RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15045
(363 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 = 175 bits (447), Expect = 4e-54
Identities = 62/194 (31%), Positives = 96/194 (49%), Gaps = 12/194 (6%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
SK P P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF
Sbjct: 2 SKSESPKE--PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 150 IRFSSHESALKAM-LKKHKIGNRICDVRIP---ESTKIGTEEPVASKVFVGSLTPDLTES 205
+ +++ E AM + HK+ R+ + + E ++ K+FVG + D E
Sbjct: 60 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 206 DLREHFEYYGAVVDVLIP-----KPFREFAFVTFE-LDSVAKSLIGQHVNIKDKKVVVME 259
LR++FE YG + + I R FAFVTF+ DSV K +I ++ + V +
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
Query: 260 ATPKKKMNERQDNR 273
A K++M ++
Sbjct: 180 ALSKQEMASASSSQ 193
>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 = 172 bits (439), Expect = 2e-53
Identities = 45/168 (26%), Positives = 87/168 (51%), Gaps = 9/168 (5%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
++ + + G+ W T+++L+EYF ++GT+ + D TGRS+GFGF+ F S +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 162 MLKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVL 221
+ +H + ++ D + E+ K+FVG + PD+ + E F +G ++D
Sbjct: 62 VKTQHILDGKVIDPKRAIPRD---EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 222 IP-----KPFREFAFVTFE-LDSVAKSLIGQHVNIKDKKVVVMEATPK 263
+ R F FVT++ D+V + + ++ KD+K+ + A P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 63.7 bits (156), Expect = 2e-12
Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTFE-LDSVAKSLI 244
K+F+G L D TE +LRE+F YG V D+ I K P R F F++FE SV + +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 245 GQHVNIKDKKVVVMEATPKKKMN 267
QH+ + K + A P+ + +
Sbjct: 64 TQHI-LDGKVIDPKRAIPRDEQD 85
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 118 bits (299), Expect = 5e-32
Identities = 32/203 (15%), Positives = 80/203 (39%), Gaps = 19/203 (9%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+ + + + V I + ++ +++ F FG ++ ++ D
Sbjct: 6 SMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV 65
Query: 141 TGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDV--------RIPESTKIGTEEPVA 190
T + KGF F+ + E+A A+ + +G R V P ++ E
Sbjct: 66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAKSLIG 245
++++V S+ DL++ D++ FE +G + + + + + F+ +E ++ +
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV- 184
Query: 246 QHVN---IKDKKVVVMEATPKKK 265
+N + + + V +A
Sbjct: 185 SSMNLFDLGGQYLRVGKAVTPPM 207
>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 = 114 bits (287), Expect = 8e-31
Identities = 40/168 (23%), Positives = 74/168 (44%), Gaps = 18/168 (10%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T+L+V +P T + + F G +E + DK TG+S G+GF+ + + A KA+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 163 --LKKHKIGNRICDVR--IPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV 218
L ++ + V P S I + ++V L +T+ +L + F YG ++
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRD-----ANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 219 D--VLIPKPF---REFAFVTFELDSVAKSLI----GQHVNIKDKKVVV 257
+L+ + R F+ F+ A+ I GQ + + + V
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 111 bits (279), Expect = 2e-30
Identities = 43/98 (43%), Positives = 61/98 (62%), Gaps = 6/98 (6%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ KR + +DL+VLG+PW T+ DLKEYF FG + VK D TG
Sbjct: 1 GSSGSSGVKR------AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTG 54
Query: 143 RSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRIPES 180
SKGFGF+RF+ +E+ +K M ++H I R CD ++P S
Sbjct: 55 HSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS 92
Score = 66.5 bits (163), Expect = 5e-14
Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTF 234
S+ + S + V L TE DL+E+F +G V+ V + K + F FV F
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 235 E-LDSVAKSLIGQHVNIKDKKVVVMEATPKKKMN 267
++ K + +H+ I + K+ +
Sbjct: 65 TEYETQVKVMSQRHM-IDGRWCDCKLPNSKQSQD 97
>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 = 110 bits (278), Expect = 2e-29
Identities = 34/163 (20%), Positives = 63/163 (38%), Gaps = 9/163 (5%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LK 164
L + + + +LK + V VD TG ++ FG++ F S E KA+ L
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALELT 74
Query: 165 KHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK 224
K+ + P+ A + +L+ ++TE +L+E FE + V
Sbjct: 75 GLKVFGNEIKLEKPKGRDSKKVRA-ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDG 133
Query: 225 PFREFAFVTFE-LDSVAKSLIGQHVN---IKDKKVVVMEATPK 263
+ A++ F+ K+L + I + V + K
Sbjct: 134 KSKGIAYIEFKSEADAEKNL--EEKQGAEIDGRSVSLYYTGEK 174
Score = 69.2 bits (170), Expect = 3e-14
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 96 DNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH 155
D+ L+ + + T+++LKE FE +++ G+SKG +I F S
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSE 146
Query: 156 ESALKAMLKKH--KIGNR 171
A K + +K +I R
Sbjct: 147 ADAEKNLEEKQGAEIDGR 164
Score = 59.9 bits (146), Expect = 6e-11
Identities = 17/95 (17%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTFE-LDS 238
G+E +F+G+L P+ + ++L+ A D+ + R+F +V FE +
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66
