + DV I+ + + S
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGS 68
Query: 203 RGFGFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPK 240
+GFGF+TF ++ + +H ++G+KI+ +AT +
Sbjct: 69 KGFGFVTFENSADADRARE-KLHGTVVEGRKIEVNNATAR 107
Score = 69.7 bits (171), Expect = 4e-15
Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
P+ + K K++ V + +++ F QFGK+ + ++ +++ +GF
Sbjct: 16 PRGSHMNTENKSQP--KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGF 71
Query: 294 GFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
GFVTFEN D ++H +++ +K+E A +
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 83.5 bits (207), Expect = 4e-20
Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 7/89 (7%)
Query: 147 GDSGRSTPTGD--DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
G SG S KLF+ GL + + E+L E G V D+ ++ + + +G
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
++ + + + +DG I
Sbjct: 60 LAYVEYENESQASQA----VMKMDGMTIK 84
Score = 68.1 bits (167), Expect = 2e-14
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
R K+F+ G+ + EE++ G V++ ++ + + + +G +V +
Sbjct: 7 GVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEY 65
Query: 299 ENEE 302
ENE
Sbjct: 66 ENES 69
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 83.5 bits (207), Expect = 5e-20
Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 9/102 (8%)
Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
+ + +L+VG L + + + LR F FG + + +M D T RS+
Sbjct: 9 SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPK 240
G+GFITF++ E +K + L+G ++ + H T +
Sbjct: 69 GYGFITFSDSECAKKA----LEQLNGFELAGRPMKVGHVTER 106
Score = 72.3 bits (178), Expect = 5e-16
Identities = 19/66 (28%), Positives = 37/66 (56%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
A N K +++VG + + + + ++ F FG++E ++MD +T R +G+GF+
Sbjct: 14 AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73
Query: 297 TFENEE 302
TF + E
Sbjct: 74 TFSDSE 79
>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 = 84.0 bits (208), Expect = 6e-20
Identities = 22/121 (18%), Positives = 46/121 (38%), Gaps = 16/121 (13%)
Query: 133 REAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL 192
RE + V +G G RS LFV G+ + + E + + F +G + ++
Sbjct: 1 REDYDSVEQDGDEPGPQ-RSVE------GWILFVTGVHEEATEEDIHDKFAEYGEIKNIH 53
Query: 193 IMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGN 247
+ D T +G+ + + + + + L+G+ + + + PK
Sbjct: 54 LNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDWCFVRGPPKGKR 109
Query: 248 R 248
R
Sbjct: 110 R 110
Score = 70.1 bits (172), Expect = 6e-15
Identities = 12/52 (23%), Positives = 32/52 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FV GV ++ + E++ F+++G+++ + +D++T +G+ V +E +
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
>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 = 84.4 bits (209), Expect = 6e-20
Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 10/132 (7%)
Query: 125 FVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGM 184
V + + QL + + + + L V + +LR+ F
Sbjct: 6 LVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFER 65
Query: 185 FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATP 239
+G + V I+ D T++SRG+GF+ F + ++ I L+G I K A
Sbjct: 66 YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA----IAGLNGFNILNKRLKVALAAS 121
Query: 240 K-NRPKIGNRTK 250
RP I
Sbjct: 122 GHQRPGIAGAVG 133
Score = 75.2 bits (185), Expect = 1e-16
Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
+H P + + + V + +++ F ++G +E ++ D++T++ RG+
Sbjct: 27 QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 294 GFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
GFV F++ I ++ I NK+++ A
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123
>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 = 82.2 bits (204), Expect = 8e-20
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 4/85 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L++G L+W T+ E L E G + ++ ++ +S+GF + + +K++
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 221 -KVPIHTLDGKKIDPKHATPKN-RP 243
+P L G+ +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHHH 87
Score = 64.9 bits (159), Expect = 2e-13
Identities = 10/82 (12%), Positives = 29/82 (35%), Gaps = 3/82 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
+++G ++ T+ E++ G + E ++ + +GF V +E +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+ + + + E
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLE 84
>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 = 83.1 bits (206), Expect = 8e-20
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + +FV L ++ +KL+E F M G V I++D +SRG G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+TF + + I +G+ +
Sbjct: 60 TVTFEQSIEAVQA----ISMFNGQLLF 82
Score = 59.2 bits (144), Expect = 3e-11
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 2/101 (1%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV 304
G +FV + +++K FS G V +L D + + RG G VTFE E V
Sbjct: 12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAV 70
Query: 305 DHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
I + ++ ++ + K + + GP
Sbjct: 71 QAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111
>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 = 83.1 bits (206), Expect = 9e-20
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 9/105 (8%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
+G + G + + P A LF+ L + + L + F FG V + D T
Sbjct: 6 SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 65
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKN 241
S+ FGF+++ P + + I +++G +I K KN
Sbjct: 66 SKCFGFVSYDNPVSAQAA----IQSMNGFQIGMKRLKVQLKRSKN 106
Score = 70.8 bits (174), Expect = 2e-15
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
+F+ + Q+ +++ F FG V + +D+QT + FGFV+++N I
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVG 338
++ I K+++ + + K ++ G
Sbjct: 87 MNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 82.7 bits (205), Expect = 1e-19
Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 5/93 (5%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S KLFVG L+ Q S E + F FG + + +++ P S+G
Sbjct: 1 GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATP 239
F+ F+ + IH L G + P ++
Sbjct: 60 FVKFSSHTEAQAA----IHALHGSQTMPGASSS 88
Score = 67.3 bits (165), Expect = 3e-14
Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
G R +K+FVG +++ S E+V F FG ++E +L +G FV F
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKF 63
Query: 299 EN-EEVVDHICEIHFHMI---KNKKVECKKAQPKE 329
+ E I +H + + K A +
Sbjct: 64 SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK 98
>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 = 81.9 bits (203), Expect = 2e-19
Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 9/93 (9%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
D + +FVG + ++ + E+L++ F G V ++ D T + +G+GF + + ET
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 217 EKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
+ L+G++ + +A + +
Sbjct: 64 LSA----MRNLNGREFSGRALRVDNAASEKNKE 92
Score = 70.7 bits (174), Expect = 2e-15
Identities = 16/60 (26%), Positives = 36/60 (60%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
P + + +FVG + + + E++K FS+ G V ++ D++T + +G+GF ++++E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 81.2 bits (201), Expect = 4e-19
Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 6/86 (6%)
Query: 148 DSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF 207
DSG G + KL V L + S ++E F FG + + D + RS G
Sbjct: 17 DSGFGGGAGVET-GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTAD 74
Query: 208 ITFAEPETVEKVLKVPIHTLDGKKID 233
+ F K +K +G +D
Sbjct: 75 VHFERKADALKAMK----QYNGVPLD 96
Score = 57.7 bits (140), Expect = 9e-11
Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFG 294
+ K+ V + S +++ F++FG +++ + D ++ R G
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTA 73
Query: 295 FVTFENEE 302
V FE +
Sbjct: 74 DVHFERKA 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 = 81.3 bits (201), Expect = 5e-19
Identities = 19/107 (17%), Positives = 44/107 (41%), Gaps = 1/107 (0%)
Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
S + ++VG + + ++++ L +F G++ + I+ D + +
Sbjct: 19 TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK 78
Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK 250
G+ +I FAE +V+ + + G+ I N P I + +
Sbjct: 79 GYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT-NMPGISSTDR 124
Score = 74.8 bits (184), Expect = 1e-16
Identities = 14/81 (17%), Positives = 39/81 (48%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
+ ++VG V ++A++++A+FS G + +L D+ + +G+ ++ F VD
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 309 EIHFHMIKNKKVECKKAQPKE 329
+ + + + ++ +
Sbjct: 96 AMDETVFRGRTIKVLPKRTNM 116
>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 = 80.3 bits (199), Expect = 6e-19
Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 11/107 (10%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S L+V L E+LR+ F FG +T +M + RS+GFG
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
F+ F+ PE K + ++G+ + K A K + G
Sbjct: 59 FVCFSSPEEATKA----VTEMNGRIVATKPLYVALAQRKEERQSGPS 101
Score = 64.5 bits (158), Expect = 3e-13
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
++V + E ++ FS FG + ++M+ R +GFGFV F + EE + E
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 310 IHFHMIKNKKVECKKAQPKE 329
++ ++ K + AQ KE
Sbjct: 75 MNGRIVATKPLYVALAQRKE 94
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 80.0 bits (198), Expect = 8e-19
Identities = 20/117 (17%), Positives = 45/117 (38%), Gaps = 16/117 (13%)
Query: 132 VREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDV 191
+RE + V +G G RS LFV G+ + + E + + F +G + ++
Sbjct: 1 MREDYDSVEQDGDEPGPQ-RSVE------GWILFVTGVHEEATEEDIHDKFAEYGEIKNI 53
Query: 192 LIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
+ D T +G+ + + + + + L+G+ + + + P
Sbjct: 54 HLNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDWCFVRGPP 106
Score = 68.1 bits (167), Expect = 2e-14
Identities = 12/52 (23%), Positives = 32/52 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FV GV ++ + E++ F+++G+++ + +D++T +G+ V +E +
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
>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 = 79.2 bits (196), Expect = 2e-18
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S DD L+VG LS + + + F G ++ + + + +
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYC 58
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
F+ F E L ++G+KI
Sbjct: 59 FVEFYEHRDAAAALA----AMNGRKIL 81
Score = 62.3 bits (152), Expect = 2e-12
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+ + ++VG +S+D + + FSQ G + M+ + + + + FV F
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAA 70
Query: 307 -ICEIHFHMIKNKKVECKKAQPKE 329
+ ++ I K+V+ A
Sbjct: 71 ALAAMNGRKILGKEVKVNWATTPS 94
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 78.8 bits (195), Expect = 2e-18
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 10/87 (11%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S ++LFVG L + E++R+ F +G +V I KD +GFG
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
FI E LD +
Sbjct: 55 FIRLETRTLAEIA----KVELDNMPLR 77
Score = 72.7 bits (179), Expect = 3e-16
Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
+ R++ +FVG + D + EE++ F ++GK E + + +GFGF+
Sbjct: 5 SSGGEKTFTQRSR-LFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIR 57
Query: 298 FENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQA 333
E + + E+ ++ K++ + A ++ +
Sbjct: 58 LETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++VG L + +SE+++E F FG V +V ++ D T++ +GFGF+ E E+V +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEA--- 58
Query: 223 PIHTLDGKKID 233
I LD
Sbjct: 59 -IAKLDNTDFM 68
Score = 78.4 bits (194), Expect = 3e-18
Identities = 27/80 (33%), Positives = 47/80 (58%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+ I+VG + ++E+VK FSQFGKV ++ D++TK+ +GFGFV + E V + I +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 310 IHFHMIKNKKVECKKAQPKE 329
+ + + +A PK+
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
>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 = 79.7 bits (197), Expect = 2e-18
Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 5/85 (5%)
Query: 149 SGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
T AKL V L + S ++E F FG + + D + RS G +
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 81
Query: 209 TFAEPETVEKVLKVPIHTLDGKKID 233
F K +K G +D
Sbjct: 82 HFERRADALKAMK----QYKGVPLD 102
Score = 61.2 bits (149), Expect = 7e-12
Identities = 14/106 (13%), Positives = 43/106 (40%), Gaps = 5/106 (4%)
Query: 234 PKHATPKNRPKIGNRTK---KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH 290
+H + G + K+ V + S +++ F++FG +++ + D ++ R
Sbjct: 17 WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRS 75
Query: 291 RGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL 335
G V FE + + + + + + ++ + + ++ +
Sbjct: 76 LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 121
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 79.4 bits (196), Expect = 2e-18
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
G ++ L+ L++ +G V +V I+ P T++ G + F
Sbjct: 1 GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60
Query: 216 VEKVLKVPIHTLDGKKID 233
++ + L +
Sbjct: 61 AKET----VKNLHLTSVM 74
Score = 70.9 bits (174), Expect = 2e-15
Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
K++ ++ + +K ++G+VEE +L+ +T++H G V F + +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 309 EIHFHMIKNKKVECKKAQPKE 329
+H + + + +
Sbjct: 67 NLHLTSVMGNIIHAQLDIKGQ 87
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVL-IMKDPITQRSRGFGFITFAEPETVE 217
S+ +F+G L + + L + F FG + IM+DP T S+G+ FI FA + +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 218 KVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNR 248
I ++G+ + + +A K+ G
Sbjct: 63 AA----IEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
Score = 65.3 bits (160), Expect = 1e-13
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVDH-IC 308
IF+G + + + + FS FG + +T +M D T +G+ F+ F + + D I
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 309 EIHFHMIKNKKVECKKAQPKE 329
++ + N+ + A K+
Sbjct: 67 AMNGQYLCNRPITVSYAFKKD 87
>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 = 78.5 bits (194), Expect = 2e-18
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAE 212
+G +A L++G L + F G V V I+++ +T G+ F+ FA+
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
Query: 213 PETVEKVLKVPIHTLDGKKID 233
T EK +H ++GK +
Sbjct: 62 LATAEKC----LHKINGKPLP 78
Score = 53.9 bits (130), Expect = 1e-09
Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 2/75 (2%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFG-KVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
+++G + + F+ G V ++ ++ T G+ FV F + +
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 307 ICEIHFHMIKNKKVE 321
+ +I+ +
Sbjct: 69 LHKINGKPLPGATPA 83
>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 = 78.9 bits (195), Expect = 3e-18
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 11/93 (11%)
Query: 145 SSGDSGRSTPTG----DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
SSG SG S +++VG L ++ + + F +GA+ D+ +
Sbjct: 2 SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
F F+ F +P E ++ DG D
Sbjct: 59 GGPPFAFVEFEDPRDAEDA----VYGRDGYDYD 87
Score = 63.9 bits (156), Expect = 6e-13
Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
R GN +I+VG + D ++++ F ++G + + + + F FV F
Sbjct: 12 GVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEF 68
Query: 299 ENEE 302
E+
Sbjct: 69 EDPR 72
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 80.7 bits (199), Expect = 3e-18
Identities = 21/130 (16%), Positives = 37/130 (28%), Gaps = 5/130 (3%)
Query: 104 KSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAK 163
++ R + + + + + T AK
Sbjct: 31 RNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAK 90
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L V L + S ++E F FG + + D + RS G + F K +K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK-- 147
Query: 224 IHTLDGKKID 233
G +D
Sbjct: 148 --QYKGVPLD 155
Score = 63.3 bits (154), Expect = 4e-12
Identities = 14/110 (12%), Positives = 42/110 (38%), Gaps = 2/110 (1%)
Query: 227 LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ 286
L K + + K+ V + S +++ F++FG +++ + D +
Sbjct: 66 LPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-R 124
Query: 287 TKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANL 335
+ R G V FE + + + + + + ++ + + ++ +
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 174
>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 = 78.1 bits (193), Expect = 3e-18
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 9/82 (10%)
Query: 152 STPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
+ + L LS+ + ++L+E F + +S+G +I F
Sbjct: 7 PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFK 61
Query: 212 EPETVEKVLKVPIHTLDGKKID 233
EK L+ G +ID
Sbjct: 62 SEADAEKNLE----EKQGAEID 79
Score = 62.7 bits (153), Expect = 1e-12
Identities = 8/53 (15%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ + +S + + +E+K F ++ + Q + +G ++ F++E
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEA 64
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 78.5 bits (194), Expect = 4e-18
Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 1/102 (0%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S +VG L + T + F + V +++D T + +GF
Sbjct: 1 GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
++ F E +++++ L L + + A + + K G
Sbjct: 60 YVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSGPS 101
Score = 60.0 bits (146), Expect = 1e-11
Identities = 12/80 (15%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+VG + +T ++ A F + ++ D+ T + +GF +V F+ + +
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 310 IHFHMIKNKKVECKKAQPKE 329
++ ++ + A+ ++
Sbjct: 75 YDGALLGDRSLRVDIAEGRK 94
>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 = 77.7 bits (192), Expect = 7e-18
Identities = 25/94 (26%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 145 SSGDSGRSTP-----TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPIT 199
SSG+ R P +P + L++ LS + + L F F I +T
Sbjct: 5 SSGEEIRKIPMFSSYNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT 63
Query: 200 QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
R RG FITF E + L ++G K+
Sbjct: 64 GRMRGQAFITFPNKEIAWQALH----LVNGYKLY 93
Score = 70.8 bits (174), Expect = 3e-15
Identities = 16/86 (18%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
G K +++ +S + ++ + F++F + + + T R RG F+TF N+E+
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81
Query: 306 H-ICEIHFHMIKNKKVECKKAQPKEA 330
+ ++ + + K + + + K+
Sbjct: 82 QALHLVNGYKLYGKILVIEFGKNKKQ 107
>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 = 80.9 bits (199), Expect = 7e-18
Identities = 18/114 (15%), Positives = 43/114 (37%), Gaps = 3/114 (2%)
Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPI 198
V + + L++G L+W T+ E L E G + ++ ++
Sbjct: 48 VGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA 107
Query: 199 TQRSRGFGFITFAEPETVEKVL-KVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
+S+GF + + +K++ +P L G+ + + +++K
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161
Score = 65.9 bits (160), Expect = 1e-12
Identities = 17/130 (13%), Positives = 40/130 (30%), Gaps = 3/130 (2%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG--KVEETVMLMDQQTKRHR 291
K A P + +++G ++ T+ E++ G + E ++ + +
Sbjct: 53 GKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112
Query: 292 GFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRM 350
GF V +E + + + + + Q + K G +
Sbjct: 113 GFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172
Query: 351 AAPAPITPAT 360
A P +
Sbjct: 173 KAGPPGGSSR 182
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 77.8 bits (192), Expect = 9e-18
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+ P LF+ L + + L F FG V + D T S+ FGF++F P++
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 217 EKVLKVPIHTLDGKKIDPK 235
+ I ++G ++ K
Sbjct: 96 QVA----IKAMNGFQVGTK 110
Score = 62.8 bits (153), Expect = 2e-12
Identities = 20/101 (19%), Positives = 45/101 (44%), Gaps = 1/101 (0%)
Query: 227 LDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQ 286
L + A + G +F+ + Q+ + ++ + F FG V + +D+Q
Sbjct: 18 LASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77
Query: 287 TKRHRGFGFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQ 326
T + FGFV+F+N + I ++ + K+++ + +
Sbjct: 78 TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>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 = 77.3 bits (191), Expect = 1e-17
Identities = 19/118 (16%), Positives = 42/118 (35%), Gaps = 16/118 (13%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
S +F+ L ++ L + F FG + ++ D S+G+GF+ F E E+
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60
Query: 219 VLKVPIHTLDGKKIDPK-----HATPKN-RPKIGNRTKK----IFVGGVSQDTSAEEV 266
I ++G ++ + + R K +++ ++
Sbjct: 61 A----IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAAA 114
Score = 66.5 bits (163), Expect = 9e-14
Identities = 17/82 (20%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-I 307
+ IF+ + + + + FS FG + ++ D +G+GFV FE +E + I
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+++ ++ ++KV + + ++
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRK 84
>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 = 76.9 bits (190), Expect = 1e-17
Identities = 22/103 (21%), Positives = 40/103 (38%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S F+G L + + E ++E+F L + +R +GFG
Sbjct: 1 GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRT 249
+ F + +++ L + +L K+I A G +
Sbjct: 61 YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPSS 103
Score = 62.3 bits (152), Expect = 2e-12
Identities = 15/80 (18%), Positives = 33/80 (41%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
F+G + D + E +K +F + +R +GFG+ FE+ + +
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 310 IHFHMIKNKKVECKKAQPKE 329
++ + NK++ A +
Sbjct: 76 LNEESLGNKRIRVDVADQAQ 95
>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 = 78.7 bits (194), Expect = 1e-17
Identities = 16/115 (13%), Positives = 40/115 (34%), Gaps = 9/115 (7%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
++ D LFV + + ++++E F +G + ++ + D T
Sbjct: 53 RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 112
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRTKK 251
S+G+ + + + L+G +I + K ++ K+
Sbjct: 113 SKGYALVEYETHKQALAA----KEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163
Score = 70.6 bits (173), Expect = 8e-15
Identities = 10/54 (18%), Positives = 29/54 (53%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FV + ++ +E++ F +G+++ + +D++T +G+ V +E +
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
>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 = 76.2 bits (188), Expect = 2e-17
Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 15/105 (14%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + L+V L TS E + + F + K R +
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYA 54
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKH-----ATPKNRPKIG 246
F+ F+ E + +K L+GK +D A P ++ G
Sbjct: 55 FVHFSNREDAVEAMK----ALNGKVLDGSPIEVTLAKPVDKDSSG 95
Score = 64.2 bits (157), Expect = 3e-13
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHI 307
K ++V + TS E ++ F+ ++ K+ R + FV F N E+ V+ +
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEAM 68
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
++ ++ +E A+P +
Sbjct: 69 KALNGKVLDGSPIEVTLAKPVD 90
>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 = 2e-17
Identities = 15/104 (14%), Positives = 36/104 (34%), Gaps = 11/104 (10%)
Query: 148 DSGRSTPTGDD--PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
+ G LFV + + ++++E F +G + ++ + D T S+G+
Sbjct: 11 EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY 70
Query: 206 GFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPK 244
+ + + L+G +I + K +
Sbjct: 71 ALVEYETHKQALAA----KEALNGAEIMGQTIQVDWCFVKGPKR 110
Score = 67.7 bits (166), Expect = 2e-14
Identities = 11/64 (17%), Positives = 32/64 (50%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ P+ +FV + ++ +E++ F +G+++ + +D++T +G+ V +
Sbjct: 16 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 299 ENEE 302
E +
Sbjct: 76 ETHK 79
>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 = 76.2 bits (188), Expect = 2e-17
Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 17/102 (16%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD--------VLIMKDPITQR 201
G + +FV GL + E + +YF G + + + D T +
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HAT 238
+G ++F +P + + I DGK+ AT
Sbjct: 62 LKGEATVSFDDPPSAKAA----IDWFDGKEFSGNPIKVSFAT 99
Score = 65.4 bits (160), Expect = 1e-13
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTKRH 290
+ + IFV G+ ++ + E V YF Q G ++ + D++T +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 291 RGFGFVTFENEEVVD 305
+G V+F++
Sbjct: 63 KGEATVSFDDPPSAK 77
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 79.0 bits (194), Expect = 3e-17
Identities = 23/201 (11%), Positives = 56/201 (27%), Gaps = 50/201 (24%)
Query: 161 SAKLFVGGLSWQTSSE-KLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
S L V GL + ++ F ++G V V MK G + A+ V++
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRA 58
Query: 220 LKVPIHTLDGKKI---------------------------------------DPKHATPK 240
I L+ +
Sbjct: 59 ----ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114
Query: 241 NRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ +I + + + + + E + G T + + G + +++
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDS 174
Query: 301 -EEVVDHICEIHFHMIKNKKV 320
+ ++ + ++ + +KN
Sbjct: 175 KSDALETLGFLNHYQMKNPNG 195
Score = 54.7 bits (131), Expect = 7e-09
Identities = 8/77 (10%), Positives = 17/77 (22%), Gaps = 4/77 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
S L + + E E G + G + + +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 219 VLKVPIHTLDGKKIDPK 235
L L+ ++
Sbjct: 181 TLG----FLNHYQMKNP 193
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 75.2 bits (185), Expect = 4e-17
Identities = 13/95 (13%), Positives = 36/95 (37%), Gaps = 1/95 (1%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+D + +++ G + + ++E+ G V ++ + + + +G F+ F E+
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESA 65
Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
+K ++ P + K R +
Sbjct: 66 KKFVETPGQKYKETDLLILFKDDYFAKKNEERKQN 100