Query: 239 VAKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNR 273
+ K+L + + ++ + + + R
Sbjct: 67 LEKALELTGLKVFGNEIKLEKPKGRDSKKVRAART 101
>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 = 109 bits (275), Expect = 5e-29
Identities = 37/170 (21%), Positives = 67/170 (39%), Gaps = 18/170 (10%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFG-----TLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
L V IP+ T+ + ++F T N + + K F F+ F S + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 161 AM-LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVD 219
AM + +R P + P A K+F+G L L + ++E +G +
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQ---PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 123
Query: 220 VLIPK-----PFREFAFVTFELDSVAKSLIGQHVN---IKDKKVVVMEAT 261
+ K + +AF + +V I +N + DKK++V A+
Sbjct: 124 FNLVKDSATGLSKGYAFCEYVDINVTDQAI-AGLNGMQLGDKKLLVQRAS 172
Score = 80.4 bits (199), Expect = 3e-18
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 91 KRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFI 150
+R + P + L + G+P D+ +KE FG L+ N+ D TG SKG+ F
Sbjct: 83 RRPHDYQPLPGAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141
Query: 151 RFSSHESALKAM--LKKHKIGNRICDVR 176
+ +A+ L ++G++ V+
Sbjct: 142 EYVDINVTDQAIAGLNGMQLGDKKLLVQ 169
Score = 49.5 bits (119), Expect = 2e-07
Identities = 11/88 (12%), Positives = 34/88 (38%), Gaps = 11/88 (12%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----------REFAFVTFE-LDS 238
A +++VG++ +TE + + F + + + FAF+ F +D
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 239 VAKSLIGQHVNIKDKKVVVMEATPKKKM 266
+++ + + + + + + +
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPL 91
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 109 bits (274), Expect = 6e-29
Identities = 39/166 (23%), Positives = 66/166 (39%), Gaps = 14/166 (8%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
NT+L+V +P TD +L F G + + D TG S G+ F+ F+S + +A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 163 --LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDV 220
L + N+ V E + ++V +L +T+ L F YG++V
Sbjct: 63 KVLNGITVRNKRLKVSYARPGG---ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK 119
Query: 221 LIPK-----PFREFAFVTFELDSVAKSLI----GQHVNIKDKKVVV 257
I + R AFV + A+ I + + V
Sbjct: 120 NILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 72.2 bits (178), Expect = 2e-15
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 92 RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
+ P +++T+L V +P T TD+ L F ++G++ N+ DK TGR +G F+R
Sbjct: 79 YARPGGE-SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 152 FSSHESALKAM 162
++ E A +A+
Sbjct: 138 YNKREEAQEAI 148
>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 = 108 bits (271), Expect = 3e-28
Identities = 37/192 (19%), Positives = 65/192 (33%), Gaps = 34/192 (17%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFG-----TLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
L V IP+ T+ + ++F T N + + K F F+ F S + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 161 AM-LKKHKIGNRICDVRIPE-----------------STKIGTEEPVASKVFVGSLTPDL 202
AM + +R P A K+F+G L L
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL 126
Query: 203 TESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAK----SLIGQHVNIKDK 253
+ ++E +G + + K + +AF + +V L G + DK
Sbjct: 127 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DK 184
Query: 254 KVVVMEATPKKK 265
K++V A+ K
Sbjct: 185 KLLVQRASVGAK 196
Score = 77.8 bits (192), Expect = 4e-17
Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 2/98 (2%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+ + + P L + G+P D+ +KE FG L+ N+ D
Sbjct: 92 PGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA 151
Query: 141 TGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVR 176
TG SKG+ F + +A+ L ++G++ V+
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189
Score = 53.5 bits (129), Expect = 1e-08
Identities = 16/118 (13%), Positives = 45/118 (38%), Gaps = 11/118 (9%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----------PFREFAFVTFE-LDS 238
A +++VG++ +TE + + F + + + FAF+ F +D
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 239 VAKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGG 296
+++ + + + + + + + +N + + + P S + + GG
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 110 bits (277), Expect = 3e-28
Identities = 31/141 (21%), Positives = 56/141 (39%), Gaps = 7/141 (4%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
+ L V +P + T +E FG+LE + + TG+SKG+GF + +SA +A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 162 M--LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESD-LREHFEYYGAVV 218
L +G R V ++ ++ + + V L P + D L +
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213
Query: 219 DVLIPK----PFREFAFVTFE 235
+ + FA + +E
Sbjct: 214 FCQLACGQDGQLKGFAVLEYE 234
Score = 95.0 bits (237), Expect = 2e-22
Identities = 25/185 (13%), Positives = 59/185 (31%), Gaps = 27/185 (14%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
+++ G+P T+ ++ + + V + KG F+ + E A
Sbjct: 19 FRNRRKILIRGLPGDVTNQEVHDLLSDYELKY---CFV----DKYKGTAFVTLLNGEQAE 71
Query: 160 KAMLKKH--KIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAV 217
A+ H ++ R V++ P + + V +L P LT+ E +G++