Score = 75.2 bits (185), Expect = 4e-17
Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 3/89 (3%)
Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+ + NR+ +++ G D + +++K + G+V + + K +G FV F++
Sbjct: 6 KNDVKNRS--VYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSI 62
Query: 302 EVVDHICEIHFHMIKNKKVECKKAQPKEA 330
E E K + A
Sbjct: 63 ESAKKFVETPGQKYKETDLLILFKDDYFA 91
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 74.5 bits (184), Expect = 5e-17
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ ++FV L + + + L++ F G V I + +S+G G + F PE E+
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 65
Query: 221 -KVPIHTLDGKKIDPKHATPKNRPKIG 246
+ L G++ID + + P G
Sbjct: 66 RMMNGMKLSGREIDVRIDRNASGPSSG 92
Score = 59.1 bits (144), Expect = 2e-11
Identities = 16/85 (18%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+ +IFV + D + + +K F++ G V + M+ + +G G V FE+ EV +
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
Query: 306 H-ICEIHFHMIKNKKVECKKAQPKE 329
++ + ++++ + +
Sbjct: 63 RACRMMNGMKLSGREIDVRIDRNAS 87
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 75.1 bits (185), Expect = 7e-17
Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 17/97 (17%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFI 208
D+ + +FV GL + E + +YF G + + + D T + +G +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 209 TFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPK 240
+F +P + + I DGK+ AT +
Sbjct: 63 SFDDPPSAKAA----IDWFDGKEFSGNPIKVSFATRR 95
Score = 65.1 bits (159), Expect = 3e-13
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTKRHRGFGFVTFE 299
IFV G+ ++ + E V YF Q G ++ + D++T + +G V+F+
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 300 NEEVVD 305
+
Sbjct: 66 DPPSAK 71
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 75.7 bits (186), Expect = 1e-16
Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
P K++VG L + +L FG +G + V + ++P GF F+ F
Sbjct: 63 HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF 117
Query: 211 AEPETVEKVLKVPIHTLDGKKID 233
+P + LDG+ +
Sbjct: 118 EDPRDAADA----VRELDGRTLC 136
Score = 65.3 bits (159), Expect = 5e-13
Identities = 21/118 (17%), Positives = 38/118 (32%), Gaps = 21/118 (17%)
Query: 200 QRSRGFGFITFAEPETVEKVLK---------------VPIHTLDGKKIDPKHATPKNRPK 244
+ +G + T EKV K T + H +R
Sbjct: 10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDS 69
Query: 245 IGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K ++VG + + + E++ F +G + + + GF FV FE+
Sbjct: 70 CPLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPR 121
>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 = 74.2 bits (183), Expect = 1e-16
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+ L++ L ++L FG V I++D + SRG GF E
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKC 79
Query: 217 EKVLKVPIHTLDGKKIDPK 235
E V I +GK I
Sbjct: 80 EAV----IGHFNGKFIKTP 94
Score = 60.3 bits (147), Expect = 1e-11
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 2/85 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
+++ + +E++ FG+V T +L D + RG GF E+ E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH 85
Query: 310 IHFHMIKNKKVECKKAQPKEAVQAN 334
+ IK +P +
Sbjct: 86 FNGKFIKTPPGVSAPTEPLLCKFSG 110
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 73.0 bits (180), Expect = 2e-16
Identities = 26/107 (24%), Positives = 43/107 (40%), Gaps = 25/107 (23%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG++ S KL VG +S ++++LR F +G V + I+ +
Sbjct: 2 SSGSSGKA--------STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KD 45
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIG 246
+ F+ E + I LD + K +T + R G
Sbjct: 46 YAFVHMERAEDAVEA----IRGLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 64.9 bits (159), Expect = 2e-13
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVV 304
G + K+ VG +S + +E++A F ++G V E ++ + + FV E E+ V
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIE-CDIV-------KDYAFVHMERAEDAV 58
Query: 305 DHICEIHFHMIKNKKVECKKAQPKE 329
+ I + + K++ + + +
Sbjct: 59 EAIRGLDNTEFQGKRMHVQLSTSRL 83
>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 = 76.1 bits (187), Expect = 2e-16
Identities = 32/204 (15%), Positives = 67/204 (32%), Gaps = 45/204 (22%)
Query: 161 SAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
++ L V L+ + + + L FG++G V V I+ + + + A+ +
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57
Query: 220 LK-VPIHTLDGKKIDPKHAT--------------------------------PKNRPKIG 246
+ + H L GK I + KN I
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVD 305
+ + + + S E++K FS G V + + R + + EE V
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQ 173
Query: 306 HICEIH-FHMIKNKKVECKKAQPK 328
+ ++H + +N + ++
Sbjct: 174 ALIDLHNHDLGENHHLRVSFSKST 197
Score = 50.3 bits (120), Expect = 2e-07
Identities = 18/87 (20%), Positives = 24/87 (27%), Gaps = 8/87 (9%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G P SA L + + S E L+ F G V Q+ R I
Sbjct: 109 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQ 164
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKH 236
E + L L + H
Sbjct: 165 MGSVEEAVQAL----IDLHNHDLGENH 187
Score = 40.3 bits (94), Expect = 4e-04
Identities = 10/87 (11%), Positives = 31/87 (35%), Gaps = 9/87 (10%)
Query: 245 IGNRTKKIFVGGVSQDT-SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
+GN + V ++ + + + + F +G V+ +L + V +
Sbjct: 1 MGNSV--LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQ 53
Query: 304 VDH-ICEIHFHMIKNKKVECKKAQPKE 329
+ ++ H + K + ++ +
Sbjct: 54 AQLAMSHLNGHKLHGKPIRITLSKHQN 80
>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 = 73.7 bits (181), Expect = 3e-16
Identities = 20/113 (17%), Positives = 42/113 (37%)
Query: 233 DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
P +++ G+ + + V +F + VE+++ + + G
Sbjct: 9 SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 68
Query: 293 FGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
GFV F NE H + N+ ++ K ++ ++ KR+ GP
Sbjct: 69 EGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGP 121
Score = 64.5 bits (157), Expect = 5e-13
Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 2/110 (1%)
Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQR 201
GKS RS +++ GL ++ ++ + ++F V D + I P +
Sbjct: 7 GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGK 65
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
+ G GF+ F + L + + I T K + + +K
Sbjct: 66 ATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRK 115
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 72.7 bits (179), Expect = 3e-16
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K++VG L +L F +G + V I ++P GF F+ F +P E
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDA--- 53
Query: 223 PIHTLDGKKID 233
+ LDGK I
Sbjct: 54 -VRGLDGKVIC 63
Score = 57.7 bits (140), Expect = 6e-11
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K++VG + E++ FS +G + V + + GF FV FE+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRT-VWIA----RNPPGFAFVEFEDPR 48
>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 = 72.7 bits (179), Expect = 4e-16
Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 147 GDSGRSTPTGDDPT--SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ-RSR 203
G P F+G L + + E ++E+F ++ V + ++P R +
Sbjct: 3 GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61
Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKN 241
GFG+ F + +++ L + +L ++I A
Sbjct: 62 GFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 99
Score = 60.7 bits (148), Expect = 6e-12
Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT-KRHRGFGFVTFENEEVVDHIC 308
F+G + D + E +K +F + + + +R +GFG+ FE+ + +
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
Query: 309 EIHFHMIKNKKVECKKAQPKE 329
++ + N+++ A +
Sbjct: 79 SLNEESLGNRRIRVDVADQAQ 99
>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 = 72.8 bits (179), Expect = 4e-16
Identities = 24/116 (20%), Positives = 44/116 (37%), Gaps = 17/116 (14%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPI 198
G SG S +D ++ ++V GL+ + + L ++F G V + I D
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 199 TQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIGNRT 249
T + +G +++ +P T + + DGK A K G +
Sbjct: 61 TGKPKGDATVSYEDPPTAKAA----VEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
Score = 65.5 bits (160), Expect = 1e-13
Identities = 16/102 (15%), Positives = 41/102 (40%), Gaps = 9/102 (8%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETV--------MLMDQQTK 288
+ P + I+V G++ + +++ +F Q G V+ + +D++T
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62
Query: 289 RHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
+ +G V++E+ + + K++ A+ K
Sbjct: 63 KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
>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 = 72.2 bits (178), Expect = 4e-16
Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 26/104 (25%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG + K+FVG +S +S++LR F G V + ++K
Sbjct: 2 SSGSSGNTW---------KIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------D 44
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRP 243
+ F+ + + I L+GK++ K +T +
Sbjct: 45 YAFVHMEKEADAKAA----IAQLNGKEVKGKRINVELSTKGQKK 84
Score = 63.8 bits (156), Expect = 4e-13
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHI 307
T KIFVG VS +++E+++ F + G+V E ++ + + FV E + I
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIE-CDVV-------KDYAFVHMEKEADAKAAI 60
Query: 308 CEIHFHMIKNKKVECKKAQPKE 329
+++ +K K++ + + +
Sbjct: 61 AQLNGKEVKGKRINVELSTKGQ 82
>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 = 71.9 bits (177), Expect = 5e-16
Identities = 22/106 (20%), Positives = 37/106 (34%), Gaps = 23/106 (21%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S KL++G LS +++ LR+ FG G+
Sbjct: 1 GSSGSSGMN-------KLYIGNLSPAVTADDLRQLFGDRKLPLAG------QVLLKSGYA 47
Query: 207 FITFAEPETVEKVLKVPIHTLD------GKKIDPKHATPKNRPKIG 246
F+ + + + I TL GK ++ ++ K G
Sbjct: 48 FVDYPDQNWAIRA----IETLSGKVELHGKIMEVDYSVSKKLRSSG 89
Score = 65.0 bits (159), Expect = 2e-13
Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
K+++G +S +A++++ F + Q G+ FV + ++ I
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIE 62
Query: 309 EIHFHM-IKNKKVECKKAQPKE 329
+ + + K +E + K+
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKK 84
>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 = 72.5 bits (178), Expect = 5e-16
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 1/95 (1%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
N P N + + G+ S EE+ +FS V + L R G FV F
Sbjct: 6 SGNSPDTAN-DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64
Query: 299 ENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
++E+ + + H I ++ +E K+ E +
Sbjct: 65 ASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTS 99
Score = 69.8 bits (171), Expect = 4e-15
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 3/96 (3%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG S T +D + + GL + S E++ ++F V + + + RS G
Sbjct: 2 SSGSSGNSPDTANDGF---VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG 58
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPK 240
F+ FA E EK LK + + I+ ++
Sbjct: 59 EAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRA 94
>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 = 71.4 bits (175), Expect = 1e-15
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 5/87 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDP-ITQRSRGFGFITFAEPETVE--- 217
+LF+GG+ E++ E V DV++ ++RGF F+ +
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRPK 244
+ L L G +I A P+
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEIDVD 96
Score = 63.3 bits (154), Expect = 9e-13
Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 5/87 (5%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM--DQQTKRHRGFGFVTFENEEVVDHIC 308
++F+GG+ + EE+ ++ + V++ ++RGF FV +E+
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 309 EI---HFHMIKNKKVECKKAQPKEAVQ 332
+ ++ A+P+ V
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEIDVD 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 = 70.7 bits (174), Expect = 1e-15
Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 21/102 (20%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G S +G KLF+G L + + +++R F +G V + I+K +GF+
Sbjct: 1 GSSGSSG----MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVH 48
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK-----HATPKNRPKIG 246
+ E I L K+ + K++ G
Sbjct: 49 IEDKTAAEDA----IRNLHHYKLHGVNINVEASKNKSKASSG 86
Score = 63.4 bits (155), Expect = 6e-13
Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
K+F+G + ++ + +E+++ F Q+GKV E ++ + +GFV E+ D
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLE-CDII-------KNYGFVHIEDKTAAEDA 58
Query: 307 ICEIHFHMIKNKKVECKKAQPKE 329
I +H + + + + ++ K
Sbjct: 59 IRNLHHYKLHGVNINVEASKNKS 81
>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 = 70.0 bits (172), Expect = 3e-15
Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 4/87 (4%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + P + V + + S +++ ++F + + + +K G
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+ F + + L+ + I
Sbjct: 61 MVAFESRDEATAAVI----DLNDRPIG 83
Score = 58.9 bits (143), Expect = 2e-11
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
I V + S +E+ +F + + +V L + G V FE+ +E
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 307 ICEIHFHMIKNKKVECKKA 325
+ +++ I ++KV+
Sbjct: 74 VIDLNDRPIGSRKVKLSGP 92
>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 = 72.7 bits (178), Expect = 6e-15
Identities = 34/210 (16%), Positives = 67/210 (31%), Gaps = 44/210 (20%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
S + P ++ L V L+ + + + L FG++G V V I+ + +
Sbjct: 18 GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KK 72
Query: 204 GFGFITFAEPETVEKVLK-VPIHTLDGKKIDPKHAT------------------------ 238
+ A+ + + + H L GK I +
Sbjct: 73 ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132
Query: 239 --------PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH 290
KN I + + + + S E++K FS G V + ++
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKD 188
Query: 291 RGFGFVTFEN-EEVVDHICEIHFHMIKNKK 319
R + + EE V + ++H H +
Sbjct: 189 RKMALIQMGSVEEAVQALIDLHNHDLGENH 218
Score = 36.9 bits (85), Expect = 0.007
Identities = 9/86 (10%), Positives = 29/86 (33%), Gaps = 7/86 (8%)
Query: 246 GNRTKKIFVGGVSQDT-SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV 304
G + V ++ + + + + F +G V+ +L + V +
Sbjct: 31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQA 85
Query: 305 DH-ICEIHFHMIKNKKVECKKAQPKE 329
+ ++ H + K + ++ +
Sbjct: 86 QLAMSHLNGHKLHGKPIRITLSKHQN 111
>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 = 68.1 bits (167), Expect = 1e-14
Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 4/87 (4%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + P + V + + S +++ ++F + + + +K G
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+ F + + L+ + I
Sbjct: 61 MVAFESRDEATAAVI----DLNDRPIG 83
Score = 64.6 bits (158), Expect = 3e-13
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
I V + S +E+ +F + + +V L + G V FE+ +E
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 307 ICEIHFHMIKNKKVECKKAQPKEA 330
+ +++ I ++KV+ +
Sbjct: 74 VIDLNDRPIGSRKVKLVLGSGPSS 97
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 68.1 bits (167), Expect = 2e-14
Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 17/91 (18%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
+ ++ +LFV +L E FG FG + +V I+ GF F+ F E E+
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78
Query: 217 EKVLKVPIHTLDGKKIDPK-----HATPKNR 242
K I + GK + ++ +
Sbjct: 79 AKA----IEEVHGKSFANQPLEVVYSKLPAK 105
Score = 63.9 bits (156), Expect = 6e-13
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 9/97 (9%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
P+ + +R + ++FV D E+ F FG ++E V ++ GF
Sbjct: 16 PRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE-VKIL-------NGF 67
Query: 294 GFVTFEN-EEVVDHICEIHFHMIKNKKVECKKAQPKE 329
FV FE E I E+H N+ +E ++
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104
>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 = 68.2 bits (167), Expect = 2e-14
Identities = 11/102 (10%), Positives = 33/102 (32%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + + + + + + ++ + + + + G
Sbjct: 1 GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
+ F + K ++ L+G++ T ++ +I
Sbjct: 61 LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKN 102
Score = 66.7 bits (163), Expect = 7e-14
Identities = 9/87 (10%), Positives = 27/87 (31%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ + + + + +V + E V ++ + G V F+NE+
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKE 329
+H + ++ ++
Sbjct: 69 DARKSERLHRKKLNGREAFVHVVTLED 95
>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 = 66.5 bits (163), Expect = 5e-14
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 19/89 (21%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG + LFV L+ + E L + F FG + V +KD
Sbjct: 2 SSGSSGMAKVK-------VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------- 46
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
+ FI F E + K ++ ++GK ++
Sbjct: 47 YAFIHFDERDGAVKAME----EMNGKDLE 71
Score = 65.0 bits (159), Expect = 2e-13
Identities = 21/99 (21%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDH 306
+ K +FV ++ + E ++ FSQFGK+E K+ + + F+ F+ + V
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLER--------VKKLKDYAFIHFDERDGAVKA 61
Query: 307 ICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
+ E++ ++ + +E A+P + + ++ GP
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 66.7 bits (163), Expect = 5e-14
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
+ + L F G V ++ D T +++GF F+ +K++K
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS-- 73
Query: 225 HTLDGKKIDPKH 236
GK++D KH
Sbjct: 74 --FHGKRLDLKH 83
Score = 51.3 bits (123), Expect = 1e-08
Identities = 11/50 (22%), Positives = 21/50 (42%)
Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ + + + FS+ GKV +D+ T + +GF FV +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65
>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 = 66.6 bits (163), Expect = 7e-14
Identities = 16/115 (13%), Positives = 44/115 (38%), Gaps = 15/115 (13%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ L++ L ++ ++E++ + FG +G + + + P +RG ++ + + +
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNA- 63
Query: 221 KVPIHTLDGKKIDPKHATPKNRP-KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG 274
+ L G + NR + + E++K ++G
Sbjct: 64 ---VDHLSGFNVS-------NRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108
Score = 56.6 bits (137), Expect = 2e-10
Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 12/98 (12%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE---- 302
NR +++ + +AEE+ F ++G + + + + + T RG +V +E+
Sbjct: 8 NRI--LYIRNLPYKITAEEMYDIFGKYGPIRQ-IRVGN--TPETRGTAYVVYEDIFDAKN 62
Query: 303 VVDHICEIHFHMIKNKKVECKKAQPKEAVQANLLVGKR 340
VDH+ + N+ + A Q K
Sbjct: 63 AVDHLSGFNVS---NRYLVVLYYNANRAFQKMDTKKKE 97
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 66.3 bits (162), Expect = 8e-14
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 12/96 (12%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSS------EKLREYFGMFGAVTDVLIMKDPITQ 200
GD + P D + + V + + + F FG +T+ ++
Sbjct: 1 GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DG 58
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKH 236
+++G+ F+ +A P +K DG K+D +H
Sbjct: 59 KTKGYIFLEYASPAHAVDAVK----NADGYKLDKQH 90
Score = 48.6 bits (116), Expect = 1e-07
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 250 KKIFVGGVSQDTSA------EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
I V V Q + FS+FGK+ ++ + +G+ F+ + +
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPA 72
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 64.6 bits (158), Expect = 2e-13
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 9/84 (10%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G S +G+D T L+VGGL + LR +F FG + + +++ + FI
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54
Query: 210 FAEPETVEKVLKVPIHTLDGKKID 233
FA + E + + + ++
Sbjct: 55 FATRQAAEVAAE---KSFNKLIVN 75
Score = 54.6 bits (132), Expect = 5e-10
Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
T ++VGG+ + +++ +F QFG++ ++ + F+ F +
Sbjct: 12 ITT--LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQ 59
>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 = 65.2 bits (159), Expect = 2e-13
Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 4/112 (3%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SG+ P D + V G+ + +R++F V V ++KD R+ G
Sbjct: 2 SSGSSGKPLPINPDDLY--VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNG 57
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGG 256
G + F P+ + LK + + ++ AT + G G
Sbjct: 58 NGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109
Score = 59.8 bits (145), Expect = 2e-11
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+ V G+ +V+ +F +V+ +L D R+ G G V F + + + +
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVG-RNNGNGLVKFLSPQDTFEALKRN 76
Query: 312 FHMIKNKKVECKKAQPKEAVQA 333
++ + VE A ++ V A
Sbjct: 77 RMLMIQRYVEVSPATERQWVAA 98
>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 = 65.7 bits (160), Expect = 2e-13
Identities = 17/91 (18%), Positives = 35/91 (38%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ + + G+ + EE+ +FS V + L + G FV F
Sbjct: 32 RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQF 91
Query: 299 ENEEVVDHICEIHFHMIKNKKVECKKAQPKE 329
++E+ + H I ++ +E K+ +E
Sbjct: 92 ASQELAEKALGKHKERIGHRYIEVFKSSQEE 122
Score = 65.3 bits (159), Expect = 3e-13
Identities = 26/122 (21%), Positives = 50/122 (40%), Gaps = 24/122 (19%)
Query: 148 DSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF 207
GR + + D + + GL + + E++ ++F V + + + + G F
Sbjct: 29 QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88
Query: 208 ITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK 267
+ FA E EK L K++ +IG+R ++F +S EEV+
Sbjct: 89 VQFASQELAEKALG------------------KHKERIGHRYIEVFK------SSQEEVR 124
Query: 268 AY 269
+Y
Sbjct: 125 SY 126
>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 = 64.7 bits (158), Expect = 2e-13
Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 20/108 (18%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + T + + GL ++ + + +F V I P R G
Sbjct: 1 GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEA 58
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFV 254
+ FA E + K++ + +R ++F+
Sbjct: 59 DVEFATHEDAVAAMA------------------KDKANMQHRYVELFL 88
Score = 54.3 bits (131), Expect = 1e-09
Identities = 11/82 (13%), Positives = 25/82 (30%), Gaps = 2/82 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+ + G+ + ++ +FS + V + R G V F E
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75
Query: 312 FHMIKNKKVECKKAQPKEAVQA 333
++++ VE +
Sbjct: 76 KANMQHRYVELFLNSTAGTSGS 97
>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 = 64.2 bits (157), Expect = 3e-13
Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 16/87 (18%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G++ PT +L+VGGL TS L F FG++ + + F +I
Sbjct: 12 GKANPT------TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQ 59
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKH 236
+ + + + G +
Sbjct: 60 YESLDAAQAACA----KMRGFPLGGPD 82
Score = 62.6 bits (153), Expect = 1e-12
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 10/67 (14%)
Query: 240 KNRPKIG----NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
+ KIG N T +++VGG+ +TS + F +FG + + + F +
Sbjct: 4 GSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAY 57
Query: 296 VTFENEE 302
+ +E+ +
Sbjct: 58 IQYESLD 64
>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 = 64.7 bits (158), Expect = 3e-13
Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 17/96 (17%)
Query: 145 SSGDSGRSTPTG-------DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
SSG SG + P + ++ GG++ + + +R+ F FG + ++ + +
Sbjct: 2 SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE- 60
Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
+G+ F+ F+ E+ I +++G I+
Sbjct: 61 -----KGYSFVRFSTHESAAHA----IVSVNGTTIE 87
Score = 58.9 bits (143), Expect = 3e-11
Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
++ GG++ + + ++ FS FG++ E + + +G+ FV F E H I +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 311 HFHMIKNKKVECKKAQPKEAVQAN 334
+ I+ V+C + + +
Sbjct: 82 NGTTIEGHVVKCYWGKESPDMTSG 105
>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 = 64.2 bits (157), Expect = 3e-13
Identities = 18/99 (18%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFV 296
++ + R T ++V G +D + ++ FS FG + + R FV
Sbjct: 5 SSGERRAPRKGNT--LYVYG--EDMTPTLLRGAFSPFGNIIDL------SMDPPRNCAFV 54
Query: 297 TFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQAN 334
T+E E D + E++ +++ +++ A+ + + +
Sbjct: 55 TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93
Score = 61.1 bits (149), Expect = 3e-12
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 12/87 (13%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S L+V G + LR F FG + D+ + R
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCA 52
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
F+T+ + E+ ++ + L+G +++
Sbjct: 53 FVTYEKMESADQA----VAELNGTQVE 75
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 64.2 bits (157), Expect = 4e-13
Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 13/99 (13%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFI 208
G S +G + LFVG L+ L E+F ++ + ++ D T S+G+GF+
Sbjct: 1 GSSGSSGPE---YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFV 56
Query: 209 TFAEPETVEKVL-----KVPIHTLDGKKIDPKHATPKNR 242
F + ++ L V L K + A PK
Sbjct: 57 KFTDELEQKRALTECQGAVG---LGSKPVRLSVAIPKAS 92
Score = 50.4 bits (121), Expect = 3e-08
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
+FVG ++ D + +F + ++ QT +G+GFV F +E + E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 311 HFHM-IKNKKVECKKAQPKE 329
+ + +K V A PK
Sbjct: 72 QGAVGLGSKPVRLSVAIPKA 91
>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 = 69.1 bits (168), Expect = 5e-13
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFV +++ T+ KLR F ++G + + ++ + + RG+ FI + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER----DMHSA 160
Query: 224 IHTLDGKKID 233
DGKKID
Sbjct: 161 YKHADGKKID 170
Score = 69.1 bits (168), Expect = 5e-13
Identities = 20/92 (21%), Positives = 44/92 (47%), Gaps = 2/92 (2%)