Sbjct: 72 AAINAFHQSRLRERELSVQLQ---------PTDALLCVANLPPSLTQQQFEELVRPFGSL 122
Query: 218 VDVLIPKPF-----REFAFVTFELDSVAKSLIGQHVN---IKDKKVVVMEATPKKKMNER 269
+ + + F + A + + + + V +
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAK-SDLLGKPLGPRTLYVHWTDAGQLTPAL 181
Query: 270 QDNRN 274
+R
Sbjct: 182 LHSRC 186
Score = 75.8 bits (187), Expect = 8e-16
Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 4/85 (4%)
Query: 95 PDNSGPVQNTDLVVLGIPWTFTDND-LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFS 153
+ + L V +P F D D L + F + + G+ KGF + +
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYE 234
Query: 154 SHESALKAM--LKKHKIGNRICDVR 176
+ E A +A +G V
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHLRVS 259
Score = 49.6 bits (119), Expect = 5e-07
Identities = 14/101 (13%), Positives = 36/101 (35%), Gaps = 9/101 (8%)
Query: 166 HKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP 225
H + R+ + + + K+ + L D+T ++ + Y +
Sbjct: 1 HMLDPEEIRKRLEHTER---QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKY- 56
Query: 226 FREFAFVTFELDSVAKSLIGQHVN---IKDKKVVVMEATPK 263
+ AFVT A++ I + ++++++ V
Sbjct: 57 -KGTAFVTLLNGEQAEAAI-NAFHQSRLRERELSVQLQPTD 95
>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 = 104 bits (262), Expect = 4e-27
Identities = 37/141 (26%), Positives = 68/141 (48%), Gaps = 9/141 (6%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG--RSKGFGFIRFSSHESALKA 161
+ V +P T+++ DL+E FEQ+G + NV D++ +SKG F+ F + ++AL+A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 162 MLK---KHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV 218
+ +++ + K+F+G ++ TE+D+R F +G +
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 219 DVLIPK----PFREFAFVTFE 235
+ I + R AFVTF
Sbjct: 124 ECRILRGPDGLSRGCAFVTFT 144
Score = 76.9 bits (190), Expect = 5e-17
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 89 QSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFG 148
Q K + + + V++ L + I T+ND++ F FG +E + G S+G
Sbjct: 81 QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCA 139
Query: 149 FIRFSSHESALKAMLKKH 166
F+ F++ A A+ H
Sbjct: 140 FVTFTTRAMAQTAIKAMH 157
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 105 bits (264), Expect = 5e-27
Identities = 48/226 (21%), Positives = 79/226 (34%), Gaps = 33/226 (14%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
S S SYP S L V + T+ L E F G + V D T RS
Sbjct: 4 GSMNPSAPSYPMAS-------LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRS 56
Query: 145 KGFGFIRFSSHESALKAM--LKKHKIGNRICDV----RIPESTKIGTEEPVASKVFVGSL 198
G+ ++ F A +A+ + I + + R P K G +F+ +L
Sbjct: 57 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV-----GNIFIKNL 111
Query: 199 TPDLTESDLREHFEYYGAVVDVLIPKPF---REFAFVTFELDSVAKSLIGQHVN---IKD 252
+ L + F +G ++ + + + FV FE A+ I + +N + D
Sbjct: 112 DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI-EKMNGMLLND 170
Query: 253 KKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNG 298
+KV V +K+ R + Y G +G
Sbjct: 171 RKVFVGRFKSRKEREAELGARAK--------EFYPYDVPDYAGSSG 208
>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 = 105 bits (264), Expect = 1e-26
Identities = 46/234 (19%), Positives = 82/234 (35%), Gaps = 29/234 (12%)
Query: 95 PDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSS 154
P Q L V +P T+ D K FE++G E + V + R +GFGFIR S
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFI----NRDRGFGFIRLES 67
Query: 155 HESALKAM--LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFE 212
A A L + +R +R + + V +L+P ++ L + F
Sbjct: 68 RTLAEIAKAELDGTILKSRPLRIR---------FATHGAALTVKNLSPVVSNELLEQAFS 118
Query: 213 YYGAVVDVLIP-----KPFREFAFVTFELDSVAKSLI-----GQHVNIKDKKVVVME-AT 261
+G V ++ + FV F A+ + G + + V++E
Sbjct: 119 QFGPVEKAVVVVDDRGRA-TGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPME 177
Query: 262 PKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGYYDNRQQQQGGYNNKRR 315
+ + ++ + R Q G Y +R + ++R
Sbjct: 178 QFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQR 231
>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 = 104 bits (262), Expect = 4e-26
Identities = 35/179 (19%), Positives = 74/179 (41%), Gaps = 14/179 (7%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
+ L + P ++T ++++ + + + S+ F +I +S E A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Query: 159 LKAM--LKKHKIGNRICDVRIPESTKIGTEEPVAS----KVFVGSLTPDLT-ESDLREHF 211
+ L KI ++ + A+ ++ + +L+ +L E+ LRE F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232
Query: 212 EYYGAVVDVLIPKPFRE------FAFVTFE-LDSVAKSLIGQHVNIKDKKVVVMEATPK 263
E +G++ + IP +E AF+ FE DS ++L + ++++ V A K
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK 291
Score = 100 bits (251), Expect = 2e-24
Identities = 34/187 (18%), Positives = 79/187 (42%), Gaps = 22/187 (11%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
+ T ++V +P ++ N + +YF+ G + +V V + ++ F I F+ ++ AL A
Sbjct: 40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPII--HVDVADSLKKNFRFARIEFARYDGALAA 97
Query: 162 MLKKHK-IGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAV-VD 219
+ K HK +G V +++ + P T+ ++R+ + V +
Sbjct: 98 ITKTHKVVGQNEIIVSHLTEC----------TLWMTNFPPSYTQRNIRDLLQDINVVALS 147
Query: 220 VLIPKP----FREFAFVTFELDSVAKSLIGQH--VNIKDKKVVVMEATPKKKMNERQDNR 273
+ +P R FA++ A+ + + + I+ +V + P +K ++ +