Query: 239 PKNRPKI-GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
P N P G+ K +FV V+ DT+ +++ F +G ++ M+ +++ + RG+ F+
Sbjct: 91 PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150
Query: 298 FENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
+E+E + I ++V + +
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 63.0 bits (154), Expect = 8e-13
Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 18/102 (17%)
Query: 153 TPTGDDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
T + P ++LF+G L + S++ L F +G + + I FGFI F
Sbjct: 2 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD 53
Query: 212 EPETVEKVLKVPIHTLDGK-----KIDPKHATPKNRPKIGNR 248
P++V I + K+ + ++ RP+ +
Sbjct: 54 NPQSVRDA----IECESQEMNFGKKLILEVSSSNARPQFDHG 91
Score = 53.4 bits (129), Expect = 2e-09
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 249 TKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH- 306
++F+G + ++ S E++ FS +G + + + FGF+ F+N + V
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDA 61
Query: 307 ICEIHFHMIKNKKVECKKAQPK 328
I M KK+ + +
Sbjct: 62 IECESQEMNFGKKLILEVSSSN 83
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 63.4 bits (154), Expect = 1e-12
Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 3/100 (3%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKV---EETVMLMDQQTKRHRGF 293
+ + + + G+ +AEEV A+F Q + +E ++ + R G
Sbjct: 11 SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70
Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
FV F EE + H ++ + +E ++ E Q
Sbjct: 71 AFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQV 110
Score = 58.0 bits (140), Expect = 8e-11
Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 5/113 (4%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG----MFGAVTDVLIMKDP 197
G S + + GL + ++E++ +FG + G +L + P
Sbjct: 4 GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63
Query: 198 ITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTK 250
R G F+ FA E + L+ L + I+ +T ++ NR
Sbjct: 64 -DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFS 115
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 19/107 (17%), Positives = 36/107 (33%), Gaps = 18/107 (16%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKDPITQ 200
+ ++LF+G L + S++ L F +G + + I
Sbjct: 3 SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN----- 57
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGK-----KIDPKHATPKNR 242
FGFI F P++V I + K+ + ++ R
Sbjct: 58 ---AFGFIQFDNPQSVRDA----IEXESQEMNFGKKLILEVSSSNAR 97
Score = 58.9 bits (143), Expect = 2e-11
Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 229 GKKIDPKHATPKNRPKIGNRTKKIFVGGVS-QDTSAEEVKAYFSQFGKVEETVMLMDQQT 287
G H + P+ + ++F+G + ++ S E++ FS +G + + +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------ 55
Query: 288 KRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKK--VECKKAQPK 328
FGF+ F+N + V I M KK +E + +
Sbjct: 56 --KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97
>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 = 62.1 bits (151), Expect = 2e-12
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 11/87 (12%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S + ++ V GL S + L+++ G V + +D G G
Sbjct: 1 GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 53
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+ F E + + LD K
Sbjct: 54 VVEFVRKEDMTYA----VRKLDNTKFR 76
Score = 52.1 bits (125), Expect = 7e-09
Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 8/92 (8%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
P ++ V G+ S +++K + + G V + D G G V F
Sbjct: 5 SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF 57
Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
+E + + + ++ ++ + E + K
Sbjct: 58 VRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 89
>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 = 13/76 (17%), Positives = 21/76 (27%), Gaps = 10/76 (13%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
P ++G + + L F FG + D + +G FI + E
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAA 77
Query: 218 KVLKVPIHTLDGKKID 233
I L
Sbjct: 78 VC----IVALANFPFQ 89
Score = 56.9 bits (138), Expect = 1e-10
Identities = 11/100 (11%), Positives = 30/100 (30%), Gaps = 11/100 (11%)
Query: 234 PKHATPKNRPKIGNRTK----KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR 289
P P+ I ++G + + ++ F FG + +
Sbjct: 8 PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------P 61
Query: 290 HRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
+G F+ ++ E I + + + + + +
Sbjct: 62 EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 60.6 bits (147), Expect = 6e-12
Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 9/91 (9%)
Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS 202
G S S P P +A ++VG L L+ G+V L Q
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRL-----TWQGP 55
Query: 203 RGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
R F+ + + ++ + L G ++
Sbjct: 56 RRRAFLHYPDSAAAQQAVS----CLQGLRLG 82
Score = 47.9 bits (114), Expect = 2e-07
Identities = 12/99 (12%), Positives = 32/99 (32%), Gaps = 7/99 (7%)
Query: 233 DPKHATPKNRPKIGNRTK-KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR 291
+ P + P G ++VG + +D ++K + G V + + R
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPR 56
Query: 292 GFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
F+ + + + + + + A+ +
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95
>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 = 60.6 bits (147), Expect = 9e-12
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 15/88 (17%)
Query: 164 LFVGGLSWQTSSE---KLREYFGMFGAVTDVLIMKDPIT---QRSRGFGFITFAEPETVE 217
+FV GLS + + K EYFG FG + V+I Q ++T+ E
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 218 KVLKVPIHTLDGKKIDPK-----HATPK 240
+ I ++ +D + T K
Sbjct: 78 RA----IQCVNNVVVDGRTLKASLGTTK 101
Score = 56.4 bits (136), Expect = 3e-10
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 7/84 (8%)
Query: 252 IFVGGVSQDTSAEEV---KAYFSQFGKVEETVMLMDQQT---KRHRGFGFVTFENEEVVD 305
+FV G+SQ + EV YF +FGK+ + V+ + +VT+ E
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 306 H-ICEIHFHMIKNKKVECKKAQPK 328
I ++ ++ + ++ K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
>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 = 20/114 (17%), Positives = 39/114 (34%), Gaps = 21/114 (18%)
Query: 145 SSGDSGRSTPTG---------DDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIM 194
SSG SG S ++++F+G L+ + + F +G V +
Sbjct: 2 SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH 61
Query: 195 KDPITQRSRGFGFITFAEPETVEKVLKVPIH--TLDGKKIDPKHATPKNRPKIG 246
K G+ F+ ++ + + L G+ +D A + G
Sbjct: 62 K--------GYAFVQYSNERHARAAVLG-ENGRVLAGQTLDINMAGEPKPDRSG 106
Score = 58.2 bits (141), Expect = 6e-11
Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 12/100 (12%)
Query: 231 KIDPKHATPKNRPKIGNRTKKIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKR 289
K+ + T KN PK N ++F+G ++ +V+ FS++G+V +
Sbjct: 11 KLQASNVTNKNDPKSINS--RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------- 60
Query: 290 HRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
H+G+ FV + NE + + ++ + ++ A
Sbjct: 61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 59.8 bits (145), Expect = 1e-11
Identities = 12/88 (13%), Positives = 33/88 (37%), Gaps = 4/88 (4%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
R +K+ + + E + + Q+G VE + VT+ +++
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQAR 68
Query: 306 H-ICEIHFHMIKNKKVECKKAQPKEAVQ 332
+ +++ ++N ++ + A Q
Sbjct: 69 QALDKLNGFQLENFTLKVAYIPDEMAAQ 96
Score = 57.8 bits (140), Expect = 6e-11
Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 7/87 (8%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S KL + + E L +G V +
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVV 57
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+T++ + + + L+G +++
Sbjct: 58 NVTYSSKDQARQA----LDKLNGFQLE 80
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 59.5 bits (145), Expect = 1e-11
Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
+ + +++ L+ + ++L++ F FG + D+L+ + + RG F+ F E
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60
Query: 213 PETVEKVLK 221
+ L+
Sbjct: 61 VSSATNALR 69
Score = 56.1 bits (136), Expect = 3e-10
Identities = 22/104 (21%), Positives = 50/104 (48%), Gaps = 13/104 (12%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRG 292
A P+ RP N T I++ +++ +E+K A FS+FG++ + +++ ++ + RG
Sbjct: 1 AVPETRP---NHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD-ILVS--RSLKMRG 52
Query: 293 FGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
FV F+ + + + +K + + A+ + A +
Sbjct: 53 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
>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 = 59.8 bits (145), Expect = 2e-11
Identities = 23/108 (21%), Positives = 46/108 (42%), Gaps = 12/108 (11%)
Query: 222 VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM 281
VP + G + P+ GN ++V G +D + ++ FS FG + + M
Sbjct: 15 VPRGSHMGPFRRSDSFPERRAPRKGNT---LYVYG--EDMTPTLLRGAFSPFGNIIDLSM 69
Query: 282 LMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPK 328
R FVT+E E D + E++ +++ +++ A+ +
Sbjct: 70 D------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 111
Score = 55.9 bits (135), Expect = 5e-10
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 12/76 (15%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
L+V G + LR F FG + D+ + R F+T+ + E+ +
Sbjct: 36 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESAD 87
Query: 218 KVLKVPIHTLDGKKID 233
+ + L+G +++
Sbjct: 88 QA----VAELNGTQVE 99
>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 = 59.5 bits (144), Expect = 4e-11
Identities = 20/110 (18%), Positives = 35/110 (31%), Gaps = 20/110 (18%)
Query: 144 KSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR 203
+ SG S T T + + GL ++ + + +F V I P R
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVT 86
Query: 204 GFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIF 253
G + FA E + K+R + +R ++F
Sbjct: 87 GEADVEFATHEEAVAAMS------------------KDRANMQHRYIELF 118
Score = 52.5 bits (126), Expect = 1e-08
Identities = 12/100 (12%), Positives = 27/100 (27%), Gaps = 2/100 (2%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
+ + + + G+ + ++ +FS V V + R G
Sbjct: 31 GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGE 88
Query: 294 GFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
V F E ++++ +E A
Sbjct: 89 ADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNG 128
>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 = 58.1 bits (141), Expect = 4e-11
Identities = 20/115 (17%), Positives = 41/115 (35%), Gaps = 27/115 (23%)
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
G S +G + + + G + + + + E+ + I+++ G+ F+
Sbjct: 1 GSSGSSGTTCHT--VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVD 56
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAE 264
F+ E V++ LK NR +G R I V ++ S
Sbjct: 57 FSNEEEVKQALK------------------CNREYMGGR--YIE---VFREKSGP 88
Score = 52.7 bits (127), Expect = 3e-09
Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 2/85 (2%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
G + + G + + + V + + V + ++ G+ FV F NEE V
Sbjct: 7 GTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA--IRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 306 HICEIHFHMIKNKKVECKKAQPKEA 330
+ + + + +E + + +
Sbjct: 65 QALKCNREYMGGRYIEVFREKSGPS 89
>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 = 57.9 bits (140), Expect = 6e-11
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 2/84 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKV--EETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
I G+ + E+V +FS E + + + + RG + E+E+ V E
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73
Query: 310 IHFHMIKNKKVECKKAQPKEAVQA 333
H + + VE + ++
Sbjct: 74 KHRMYMGQRYVEVYEINNEDVDAL 97
Score = 49.1 bits (117), Expect = 9e-08
Identities = 11/91 (12%), Positives = 30/91 (32%), Gaps = 4/91 (4%)
Query: 164 LFVGGLSWQTSSEKLREYFGMF---GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ GL W + E + +F + + + + RG I + V+K L
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESEQDVQKAL 72
Query: 221 KVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
+ + + ++ ++ + +
Sbjct: 73 EKHRMYMGQRYVEVYEINNEDVDALMKSLQV 103
>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 = 58.9 bits (142), Expect = 7e-11
Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 2/99 (2%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE--ETVMLMDQQTKRHRGFG 294
G + + G+ S E+V+ + S + V + + R G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 295 FVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAVQA 333
FV +E+ V + + ++ +E K+ E
Sbjct: 92 FVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWV 130
Score = 49.2 bits (117), Expect = 2e-07
Identities = 15/93 (16%), Positives = 28/93 (30%), Gaps = 4/93 (4%)
Query: 143 GKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMF---GAVTDVLIMKDPIT 199
G G + + + GL W S E ++ + V +
Sbjct: 26 GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-E 84
Query: 200 QRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI 232
R G F+ + V+ LK ++ + I
Sbjct: 85 GRQSGEAFVELGSEDDVKMALKKDRESMGHRYI 117
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 55.9 bits (135), Expect = 2e-10
Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 164 LFVGGL------SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
+ V + + + + F FG +T+ ++ +++G+ F+ +A P
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 218 KVLKVPIHTLDGKKIDPKH 236
+K DG K+D +H
Sbjct: 62 DAVK----NADGYKLDKQH 76
Score = 44.7 bits (106), Expect = 2e-06
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 252 IFVGGVSQDTSA------EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
I V V Q + FS+FGK+ ++ + +G+ F+ + +
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPA 58
>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 = 56.9 bits (137), Expect = 2e-10
Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 2/96 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEET--VMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+ + G+ S E+V+ + S + V + + R G FV E+E+ V +
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVGKRVILGP 345
+ ++ +E K+ E G GP
Sbjct: 80 KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115
Score = 55.3 bits (133), Expect = 6e-10
Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 5/110 (4%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFG---MFGAVTDVLIMKDPITQR 201
SSG SG + + + GL W S E ++ + + V V + R
Sbjct: 2 SSGSSGMM-LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGR 59
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNRTKK 251
G F+ + V+ LK ++ + I+ + + +
Sbjct: 60 QSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGP 109
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 56.4 bits (136), Expect = 2e-10
Identities = 15/92 (16%), Positives = 29/92 (31%), Gaps = 8/92 (8%)
Query: 143 GKSSGDSGRSTPTGDDP-TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
SSG R + P ++ + L S + L++ T T+
Sbjct: 9 HHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRD 65
Query: 202 SRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
G G + F E + + + L+ +
Sbjct: 66 FDGTGALEFPSEEILVEA----LERLNNIEFR 93
Score = 53.3 bits (128), Expect = 3e-09
Identities = 10/92 (10%), Positives = 33/92 (35%), Gaps = 4/92 (4%)
Query: 239 PKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ K+ + +I + + + S +++K + T+ G G + F
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTGALEF 74
Query: 299 ENEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
+EE++ + ++ + + ++
Sbjct: 75 PSEEILVEALERLNNIEFRGSVITVERDDNPP 106
>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 = 56.0 bits (135), Expect = 4e-10
Identities = 18/87 (20%), Positives = 30/87 (34%), Gaps = 12/87 (13%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
GR P + ++ V GL S + L+++ G V + +D G G
Sbjct: 3 APRGRYGP-PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 54
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKID 233
+ F E + + LD K
Sbjct: 55 VVEFVRKEDMTYA----VRKLDNTKFR 77
Score = 52.5 bits (126), Expect = 7e-09
Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 8/91 (8%)
Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
+ P ++ V G+ S +++K + + G V + D G G V F
Sbjct: 7 RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV 59
Query: 300 NEEVVDH-ICEIHFHMIKNKKVECKKAQPKE 329
+E + + + ++ ++ + E + K
Sbjct: 60 RKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 90
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 56.1 bits (135), Expect = 4e-10
Identities = 12/89 (13%), Positives = 31/89 (34%), Gaps = 8/89 (8%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
S + + ++ + EKL+ G + D+++ + + G +I FA
Sbjct: 25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFAT 81
Query: 213 PETVEKVLKVPIHT-LDGKKIDPKHATPK 240
E+ + ++ G + +
Sbjct: 82 QESAQAFVEAFQGYPFQGNPLVITFSETP 110
Score = 49.5 bits (118), Expect = 1e-07
Identities = 10/100 (10%), Positives = 35/100 (35%), Gaps = 8/100 (8%)
Query: 235 KHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRH 290
+ P ++ + + ++ + E+++ A S G + + V+ + +
Sbjct: 15 DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDN 71
Query: 291 RGFGFVTFENEEVVDHICE-IHFHMIKNKKVECKKAQPKE 329
G ++ F +E E + + + ++ +
Sbjct: 72 SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111
>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 = 57.5 bits (138), Expect = 5e-10
Identities = 10/69 (14%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+++ G + + ++E+ G V ++ + + + +G F+ F E+ +K ++ P
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP 170
Query: 224 IHTLDGKKI 232
+
Sbjct: 171 GQKYKETDL 179
Score = 53.7 bits (128), Expect = 1e-08
Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGF 293
+ K + + +++ G D + +++K + G+V + + K +G
Sbjct: 94 KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL-NIQMRRTLHKAFKGS 152
Query: 294 GFVTFENEE 302
FV F++ E
Sbjct: 153 IFVVFDSIE 161
>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 = 54.7 bits (132), Expect = 6e-10
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 8/83 (9%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+ + I V + QD++ +EV + V R++ FVT N E +
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-------DRNKRTAFVTLLNGEQAQN 55
Query: 307 -ICEIHFHMIKNKKVECKKAQPK 328
I H + + K + +
Sbjct: 56 AIQMFHQYSFRGKDLIVQLQPTD 78
Score = 52.0 bits (125), Expect = 6e-09
Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 11/73 (15%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S+ + V L ++ +++ + + +K R++ F+T E +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA- 56
Query: 221 KVPIHTLDGKKID 233
I
Sbjct: 57 ---IQMFHQYSFR 66
>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 = 54.8 bits (132), Expect = 2e-09
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 15/83 (18%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAE 212
+ +++V L+ + L+ FG + + D+ +MK R +G FI
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPN 101
Query: 213 PETVEKVLKVPIHTLDGKKIDPK 235
+ K LK +G + K
Sbjct: 102 EKAAAKALK----EANGYVLFGK 120
Score = 53.3 bits (128), Expect = 7e-09
Identities = 15/131 (11%), Positives = 48/131 (36%), Gaps = 14/131 (10%)
Query: 217 EKVLKVPIHTLDGKKIDPKHATPKNRPKI--------GNRTKKIFVGGVSQDTSAEEVKA 268
++P + ++++ + + + G +I+V +++ +++K
Sbjct: 5 SDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKY 64
Query: 269 YFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFENEEVVDH-ICEIHFHMIKNKKVEC 322
F ++ + + R +G F+ NE+ + E + +++ K +
Sbjct: 65 IFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124
Query: 323 KKAQPKEAVQA 333
+ A+ Q
Sbjct: 125 QFARSARPKQD 135
>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 = 53.4 bits (128), Expect = 3e-09
Identities = 19/109 (17%), Positives = 43/109 (39%), Gaps = 11/109 (10%)
Query: 225 HTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD 284
H + P+ + + G ++ I + + D + EV + FGKV +ML
Sbjct: 7 HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-- 64
Query: 285 QQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKNKKVECKKAQPKE 329
+ + F+ EE +V++ +++ + + + + KE
Sbjct: 65 ----KGKNQAFIEMNTEEAANTMVNY-YTSVTPVLRGQPIYIQFSNHKE 108
Score = 48.4 bits (115), Expect = 2e-07
Identities = 17/109 (15%), Positives = 34/109 (31%), Gaps = 9/109 (8%)
Query: 135 AHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM 194
H +G S S + + L + ++ FG VT++L++
Sbjct: 5 HHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML 64
Query: 195 KDPITQRSRGFGFITFAEPETVEKVLKVPIHT---LDGKKIDPKHATPK 240
+ + FI E ++ L G+ I + + K
Sbjct: 65 ------KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107
>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 = 52.5 bits (126), Expect = 6e-09
Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 18/89 (20%)
Query: 145 SSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG 204
SSG SGRS + L T + +++E F FG++ VL+
Sbjct: 2 SSGSSGRSKTV--------ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGI 47
Query: 205 FGFITFAEPETVEKVLKVPIHTLDGKKID 233
+ F EP K L K
Sbjct: 48 TAIVEFLEPLEARK----AFRHLAYSKFH 72
Score = 46.3 bits (110), Expect = 1e-06
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 8/57 (14%)
Query: 246 GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
I + T A E++ FS+FG + ++ V F
Sbjct: 9 SKTV--ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPL 57
>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 = 55.3 bits (132), Expect = 9e-09
Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 11/86 (12%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLRE----YFGMFGAVTDVLIMKDPITQRSRGFGFIT 209
+ + +++ L+ + ++L++ F FG + D+L+ + + RG F+
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVI 58
Query: 210 FAEPETVEKVLKVPIHTLDGKKIDPK 235
F E + + ++ G K
Sbjct: 59 FKEVSSATNA----LRSMQGFPFYDK 80
Score = 50.6 bits (120), Expect = 3e-07
Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 13/104 (12%)
Query: 237 ATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRG 292
A P+ RP N T I++ +++ +E+K A FSQFG++ + ++ ++ + RG
Sbjct: 2 AVPETRP---NHT--IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRG 53
Query: 293 FGFVTFENEEVVDH-ICEIHFHMIKNKKVECKKAQPKEAVQANL 335
FV F+ + + + +K + + A+ + A +
Sbjct: 54 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
Score = 50.6 bits (120), Expect = 3e-07
Identities = 27/195 (13%), Positives = 49/195 (25%), Gaps = 9/195 (4%)
Query: 43 PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVN 102
+ K+ G + Q TP ++ Q + +
Sbjct: 89 TDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMT 148
Query: 103 GKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSA 162
P + GL + + G + P ++P +
Sbjct: 149 QAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNH 208
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
LF+ L +T+ L F F +V ++ F+ F
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAA--- 260
Query: 223 PIHTLDGKKIDPKHA 237
L G KI +A
Sbjct: 261 -RDALQGFKITQNNA 274
Score = 36.4 bits (83), Expect = 0.012
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 5/81 (6%)
Query: 222 VPIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM 281
+P + +++ P P +F+ + ++T+ + F+QF +E +
Sbjct: 180 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 239
Query: 282 LMDQQTKRHRGFGFVTFENEE 302
+ + FV F+NE
Sbjct: 240 VPGR-----HDIAFVEFDNEV 255
>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 = 50.5 bits (121), Expect = 1e-08
Identities = 11/76 (14%), Positives = 29/76 (38%), Gaps = 10/76 (13%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM-KDPI----TQRSRGFGFITFAEPETVE 217
+L+VG + + + E + ++F + + +P+ + + F F+ F +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 218 KVLKVPIHTLDGKKID 233
+ + DG
Sbjct: 68 QAMA-----FDGIIFQ 78
Score = 48.2 bits (115), Expect = 1e-07
Identities = 8/58 (13%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFENEE 302
++++VG + + E + +F+ ++ ++ Q + + F F+ F + +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 51.0 bits (122), Expect = 2e-08
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 9/84 (10%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI- 307
++ I + + D + EV + FGKV +ML + + F+ EE + +
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMV 69
Query: 308 --CEIHFHMIKNKKVECKKAQPKE 329
+++ + + + + KE
Sbjct: 70 NYYTSVTPVLRGQPIYIQFSNHKE 93
Score = 48.7 bits (116), Expect = 1e-07
Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 9/95 (9%)
Query: 149 SGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
S G S + + L + ++ FG VT++L++K + FI
Sbjct: 4 SHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFI 57
Query: 209 TFAEPETVEKVLKVPIH---TLDGKKIDPKHATPK 240
E ++ L G+ I + + K
Sbjct: 58 EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 92
>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 = 49.8 bits (119), Expect = 5e-08
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S S + V GL L E FG + V++M +
Sbjct: 1 GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54
Query: 207 FITFAEPETVEKVLK 221
+ F ++ ++ +
Sbjct: 55 LVEFENIDSAKECVT 69
Score = 47.1 bits (112), Expect = 4e-07
Identities = 11/89 (12%), Positives = 26/89 (29%), Gaps = 9/89 (10%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD--- 305
+ + V G+ + ++ +FG + +M + V FEN +
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECV 68
Query: 306 HICEIHFHMIKNKKVECKKAQPKEAVQAN 334
I ++ + K +
Sbjct: 69 TFAADVPVYIAGQQAFFNYSTSKRITRPG 97
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 49.4 bits (118), Expect = 6e-08
Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 11/78 (14%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P S + + GL L E FG ++ V++M + + F +
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACN 72
Query: 219 VLK----VPIHTLDGKKI 232
+ I+ + G
Sbjct: 73 AVNYAADNQIY-IAGHPA 89
Score = 49.0 bits (117), Expect = 7e-08
Identities = 9/70 (12%), Positives = 21/70 (30%), Gaps = 7/70 (10%)
Query: 234 PKHATPKNR-PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG 292
H P + + + G+ ++ +FG + V++ +
Sbjct: 5 HHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKR 58
Query: 293 FGFVTFENEE 302
V FE+
Sbjct: 59 QALVEFEDVL 68
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 47.9 bits (114), Expect = 2e-07
Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 240 KNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
G ++ + + + + + EV A FGKV +ML + + F+