Sbjct: 148 IRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK--SKRTDS 205
Query: 274 NNFDRRN 280
+ R
Sbjct: 206 ATLEGRE 212
Score = 75.0 bits (185), Expect = 2e-15
Identities = 21/94 (22%), Positives = 47/94 (50%), Gaps = 3/94 (3%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDND-LKEYFEQFGTLEFANVKVD-KNTGRS 144
+ ++S +S ++ ++++ + D + L+E FE FG++E N+ K +
Sbjct: 194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFN 253
Query: 145 KGFGFIRFSSHESALKAM-LKKHKIGNRICDVRI 177
F+ F + +SA +A+ + + +GNR V +
Sbjct: 254 NCCAFMVFENKDSAERALQMNRSLLGNREISVSL 287
>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 = 99.7 bits (249), Expect = 5e-26
Identities = 29/100 (29%), Positives = 49/100 (49%), Gaps = 4/100 (4%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV 137
+SG+S ++ + P + L + G+ + T+ L+ Y+EQ+G L V
Sbjct: 2 SSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 61
Query: 138 DKNTGRSKGFGFIRFSSHESALKAMLKK-HKIGNRICDVR 176
D + RS+GFGF+ FSS AM + H I R+ + +
Sbjct: 62 DPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPK 101
Score = 60.0 bits (146), Expect = 1e-11
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTFE-LDSVAKSLIG 245
K+F+G L+ + TE LR ++E +G + D ++ + P R F FVTF + V ++
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 246 QHVNIKDKKVVVMEATPKKKMN 267
+ +I + V A +++
Sbjct: 89 RPHSIDGRVVEPKRAVAREESG 110
>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 = 96.9 bits (242), Expect = 2e-25
Identities = 42/80 (52%), Positives = 51/80 (63%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQH 247
+S VFVG T D+TE +LRE F YG V+DV IPKPFR FAFVTF D +A+SL G+
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGED 62
Query: 248 VNIKDKKVVVMEATPKKKMN 267
+ IK V + A PK N
Sbjct: 63 LIIKGISVHISNAEPKHNSN 82
Score = 77.6 bits (192), Expect = 3e-18
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 5/82 (6%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ + V T+++L+E+F Q+G + + + F F+ F+ + A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIA 55
Query: 159 LKAMLKKHKIGNRICDVRIPES 180
+ I + E
Sbjct: 56 QSLCGEDLIIKGISVHISNAEP 77
>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 = 96.4 bits (241), Expect = 3e-25
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 108 VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK-H 166
V G+ + ++EYF FG +E + +D T + +GF FI F E K M KK H
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63
Query: 167 KIGNRICDVR 176
+G C+++
Sbjct: 64 NVGLSKCEIK 73
Score = 65.6 bits (161), Expect = 5e-14
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFE-LDSVAKSLI 244
K+FVG L+PD E +RE+F +G V + +P K R F F+TF+ + V K +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKR-RGFCFITFKEEEPVKKIME 59
Query: 245 GQHVNIKDKKVVVMEA 260
++ N+ K + A
Sbjct: 60 KKYHNVGLSKCEIKVA 75
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 96.4 bits (241), Expect = 3e-25
Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 108 VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LKKH 166
V G+ T D+K YFEQFG ++ A + DK T R +GFGF+ F S + K + H
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFH 63
Query: 167 KIGNRICDVR 176
+I N++ + +
Sbjct: 64 EINNKMVECK 73
Score = 61.3 bits (150), Expect = 1e-12
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFE-LDSVAKSLI 244
K+FVG L+ + T D++ +FE +G V D ++ + R F FVTFE D V K
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRH-RGFGFVTFESEDIVEKVCE 59
Query: 245 GQHVNIKDKKVVVMEA 260
I +K V +A
Sbjct: 60 IHFHEINNKMVECKKA 75
>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 = 95.8 bits (239), Expect = 6e-25
Identities = 41/82 (50%), Positives = 49/82 (59%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI 244
SKVFVG T D+T +L++ F YG VVDV IPKPFR FAFVTF D VA+SL
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLC 65
Query: 245 GQHVNIKDKKVVVMEATPKKKM 266
G+ + IK V + A PK
Sbjct: 66 GEDLIIKGISVHISNAEPKHNK 87
Score = 75.3 bits (186), Expect = 2e-17
Identities = 12/84 (14%), Positives = 28/84 (33%), Gaps = 5/84 (5%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+ + + V T +L+++F Q+G + + + F F+ F+ +
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDK 59
Query: 157 SALKAMLKKHKIGNRICDVRIPES 180
A + I + E
Sbjct: 60 VAQSLCGEDLIIKGISVHISNAEP 83
>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 = 95.8 bits (239), Expect = 1e-24
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 1/96 (1%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+S + S + + + G+ W T L+EYF QFG ++ V D
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62
Query: 141 TGRSKGFGFIRFSSHESALKAM-LKKHKIGNRICDV 175
T RS+GFGF+ F K + +H++ ++ D
Sbjct: 63 TKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDP 98
Score = 59.6 bits (145), Expect = 2e-11
Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 11/97 (11%)
Query: 177 IPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAF 231
+P + +G+ K+F+G L+ T+ LRE+F +G V + L+ + P R F F
Sbjct: 15 VPRGSHMGSSG---CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 232 VTFELDSVAKSLIGQ--HVNIKDKKVVVMEATPKKKM 266
VTF + ++ Q H + K + A P++
Sbjct: 72 VTFMDQAGVDKVLAQSRHE-LDSKTIDPKVAFPRRAQ 107
>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 = 95.0 bits (237), Expect = 2e-24