Sbjct: 6 SGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELA 59
Query: 300 NEE----VVDHICEIHFHMIKNKKVECKKAQPKE 329
EE +V++ + H ++N+ + + + KE
Sbjct: 60 TEEAAITMVNYYSAVTPH-LRNQPIYIQYSNHKE 92
Score = 47.9 bits (114), Expect = 2e-07
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 9/97 (9%)
Query: 147 GDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFG 206
G SG S D S L + L + + ++ FG VT++L++K +
Sbjct: 1 GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQA 54
Query: 207 FITFAEPETVEKVLKVPIH---TLDGKKIDPKHATPK 240
F+ A E ++ L + I +++ K
Sbjct: 55 FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK 91
>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 = 47.2 bits (112), Expect = 4e-07
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ GG+ S ++ + G V+ +M ++ + F + E
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTE 74
Score = 44.9 bits (106), Expect = 3e-06
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 11/81 (13%)
Query: 155 TGDDPTSA-KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
T T + + GGL S +L G V +L+ + + + F +
Sbjct: 20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTT 73
Query: 214 ETVEKVLKVPIHTLDGKKIDP 234
E ++ TL+GK++
Sbjct: 74 EESKRA----YVTLNGKEVVD 90
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 43.3 bits (101), Expect = 1e-04
Identities = 14/115 (12%), Positives = 26/115 (22%), Gaps = 3/115 (2%)
Query: 7 GGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAI 66
A Q G + +P + + +L+ T+ +
Sbjct: 25 QPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMH 84
Query: 67 LHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTS 121
LH P P Q Q + + G + P +
Sbjct: 85 LHNVPLVDPNAYMQPQVPVQMGTPLQQQQQP---MAAPAYGQPSAAMGQNMRPMN 136
Score = 37.9 bits (87), Expect = 0.006
Identities = 15/93 (16%), Positives = 23/93 (24%)
Query: 30 PHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRD 89
P L + L+ P V+ + + Q QQQQQ P
Sbjct: 64 PAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQ 123
Query: 90 LQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSA 122
+ +N D P +
Sbjct: 124 PSAAMGQNMRPMNQLYPIDLLTELPPPITDLTL 156
Score = 36.7 bits (84), Expect = 0.015
Identities = 9/65 (13%), Positives = 13/65 (20%)
Query: 30 PHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRD 89
P P G P P P + QQ D
Sbjct: 23 LQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMND 82
Query: 90 LQPNS 94
+ ++
Sbjct: 83 MHLHN 87
Score = 36.3 bits (83), Expect = 0.018
Identities = 13/99 (13%), Positives = 17/99 (17%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
G P + P + + P Q Q QQ
Sbjct: 13 QLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQ 72
Query: 81 QPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDP 119
+ N LV N T
Sbjct: 73 IDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQ 111
Score = 36.0 bits (82), Expect = 0.025
Identities = 10/77 (12%), Positives = 16/77 (20%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
P P PP ++ + QQ P Q+Q
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 81 QPPQPQPRDLQPNSNNQ 97
Q + +
Sbjct: 70 HQQIDQATTSMNDMHLH 86
Score = 34.4 bits (78), Expect = 0.079
Identities = 11/67 (16%), Positives = 13/67 (19%)
Query: 31 HHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDL 90
HH V+ L Q A Q P Q + L
Sbjct: 3 HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62
Query: 91 QPNSNNQ 97
P
Sbjct: 63 TPAQEQL 69
Score = 31.7 bits (71), Expect = 0.45
Identities = 11/92 (11%), Positives = 15/92 (16%)
Query: 30 PHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRD 89
P N P P + Q QQQ Q +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 90 LQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTS 121
Q + + P
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQV 101
Score = 29.8 bits (66), Expect = 1.8
Identities = 11/65 (16%), Positives = 16/65 (24%)
Query: 28 QIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
V + P Q + Q + + QN Q P + PP
Sbjct: 95 AYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDL 154
Query: 88 RDLQP 92
P
Sbjct: 155 TLPPP 159
Score = 27.9 bits (61), Expect = 7.2
Identities = 16/91 (17%), Positives = 23/91 (25%), Gaps = 7/91 (7%)
Query: 7 GGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAI 66
H+Q + +MN + + P P Q G P P A
Sbjct: 64 PAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQ----MGTPLQQQQQPMAAP 119
Query: 67 LHQQPTPQPQQ---QQQQPPQPQPRDLQPNS 94
+ QP+ Q Q P
Sbjct: 120 AYGQPSAAMGQNMRPMNQLYPIDLLTELPPP 150
>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 = 37.6 bits (87), Expect = 0.001
Identities = 9/81 (11%), Positives = 24/81 (29%), Gaps = 7/81 (8%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEK-LREYFGMFGAVTDVLIMKDPITQ 200
+GK + + L S+ + + +G + + ++M+
Sbjct: 6 SGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----- 60
Query: 201 RSRGFGFITFAEPETVEKVLK 221
+ FI E ++
Sbjct: 61 -MKSQAFIEMETREDAMAMVD 80
Score = 36.5 bits (84), Expect = 0.003
Identities = 15/95 (15%), Positives = 33/95 (34%), Gaps = 12/95 (12%)
Query: 233 DPKHATPKNRPKIGNRTKKIFVGGV-SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR 291
P+ + + + I + + S V +GK++ +++ R +
Sbjct: 9 KPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMK 62
Query: 292 GFGFVTFENEE----VVDHICEIHFHMIKNKKVEC 322
F+ E E +VDH C + + V+
Sbjct: 63 SQAFIEMETREDAMAMVDH-CLKKALWFQGRCVKV 96
>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 = 39.8 bits (92), Expect = 0.001
Identities = 32/233 (13%), Positives = 72/233 (30%), Gaps = 65/233 (27%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV----- 219
FV + + + + +++ KD ++ R F + + E V+K
Sbjct: 29 FVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL 87
Query: 220 ------LKVPIHTL--------------------DGKKIDPKHATPKNRPKIGNRTKKIF 253
L PI T D + + + R + + ++
Sbjct: 88 RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS---RLQPYLKLRQ-- 142
Query: 254 VGGVSQDTSAEEVKAY-FSQFGKVEETVM----LMDQQTKRHRGFG-F-VTFEN----EE 302
+ + A+ V GK T + + + + F F + +N E
Sbjct: 143 --ALLELRPAKNVLIDGVLGSGK---TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET 197
Query: 303 VVDHICEIHFHMIKNKKVECKKA----QPKEAVQA---NLLVGKR-----VIL 343
V++ + ++ + + N + ++QA LL K ++L
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250
Score = 39.8 bits (92), Expect = 0.002
Identities = 49/336 (14%), Positives = 93/336 (27%), Gaps = 95/336 (28%)
Query: 86 QPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVG---GLNVVREA------H 136
+ QP+ ++ + R D+ AK V +R+A
Sbjct: 99 KTEQRQPSMMTRMYI--------EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150
Query: 137 QLVLVNGKSSGDSGRSTPTGD---DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLI 193
+ VL++G SG++ D + W + VL
Sbjct: 151 KNVLIDGV--LGSGKTWVALDVCLSYKVQCKMDFKIFWLN--------LKNCNSPETVLE 200
Query: 194 M--------KDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKK---I-----DPKHA 237
M T RS I +++ L+ + + + + + K
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKL-RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259
Query: 238 -----------TPKNRPKI----GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVML 282
T + + T I + S + +EVK+ ++ L
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-DL 318
Query: 283 MDQQTKRH----RGFGFVTFENEEVVDHICEIHFHMIKN-KKVECKKAQPKEAVQANLLV 337
+ + E + D + N K V C K ++++L V
Sbjct: 319 PREVLTTNPRRLSIIA------ESIRDGLA-----TWDNWKHVNCDKL--TTIIESSLNV 365
Query: 338 GKRVILGPLGLR-----MAA-P--APITPATQLAAL 365
L P R ++ P A I L+ +
Sbjct: 366 -----LEPAEYRKMFDRLSVFPPSAHIPTIL-LSLI 395
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 38.6 bits (89), Expect = 0.002
Identities = 14/101 (13%), Positives = 36/101 (35%), Gaps = 16/101 (15%)
Query: 212 EPETVEKVLKVPIHTLDGKKIDPKHA-TPKNRPKIGNRTKKIFVGGVSQDTSA------- 263
E + + L+ + G++ + + K ++VGG+ ++
Sbjct: 96 EEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQ 155
Query: 264 --EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++ FS+ G ++ + + GFV F+ +
Sbjct: 156 IESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQA 190
Score = 35.5 bits (81), Expect = 0.019
Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 19/101 (18%)
Query: 157 DDPTSAKLFVGGLS---------WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGF 207
+ L+VGG+ ++R F G + + ++ S+ GF
Sbjct: 130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGF 183
Query: 208 ITFAEPETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGNR 248
+ F E + + + + + G
Sbjct: 184 VKFKYQANAEFA----KEAMSNQTLLLPSDKEWDDRREGTG 220
>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 = 38.5 bits (89), Expect = 0.004
Identities = 49/264 (18%), Positives = 77/264 (29%), Gaps = 112/264 (42%)
Query: 54 APQVNTSPP--QNAILHQQ--PTPQ------PQQQQQQPPQPQPRDLQPNSNNQLVLVNG 103
P + P ++++ + + P+P Q+Q Q L ++ LVNG
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNG 373
Query: 104 KS----SGDSGRSTPTGDDPTSAKLFVGGLNV-VREAHQLVLVNGKSSGDSGRSTPTGDD 158
SG P P S L+ GLN+ +R+A P+G D
Sbjct: 374 AKNLVVSG------P----PQS--LY--GLNLTLRKAK----------------APSGLD 403
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGM-FGAVT---------DV--LIMKDPITQRSRGFG 206
+ S KL+ F F V LI KD +
Sbjct: 404 QSRIPF---------SERKLK--FSNRFLPVASPFHSHLLVPASDLINKDLVKNN----- 447
Query: 207 FITFAEPETVEKVLKVPI-HTLDGK-------------------------KIDPKHAT-- 238
++F + +++P+ T DG AT
Sbjct: 448 -VSFNAKD-----IQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHI 501
Query: 239 ----PKNRPKIGNRTKKIFVG-GV 257
P +G T + G GV
Sbjct: 502 LDFGPGGASGLGVLTHRNKDGTGV 525
Score = 33.1 bits (75), Expect = 0.22
Identities = 48/312 (15%), Positives = 86/312 (27%), Gaps = 107/312 (34%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGM-FGAVTDVLIMKD-PITQR---SRGFGFIT-FAE 212
PT+ S+ +S+ L+E F T+ D P T + G+++ E
Sbjct: 23 PTA--------SFFIASQ-LQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE 73
Query: 213 PETV---EKVLKV-------------PIHTL-------DGKKIDPKHATPK--------- 240
P V ++VL + IH L + + K
Sbjct: 74 PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMA 133
Query: 241 NRP-----------KIGNRTKKIFV--GGVSQ--------------DTSAEEVKAYFSQF 273
RP +G ++ GG Q T V
Sbjct: 134 KRPFDKKSNSALFRAVGEGNAQLVAIFGG--QGNTDDYFEELRDLYQTYHVLVGDLIKFS 191
Query: 274 GKVEETVMLMDQQTKRH--RGFGFVTF-ENEEV---VDHI--CEIHFHMIKNKKVECKKA 325
+ ++ ++ +G + + EN D++ I +I
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI---------- 241
Query: 326 QPKEAVQ-ANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQN 384
+Q A+ +V ++ LG P + L +Q V A A A
Sbjct: 242 ---GVIQLAHYVVTAKL----LGFT-----PGELRSYLKGATGHSQGLVTAVAIAETDSW 289
Query: 385 AAAVANYGKIFE 396
+ + K
Sbjct: 290 ESFFVSVRKAIT 301
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 35.5 bits (81), Expect = 0.012
Identities = 9/71 (12%), Positives = 23/71 (32%), Gaps = 4/71 (5%)
Query: 232 IDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR 291
+ +I V + + + + FS+FG V + + TK ++
Sbjct: 29 ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQ 84
Query: 292 GFGFVTFENEE 302
+ + +
Sbjct: 85 FQALLQYADPV 95
Score = 34.3 bits (78), Expect = 0.030
Identities = 13/97 (13%), Positives = 30/97 (30%), Gaps = 8/97 (8%)
Query: 129 LNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAK----LFVGGLSWQTSSEKLREYFGM 184
+A V + S + G + V L + + + L + F
Sbjct: 10 AQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSK 69
Query: 185 FGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
FG V ++ ++ + +A+P + +
Sbjct: 70 FGTVLKIITFTKN----NQFQALLQYADPVSAQHAKL 102
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.6 bits (79), Expect = 0.014
Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 4/56 (7%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ +I V + + + + FS+FG V + + TK ++ + + +
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPV 77
Score = 33.1 bits (75), Expect = 0.045
Identities = 11/84 (13%), Positives = 27/84 (32%), Gaps = 8/84 (9%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAK----LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDP 197
+ S + G + V L + + + L + F FG V ++
Sbjct: 5 GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64
Query: 198 ITQRSRGFGFITFAEPETVEKVLK 221
++ + +A+P + +
Sbjct: 65 ----NQFQALLQYADPVSAQHAKL 84
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 35.8 bits (82), Expect = 0.020
Identities = 21/119 (17%), Positives = 29/119 (24%), Gaps = 11/119 (9%)
Query: 10 PDHHEQF------NGLIPTMNGLVQIP-HHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPP 62
D + F + PT G + P HP L G P H + +P PP
Sbjct: 10 DDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPP 69
Query: 63 QNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTS 121
+P P P + + SS D
Sbjct: 70 ----FSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKV 124
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 33.1 bits (75), Expect = 0.047
Identities = 14/83 (16%), Positives = 24/83 (28%), Gaps = 8/83 (9%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAK---LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI 198
+G S R T D K L + + + + L G V + I
Sbjct: 3 SGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKV-----QRIVI 57
Query: 199 TQRSRGFGFITFAEPETVEKVLK 221
+R+ + F +K
Sbjct: 58 FKRNGIQAMVEFESVLCAQKAKA 80
Score = 32.3 bits (73), Expect = 0.094
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 236 HATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGF 295
+ P GN+ + + + + + + GKV+ V+ KR+
Sbjct: 12 RPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVI-----FKRNGIQAM 66
Query: 296 VTFENEE 302
V FE+
Sbjct: 67 VEFESVL 73
>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 = 31.8 bits (72), Expect = 0.085
Identities = 10/92 (10%), Positives = 27/92 (29%), Gaps = 12/92 (13%)
Query: 246 GNRTKKIFVGGVSQDTSAE-EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-- 302
+ + + + + ++ FG + ++L F+ E
Sbjct: 12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTEDA 65
Query: 303 --VVDHICEIHFHMIKNKKVECKKAQPKEAVQ 332
VD+ + K V +Q + ++
Sbjct: 66 QAAVDYYTTTPAL-VFGKPVRVHLSQKYKRIK 96
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 33.4 bits (76), Expect = 0.12
Identities = 12/47 (25%), Positives = 13/47 (27%), Gaps = 4/47 (8%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
Q P +PP Q PQ Q PPQ P
Sbjct: 379 QKMQQQQ----AAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYP 421
Score = 31.8 bits (72), Expect = 0.37
Identities = 15/71 (21%), Positives = 18/71 (25%), Gaps = 1/71 (1%)
Query: 28 QIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
+ + PP G P P P P Q PPQ P
Sbjct: 374 MMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAP 433
Query: 88 RDLQPNS-NNQ 97
P +NQ
Sbjct: 434 PAAPPQGVDNQ 444
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 29.6 bits (66), Expect = 0.69
Identities = 9/50 (18%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
F G + T E++ FS G+++ + + G + F+ +
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE------GIILFKEKA 66
>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae}
SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
PDB: 1pd0_A 1pd1_A
Length = 810
Score = 30.7 bits (68), Expect = 0.86
Identities = 7/25 (28%), Positives = 9/25 (36%)
Query: 69 QQPTPQPQQQQQQPPQPQPRDLQPN 93
QP+ Q + Q P DL
Sbjct: 6 GQPSAAMGQNMRPMNQLYPIDLLTE 30
Score = 28.0 bits (61), Expect = 6.9
Identities = 8/65 (12%), Positives = 14/65 (21%), Gaps = 1/65 (1%)
Query: 53 GAPQVNT-SPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGR 111
AP S + P + P P P + +
Sbjct: 1 AAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSN 60
Query: 112 STPTG 116
++P
Sbjct: 61 ASPDY 65
>3a58_A Exocyst complex component SEC3; protein complex, PH domain, GTPase,
membrane traffic, coiled coil, exocytosis,
phosphoprotein; HET: GNP; 2.60A {Saccharomyces
cerevisiae}
Length = 320
Score = 29.9 bits (66), Expect = 1.3
Identities = 10/82 (12%), Positives = 24/82 (29%), Gaps = 5/82 (6%)
Query: 12 HHEQFNGLIPTMNG----LVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAIL 67
+ + F G +P + L + + P +K + T+ Q+
Sbjct: 217 YIQTFEGHVPELVNWDLSLFYLDERSYQRAVITNRPGSVSPIK-SPTSNFTTNTTQSVGS 275
Query: 68 HQQPTPQPQQQQQQPPQPQPRD 89
P + ++ + P
Sbjct: 276 VPFSAPTERTRRSETESVNPVS 297
>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 = 30.2 bits (67), Expect = 1.4
Identities = 9/60 (15%), Positives = 19/60 (31%), Gaps = 6/60 (10%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+ + + S + Y SQFG + + + V F +E + +
Sbjct: 56 VLIH-CPEKISENKFLKYLSQFGPINNHFF-----YESFGLYAVVEFCQKESIGSLQNGT 109
>4f6o_A Metacaspase-1; rossmann fold, hydrolase; HET: DFH; 1.68A
{Saccharomyces cerevisiae}
Length = 350
Score = 29.9 bits (66), Expect = 1.5
Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 5/50 (10%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
NG P + G PQ + PP Q T Q Q Q Q R
Sbjct: 9 NGYNNPNVNASNMYGPPQNMSLPPP-----QTQTIQGTDQPYQYSQCTGR 53
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 28.2 bits (62), Expect = 1.8
Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
S + L +G V +++ ++ + G + FA + E ++
Sbjct: 30 SKDVLLRLLQKYGEVLNLV-----LSSKKPGTAVVEFATVKAAELAVQ 72
Score = 27.0 bits (59), Expect = 4.2
Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 262 SAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNK-KV 320
S + + ++G+V V+ + + G V F + + + ++ N K+
Sbjct: 30 SKDVLLRLLQKYGEVLNLVL-----SSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKI 84
Query: 321 ECKKAQPKEA 330
+ QP++A
Sbjct: 85 SWLEGQPQDA 94
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics;
5.00A {Barmah forest virus}
Length = 253
Score = 29.2 bits (65), Expect = 1.9
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 40 GPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQ--QQQPPQPQPRDLQPNSNNQ 97
PP PP + + Q+ + A+ +Q + Q++ + PP+P+ +
Sbjct: 27 QPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQKKPKKTPPPKPKKTQKPKKPTQK 86
>1yc9_A VCEC, multidrug resistance protein; outer membrane protein,
multidrug resistanc membrane protein; HET: BOG; 1.80A
{Vibrio cholerae}
Length = 442
Score = 29.6 bits (67), Expect = 2.1
Identities = 6/32 (18%), Positives = 12/32 (37%)
Query: 359 ATQLAALQSQAQAQVQAAAAAVAAQNAAAVAN 390
A + + Q+ + A A+ A +A
Sbjct: 357 ADVVTSSQALQARINKTEQAVQQAEQALHIAT 388
>3ijr_A Oxidoreductase, short chain dehydrogenase/reducta; structural
genomics, infectious D center for structural genomics of
infectious diseases; HET: NAD; 2.05A {Bacillus anthracis
str} PDB: 3i3o_A*
Length = 291
Score = 29.0 bits (66), Expect = 2.2
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 15/55 (27%)
Query: 68 HQQPTPQPQQQQQQPP------QPQPRDLQPN--SNNQL----VLVNGKSSGDSG 110
+ P Q Q + P P P+ PN + +L VL+ G GDSG
Sbjct: 7 QKNFVTMPAQHQNKQPGIESLMNPLPQFEDPNYKGSEKLKGKNVLITG---GDSG 58
>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis,
clathrin adaptor, transport, coated PITS; 4.0A {Mus
musculus} SCOP: i.23.1.1
Length = 158
Score = 28.5 bits (63), Expect = 2.3
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEET 279
+GG QDTS + V Q ++E
Sbjct: 117 FLMGGDVQDTSKKSVLKAIEQADLLQEE 144
>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring
E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A
{Saccharomyces cerevisiae}
Length = 371
Score = 29.1 bits (64), Expect = 2.6
Identities = 11/72 (15%), Positives = 24/72 (33%), Gaps = 8/72 (11%)
Query: 35 LVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNS 94
+ + PP Q + S + + ++ T + PP P +S
Sbjct: 8 ITVRSMEGPPT--------VQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSSSS 59
Query: 95 NNQLVLVNGKSS 106
+ + ++ K S
Sbjct: 60 SFAVPTIHFKES 71
>1zgk_A Kelch-like ECH-associated protein 1; beta-propeller, kelch repeat
motif, protein binding; HET: MSE; 1.35A {Homo sapiens}
SCOP: b.68.11.1 PDB: 2flu_X 1u6d_X 1x2j_A 1x2r_A 2dyh_A
2z32_A 3ade_A
Length = 308
Score = 28.8 bits (65), Expect = 2.9
Identities = 13/68 (19%), Positives = 22/68 (32%), Gaps = 6/68 (8%)
Query: 80 QQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRSTPTGD--DPTSAK-LFVGGLNVVREAH 136
PR +L+ G G +S + +P++ L + L V R
Sbjct: 8 HHSSGLVPRGSHAPKVGRLIYTAG---GYFRQSLSYLEAYNPSNGTWLRLADLQVPRSGL 64
Query: 137 QLVLVNGK 144
+V G
Sbjct: 65 AGCVVGGL 72
>1clc_A Endoglucanase CELD; EC: 3.2.1.4; cellulase, glycosyl hydrolase;
1.90A {Clostridium thermocellum} SCOP: a.102.1.2
b.1.18.2
Length = 639
Score = 29.1 bits (65), Expect = 3.1
Identities = 7/30 (23%), Positives = 7/30 (23%), Gaps = 3/30 (10%)
Query: 27 VQIPHHPGLVHLNGPPPPPHQLVKLNGAPQ 56
PH P P LV G
Sbjct: 502 PMNPHDRRSGADGIWEPWPGYLV---GGGW 528
>2qdz_A TPSB transporter FHAC; beta barrel, potra domain, membrane,
protein transport; 3.15A {Bordetella pertussis} PDB:
3njt_A
Length = 554
Score = 29.0 bits (64), Expect = 3.3
Identities = 5/33 (15%), Positives = 10/33 (30%)
Query: 56 QVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
Q P + + +Q Q+ + R
Sbjct: 1 QAQLLPGARDLNRIDDRQRKEQLQRDIERALTR 33
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 28.7 bits (63), Expect = 3.9
Identities = 15/111 (13%), Positives = 27/111 (24%), Gaps = 4/111 (3%)
Query: 73 PQPQQQQQQPPQPQP----RDLQPNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGG 128
Q+ QPP P P P S ++ + + P+ F
Sbjct: 22 YMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSL 81
Query: 129 LNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLR 179
N V++ G + L V ++ +
Sbjct: 82 SNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLVIDEPHTDWAKYFK 132
>2dga_A Beta-glucosidase; alpha/beta barrel, hydrolase; 1.80A {Triticum
aestivum} PDB: 3aiq_A* 3air_A* 3ais_A* 3aiu_A 3aiv_A*
3aiw_A*
Length = 565
Score = 28.4 bits (64), Expect = 4.7
Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 2/70 (2%)
Query: 12 HHEQFNGLIPTMNGLVQIPHHP-GLVHLNGPPPP-PHQLVKLNGAPQVNTSPPQNAILHQ 69
HH +GL+P +G+ + H++ P + G P P
Sbjct: 4 HHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMAGTPSKPAEPIGPVFTKL 63
Query: 70 QPTPQPQQQQ 79
+P P++
Sbjct: 64 KPWQIPKRDW 73
>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine
proteinase, wild type, viral protein; 2.38A {Sindbis
virus} SCOP: b.47.1.3 PDB: 1ld4_A 3j0f_A
Length = 264
Score = 28.2 bits (62), Expect = 4.8
Identities = 9/59 (15%), Positives = 19/59 (32%), Gaps = 6/59 (10%)
Query: 41 PPPPPHQLVKLNGA------PQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPN 93
Q+ +L A Q + Q +Q +P +P+P++ +
Sbjct: 35 RNGLASQIQQLTTAVSALVIGQATRPQNPRPRPPPRQKKQAPKQPPKPKKPKPQEKKKK 93
Score = 27.1 bits (59), Expect = 9.7
Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 2/71 (2%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPP--QPQPRDLQPNSNN 96
P P Q PP+ Q + Q + +P Q L+ +
Sbjct: 57 ATRPQNPRPRPPPRQKKQAPKQPPKPKKPKPQEKKKKQPAKTKPGKRQRMALKLEADRLF 116
Query: 97 QLVLVNGKSSG 107
+ +G G
Sbjct: 117 DVKNEDGDVIG 127
>3luy_A Probable chorismate mutase; structural genomics, APC38059,
3-phenylp PSI-2, protein structure initiative; HET: PPY;
2.00A {Bifidobacterium adolescentis}
Length = 329
Score = 28.0 bits (63), Expect = 6.0
Identities = 6/39 (15%), Positives = 7/39 (17%), Gaps = 16/39 (41%)
Query: 368 QAQAQVQ----------------AAAAAVAAQNAAAVAN 390
AQ + AAA A
Sbjct: 118 HGLAQCKRFIAEHRLSTQPATSNAAACRDLIPGEIAFGP 156
>3pxp_A Helix-turn-helix domain protein; DNA-binding, basic
helix-loop-helix motif, BHLH motif, lambd repressor-like
DNA-binding fold; HET: MSE MYR; 2.30A {Chloroflexus
aurantiacus}
Length = 292
Score = 27.6 bits (62), Expect = 6.5
Identities = 5/47 (10%), Positives = 13/47 (27%), Gaps = 3/47 (6%)
Query: 349 RMAAPAPITPATQ--LAALQSQAQ-AQVQAAAAAVAAQNAAAVANYG 392
+ Q + +++ A V + A N + +
Sbjct: 87 SATYKRSPEESLQYLIDMIRNMNVPAFVTDQYVNIIAANMITIRFFN 133
>3r3s_A Oxidoreductase; structural genomics, csgid, center for structural
genomics O infectious diseases, 3-layer(ABA) sandwich,
rossmann fold; HET: NAD; 1.25A {Salmonella enterica
subsp}
Length = 294
Score = 27.5 bits (62), Expect = 7.5
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 14/62 (22%)
Query: 60 SPPQNAILHQQPTPQPQQQQQQP-------PQPQPRDLQPNSNNQL----VLVNGKSSGD 108
S + P+Q+Q P P P + + +L LV G GD
Sbjct: 2 SHLYDPTTQYYTGEYPKQKQPAPGVQAKMTPVPDCGEKSYVGSGRLKDRKALVTG---GD 58
Query: 109 SG 110
SG
Sbjct: 59 SG 60
>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain,
protein binding; HET: ADP; 2.90A {Rattus norvegicus}
SCOP: d.15.1.2 PDB: 1i42_A 1jru_A
Length = 127
Score = 26.8 bits (59), Expect = 7.6
Identities = 11/62 (17%), Positives = 20/62 (32%)
Query: 43 PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVN 102
P G Q S + P Q + + + + +P +N Q+ L +
Sbjct: 2 KPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLAD 61
Query: 103 GK 104
G
Sbjct: 62 GG 63
>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA
packaging podoviridae, virus assembly, tail tube, trunk
domain; 7.50A {Enterobacteria phage P22}
Length = 725
Score = 27.7 bits (60), Expect = 8.1
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 69 QQPTPQPQQQQQQPPQPQPRDLQ 91
QQ + QQ +Q P Q
Sbjct: 590 QQWLVEAQQAKQGQQDPAMVQAQ 612
>2jd4_A Laminin subunit alpha-1; basement membrane protein, metal binding
protein; 1.9A {Mus musculus}
Length = 383
Score = 27.6 bits (61), Expect = 8.6
Identities = 26/111 (23%), Positives = 42/111 (37%), Gaps = 8/111 (7%)
Query: 98 LVLVNGKSS----GDSGRSTPTGDDPTSAKLFVGG---LNVVREAHQLVL-VNGKSSGDS 149
L +V+GK +GR T T + L G L + H++VL V+G S
Sbjct: 250 LEIVDGKVLFHVNNGAGRITATYQPRAARALCDGKWHTLQAHKSKHRIVLTVDGNSVRAE 309
Query: 150 GRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
T + T+ ++VGG L G V ++ + + Q
Sbjct: 310 SPHTHSTSADTNDPIYVGGYPAHIKQNSLSSRASFRGCVRNLRLSRGSQVQ 360
>1ek9_A Outer membrane protein TOLC; integral membrane protein, alpha
helical barrel, beta barrel; 2.10A {Escherichia coli}
SCOP: f.5.1.1 PDB: 1tqq_A 2vde_A 2vdd_A 2wmz_A* 2xmn_A*
Length = 428
Score = 27.4 bits (61), Expect = 8.7
Identities = 11/81 (13%), Positives = 21/81 (25%), Gaps = 16/81 (19%)
Query: 329 EAVQANL--LVGKRV----ILGPLGLRMAAPAPITPATQLAALQS----QAQAQVQAAAA 378
+ L + G L + P P+ + A ++ QA+ A
Sbjct: 176 DNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLARE 235
Query: 379 AVAAQNAA------AVANYGK 393
+ A+ G
Sbjct: 236 QIRQAQDGHLPTLDLTASTGI 256
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
0.315 0.132 0.386
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,052,521
Number of extensions: 369075
Number of successful extensions: 2133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1661
Number of HSP's successfully gapped: 565
Length of query: 398
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 302
Effective length of database: 4,021,377
Effective search space: 1214455854
Effective search space used: 1214455854
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: 42 (22.0 bits)
S2: 58 (26.1 bits)