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
S ++ + V GIP + +L+EYF++FG + + D R +GFGFI F +
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Query: 157 SALKAM-LKKHKIGNRICDVR 176
S +A+ + H I + +V+
Sbjct: 64 SVDQAVNMHFHDIMGKKVEVK 84
Score = 70.7 bits (174), Expect = 1e-15
Identities = 29/93 (31%), Positives = 51/93 (54%), Gaps = 8/93 (8%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFE-L 236
G+ ++K+FVG + + E++LRE+F+ +G V +V++ +P R F F+TFE
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRP-RGFGFITFEDE 62
Query: 237 DSVAKSLIGQHVNIKDKKVVVMEATPKKKMNER 269
SV +++ +I KKV V A P+ +
Sbjct: 63 QSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSG 95
>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 = 95.1 bits (237), Expect = 2e-24
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 1/115 (0%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
+ + T + V G+P+ TD L++YFE FG +E A V D+ TG+S+G
Sbjct: 1 GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
Query: 147 FGFIRFSSHESALKAMLKK-HKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTP 200
+GF+ + +A +A I R +V + + V +
Sbjct: 61 YGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115
Score = 62.3 bits (152), Expect = 2e-12
Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTFE-LDSV 239
++ +K+FVG L T++ LR++FE +G + + ++ R + FVT +
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 240 AKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRNNF 276
++ + I +K V A K Q
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIG 109
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 92.6 bits (231), Expect = 7e-24
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LK 164
+ + G+ W T L+EYF QFG ++ V D T RS+GFGF+ F K +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 165 KHKIGNRICDVR 176
+H++ ++ D +
Sbjct: 63 RHELDSKTIDPK 74
Score = 54.4 bits (132), Expect = 5e-10
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTFELDSVAKSLIGQ 246
K+F+G L+ T+ LRE+F +G V + L+ + P R F FVTF + ++ Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 247 HVNIKDKKVV 256
+ D K +
Sbjct: 62 SRHELDSKTI 71
>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 = 93.5 bits (233), Expect = 8e-24
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S +NSG + L V G+ W+ T L+ YF Q+G + + DK T +S+GFGF
Sbjct: 3 SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62
Query: 150 IRFSSHESALKAM-LKKHKIGNRICDV 175
++F + + H + R D
Sbjct: 63 VKFKDPNCVGTVLASRPHTLDGRNIDP 89
Score = 57.6 bits (140), Expect = 8e-11
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 6/87 (6%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTF-ELDSV 239
K+FVG L T+ LR +F YG VVD +I K R F FV F + + V
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCV 71
Query: 240 AKSLIGQHVNIKDKKVVVMEATPKKKM 266
L + + + + TP+
Sbjct: 72 GTVLASRPHTLDGRNIDPKPCTPRGMQ 98
>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 = 91.5 bits (228), Expect = 2e-23
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
+ V G+ W + DLK+YF +FG + +K+D NTGRS+GFGFI F S
Sbjct: 6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS 65
Query: 158 ALKAM-LKKHKIGNRICDVR 176
K + K+H++ R+ D +
Sbjct: 66 VEKVLDQKEHRLDGRVIDPK 85
Score = 55.7 bits (135), Expect = 2e-10
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 9/84 (10%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFELDSVA 240
E A K+FVG L+ D ++ DL+++F +G VVD I R F F+ F+ +
Sbjct: 7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV 66
Query: 241 KSLIGQHVNIKDKKVVVMEATPKK 264
+ ++ Q + D +V+ PKK
Sbjct: 67 EKVLDQKEHRLDGRVI----DPKK 86
>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 = 89.5 bits (223), Expect = 1e-21
Identities = 31/162 (19%), Positives = 70/162 (43%), Gaps = 15/162 (9%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHKI 168
+ T++ LK+YF+ G + + +DK ++ + F+ + A A+ L +I
Sbjct: 8 LDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQI 66
Query: 169 GNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-- 226
N I + ++ + + + +FVG L ++ + LR F+ + + + +
Sbjct: 67 ENNIVKINWAFQSQQSSSDDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT 125
Query: 227 ---REFAFVTFELDSVAKSLI----GQHVNIKDKKVVVMEAT 261
R + FV+F A++ + GQ +N + + + A
Sbjct: 126 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLN--GRPLRINWAA 165
Score = 63.7 bits (156), Expect = 2e-12
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
A QS++S D++ +L V + D L+ F+ F + +V D TG S+G
Sbjct: 76 AFQSQQSSSDDTF-----NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 130
Query: 147 FGFIRFSSHESALKAM 162
+GF+ F+S + A AM
Sbjct: 131 YGFVSFTSQDDAQNAM 146
Score = 40.2 bits (95), Expect = 3e-04
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----REFAFVTFELDSVAKSLIGQ-- 246
++VG+L +TE L+++F+ G + ++ I +AFV + A +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 247 HVNIKDKKVVVMEATPKKKMN 267
I++ V + A ++ +
Sbjct: 63 GKQIENNIVKINWAFQSQQSS 83
>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 = 86.4 bits (215), Expect = 2e-21
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 2/84 (2%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ L + G+ TD DL + + +G + +DK T + KG+GF+ F S +A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 159 LKAM--LKKHKIGNRICDVRIPES 180
KA+ LK + ++ P S
Sbjct: 61 QKAVTALKASGVQAQMAKQSGPSS 84
Score = 47.1 bits (113), Expect = 2e-07
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSLI 244
S +++ L P T+ DL + + YG +V + + FV F+ S A+ +
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD-KTTNKCKGYGFVDFDSPSAAQKAV 64
>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 = 82.7 bits (205), Expect = 6e-20
Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G + + V GI + +++ +F ++G+++ + D+ TG SKG+GF+ F +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
Query: 159 LKAMLKKHKIGNRICDVR 176
K + + + +
Sbjct: 64 QKIVESQINFHGKKLKLG 81
Score = 74.6 bits (184), Expect = 6e-17
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFELDSVAKSLIG 245
+ VFVG + + E+++R F YG+V +V I + + FV+F D + ++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVS-KGYGFVSFYNDVDVQKIVE 68
Query: 246 QHVNIKDKKVVVMEATPKKKMNERQDN 272
+N KK+ + A K+ ++
Sbjct: 69 SQINFHGKKLKLGPAIRKQNLSTYHVQ 95
>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 = 82.4 bits (204), Expect = 1e-19
Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 8/94 (8%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S S + + + + + + L E +QFG L++ V + +T SKG F
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 150 IRFSSHESALKAM--------LKKHKIGNRICDV 175
+F + E+A K + K+ R V
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95
Score = 57.0 bits (138), Expect = 1e-10
Identities = 17/105 (16%), Positives = 38/105 (36%), Gaps = 15/105 (14%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVT 233
S+ + ++ VF+ +L+ D E L E + +G + V + + AF
Sbjct: 5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVL-HPDTEHSKGCAFAQ 63
Query: 234 FELDSVAKSLI--------GQHVNIKDKKVVVMEATPKKKMNERQ 270
F A+ + G + + +++ V A + +
Sbjct: 64 FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108
>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 = 80.5 bits (199), Expect = 1e-18
Identities = 22/83 (26%), Positives = 41/83 (49%)
Query: 80 DASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+G + R + + P N L V G+ T+ DL+E F ++G + ++ D+
Sbjct: 23 SMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ 82
Query: 140 NTGRSKGFGFIRFSSHESALKAM 162
+ RS+GF F+ F + + A +A
Sbjct: 83 QSRRSRGFAFVYFENVDDAKEAK 105
Score = 52.8 bits (127), Expect = 6e-09
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAKSLIG 245
+ V L+ TE DLRE F YG + DV I R FAFV FE AK
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 246 Q--HVNIKDKKVVVMEATPKK 264
+ + + +++ V + K+
Sbjct: 107 RANGMELDGRRIRVDFSITKR 127
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 80.7 bits (199), Expect = 1e-18
Identities = 20/100 (20%), Positives = 35/100 (35%), Gaps = 4/100 (4%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV--D 138
S + Y + + + V W TD L + G + +K +
Sbjct: 33 PSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN 92
Query: 139 KNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVR 176
+ G+SKG+ + +S S K + L + DVR
Sbjct: 93 RANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132
Score = 51.1 bits (122), Expect = 5e-08
Identities = 22/110 (20%), Positives = 38/110 (34%), Gaps = 13/110 (11%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGA--VVDVLIPKPFRE------FAFVTFE 235
+ V+VGS + T+ L + G VV++ + R +A V
Sbjct: 49 SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN-RANGQSKGYAEVVVA 107
Query: 236 LDSVAKSLIGQHVNIKD---KKVVVMEATPKKKMNERQDNRNNFDRRNDR 282
++ L+ + + K +KV V AT + R R R
Sbjct: 108 SENSVHKLL-ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRVPR 156
>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 = 79.3 bits (196), Expect = 1e-18
Identities = 24/82 (29%), Positives = 38/82 (46%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+ + QS + + +L + +P F D DL + F FG + A V +DK
Sbjct: 3 SGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62
Query: 141 TGRSKGFGFIRFSSHESALKAM 162
T SK FGF+ + + SA A+
Sbjct: 63 TNLSKCFGFVSYDNPVSAQAAI 84
Score = 48.5 bits (116), Expect = 2e-07
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 9/87 (10%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSV 239
E P + +F+ L + + DL + F +G VV + + F FV+++
Sbjct: 20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79
Query: 240 AKSLIGQHVN---IKDKKVVVMEATPK 263
A++ I Q +N I K++ V K
Sbjct: 80 AQAAI-QSMNGFQIGMKRLKVQLKRSK 105
>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 = 1e-18
Identities = 12/82 (14%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G + ++ + + LK+ ++G +E + + T + G + F+S A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 159 LKAM--LKKHKIGNRICDVRIP 178
+ + L + I ++
Sbjct: 62 KETVKNLHLTSVMGNIIHAQLD 83
Score = 54.7 bits (132), Expect = 9e-10
Identities = 15/97 (15%), Positives = 35/97 (36%), Gaps = 9/97 (9%)
Query: 187 EPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFELDSVAK 241
+ +V L ++ E+ L++ YG V +V I + A V F AK
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 242 SLIGQHVN---IKDKKVVVMEATPKKKMNERQDNRNN 275
+ ++++ + + ++ + + N
Sbjct: 63 ETV-KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVN 98
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 78.8 bits (195), Expect = 2e-18
Identities = 22/73 (30%), Positives = 39/73 (53%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S + + P N L V G+ T+ DL+E F ++G + ++ D+ + RS+GF F
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 150 IRFSSHESALKAM 162
+ F + + A +A
Sbjct: 62 VYFENVDDAKEAK 74
Score = 52.6 bits (127), Expect = 3e-09
Identities = 22/60 (36%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSLI 244
+ V L+ TE DLRE F YG + DV I ++ FAFV FE AK
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD-QQSRRSRGFAFVYFENVDDAKEAK 74
>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 = 78.5 bits (194), Expect = 3e-18
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 93 SYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
+ +G L+V + + +D D++E F +FGTL+ A V D+ +GRS G + F
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHF 77
Query: 153 SSHESALKAMLKKH--KIGNRICDVRIPES 180
ALKAM + + + R ++++ S
Sbjct: 78 ERKADALKAMKQYNGVPLDGRPMNIQLVTS 107
Score = 42.3 bits (100), Expect = 2e-05
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTFELDSVAK 241
K+ V +L ++++D++E F +G + + A V FE + A
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL 84
>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 = 78.2 bits (193), Expect = 7e-18
Identities = 24/79 (30%), Positives = 41/79 (51%)
Query: 84 NSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGR 143
Q N P +L+V IP T + L++ FE++G +E + D+ T +
Sbjct: 23 QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ 82
Query: 144 SKGFGFIRFSSHESALKAM 162
S+G+GF++F S SA +A+
Sbjct: 83 SRGYGFVKFQSGSSAQQAI 101
Score = 51.7 bits (124), Expect = 2e-08
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 14/106 (13%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELD 237
E V + V + + E LR+ FE YG + V I RE + FV F+
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD-RETRQSRGYGFVKFQSG 94
Query: 238 SVAKSLIGQHVN---IKDKKVVVMEATPKKKMNERQDNRNNFDRRN 280
S A+ I +N I +K++ V A +R N
Sbjct: 95 SSAQQAI-AGLNGFNILNKRLKVALAASGH---QRPGIAGAVGDGN 136
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 77.4 bits (191), Expect = 8e-18
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
+ +L + +P FTD DL F FG + A V +DK T SK FGF+ F + +SA A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 162 MLKKH--KIGNR 171
+ + ++G +
Sbjct: 99 IKAMNGFQVGTK 110
Score = 43.5 bits (103), Expect = 8e-06
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 15/87 (17%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE--------FAFVTFEL 236
E P +F+ L + T++DL F +G V+ K F + F FV+F+
Sbjct: 35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISA---KVFIDKQTSLSKCFGFVSFDN 91
Query: 237 DSVAKSLIGQHVN---IKDKKVVVMEA 260
A+ I + +N + K++ V
Sbjct: 92 PDSAQVAI-KAMNGFQVGTKRLKVQLK 117
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 76.6 bits (189), Expect = 8e-18
Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 4/95 (4%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S +SG T + V +P+T + +++ ++F + + + G G
Sbjct: 2 SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
Query: 150 IRFSSHESALKAMLKKHK--IGNRICDVRIPESTK 182
+ F S + A A++ + IG+R V++ +
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSR--KVKLSGPSS 94
Score = 40.7 bits (96), Expect = 5e-05
Identities = 14/91 (15%), Positives = 33/91 (36%), Gaps = 7/91 (7%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVD-VLIPKP----FREFAFV 232
S+ + +P + + V ++ ++ ++ + F Y + V + A V
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 233 TFELDSVAKSLIGQH--VNIKDKKVVVMEAT 261
FE A + + I +KV + +
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLSGPS 93
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 76.6 bits (189), Expect = 9e-18
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 1/80 (1%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE-LDSVAKSLIGQHVNI 250
VFV + + L E+F +G V V++ K FA V + + L ++
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSL 69
Query: 251 KDKKVVVMEATPKKKMNERQ 270
++ V K+ +
Sbjct: 70 GGHRLRVRPREQKEFQSPAS 89
Score = 73.1 bits (180), Expect = 1e-16
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 6/81 (7%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+SG + V G P L EYF FG + +V +DK+ G F +
Sbjct: 2 SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKGV---FAIVEMGDVG 56
Query: 157 SALKAM-LKKHKIGNRICDVR 176
+ + +H +G VR
Sbjct: 57 AREAVLSQSQHSLGGHRLRVR 77
>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 = 77.0 bits (190), Expect = 1e-17
Identities = 26/80 (32%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ K L + IP + DLK FE+FG + V D+ TG
Sbjct: 1 GSSGSSGMK--------DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTG 52
Query: 143 RSKGFGFIRFSSHESALKAM 162
KG F+ + ESALKA
Sbjct: 53 MHKGCAFLTYCERESALKAQ 72
Score = 63.5 bits (155), Expect = 7e-13
Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 10/96 (10%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-----PFREFAFVTF 234
S G ++ A K+F+G + +L E DL+ FE +G + ++ + K + AF+T+
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 235 ELDSVAKSLI----GQHV-NIKDKKVVVMEATPKKK 265
A Q ++ + V A + +
Sbjct: 63 CERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98
>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 = 76.6 bits (189), Expect = 1e-17
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 84 NSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGR 143
+ A + S L V + + T++ L+ FE FG +E + +D TGR
Sbjct: 9 SHMAAAMANNLQKGSAGPMR--LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR 66
Query: 144 SKGFGFIRFSSHESALKAM 162
SKG+GFI FS E A KA+
Sbjct: 67 SKGYGFITFSDSECAKKAL 85
Score = 53.8 bits (130), Expect = 2e-09
Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 11/96 (11%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAF 231
+ + +++VGSL ++TE LR FE +G + + + E + F
Sbjct: 14 AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD-SETGRSKGYGF 72
Query: 232 VTFELDSVAKSLIGQHVNIKD---KKVVVMEATPKK 264
+TF AK + + +N + + + V T +
Sbjct: 73 ITFSDSECAKKAL-EQLNGFELAGRPMKVGHVTERT 107
>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 = 76.1 bits (188), Expect = 2e-17
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
G+ + + L++ F ++G + V D+ T RS+GFGF+ F + + A AM +
Sbjct: 19 GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS 78
Query: 168 IGNRICDV 175
+ R V
Sbjct: 79 VDGRQIRV 86
Score = 57.3 bits (139), Expect = 8e-11
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 13/94 (13%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVT 233
S+ K+FVG L+ D E L + F YG + +V++ K RE F FVT
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD-RETQRSRGFGFVT 60
Query: 234 FELDSVAKSLI----GQHVNIKDKKVVVMEATPK 263
FE AK + G+ ++ +++ V +A
Sbjct: 61 FENIDDAKDAMMAMNGK--SVDGRQIRVDQAGKS 92
>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 = 75.7 bits (187), Expect = 2e-17
Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ L V + + T++ L+ FE FG ++ + D +TGRSKG+GFI FS E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 159 LKAM 162
+A+
Sbjct: 61 RRAL 64
Score = 55.3 bits (134), Expect = 3e-10
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 13/92 (14%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAK 241
+S ++VGSL ++TE LR FE +G + ++++ K + + F+TF A+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD-SDTGRSKGYGFITFSDSECAR 61
Query: 242 SLI----GQHVNIKDKKVVVMEATPKKKMNER 269
+ G + + + V T +
Sbjct: 62 RALEQLNGF--ELAGRPMRVGHVTERLDGGSG 91
>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 = 75.3 bits (186), Expect = 2e-17
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKV--DKNTGRSKGFGFIRFSSHESALKAM--LKK 165
+ W TD DL E G + +K ++ G+SKGF + S S+ K M L K
Sbjct: 8 NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67
Query: 166 HKIGNRICDV 175
++ + V
Sbjct: 68 RELHGQNPVV 77
Score = 49.9 bits (120), Expect = 3e-08
Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 13/90 (14%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGA--VVDVLIPKPFRE------FAFVTFELDSVAKSL 243
+++G+LT T+ DL E G ++++ + R FA V ++ +K L
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN-RANGQSKGFALVGVGSEASSKKL 61
Query: 244 IGQHVNIKD---KKVVVMEATPKKKMNERQ 270
+ + ++ + VV + + +
Sbjct: 62 M-DLLPKRELHGQNPVVTPSNKLEHHHHHH 90
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 75.3 bits (186), Expect = 3e-17
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ + + + V +P++ T+NDL F ++G + + DK+T
Sbjct: 1 GSSGSSGMSGGLAPSK-----STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR 55
Query: 143 RSKGFGFIRFSSHESALKAM 162
+SKG FI F +SA
Sbjct: 56 KSKGVAFILFLDKDSAQNCT 75
Score = 56.5 bits (137), Expect = 1e-10
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELD 237
G P S V+V +L LT +DL F YG VV V I K ++ AF+ F
Sbjct: 10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD-KDTRKSKGVAFILFLDK 68
Query: 238 SVAKSLI 244
A++
Sbjct: 69 DSAQNCT 75
>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 = 74.9 bits (185), Expect = 4e-17
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V + +T ++ DL++ F +G L + +D T + KGF F+ F E A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67
Score = 58.4 bits (142), Expect = 3e-11
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 11/90 (12%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFELDSVAKSLI 244
++FV +L+ +E DL + F YG + ++ P KP + FAFVTF A
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKP-KGFAFVTFMFPEHAVKAY 67
Query: 245 GQHVNIKD---KKVVVMEATPKKKMNERQD 271
V+ + + + V+ +T KK+ ++
Sbjct: 68 -AEVDGQVFQGRMLHVLPSTIKKEASQSGP 96
>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 = 75.0 bits (185), Expect = 4e-17
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S N N + V + + DL+E F FG++ + DK TG+SKGF F
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 150 IRFSSHESALKAM--LKKHKIGNRI 172
I F E A +A+ + + I
Sbjct: 62 ISFHRREDAARAIAGVSGFGYDHLI 86
Score = 54.2 bits (131), Expect = 1e-09
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 9/82 (10%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAKSLIG 245
+ + V +L+ D E+DL+E F +G++ + + K + FAF++F A I
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI- 74
Query: 246 QHVN---IKDKKVVVMEATPKK 264
V+ + V A P
Sbjct: 75 AGVSGFGYDHLILNVEWAKPST 96
>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 = 75.9 bits (187), Expect = 4e-17
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 92 RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
G L+V + + +D D++E F +FGTL+ A V D+ +GRS G +
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 82
Query: 152 FSSHESALKAM 162
F ALKAM
Sbjct: 83 FERRADALKAM 93
Score = 46.2 bits (110), Expect = 1e-06
Identities = 15/106 (14%), Positives = 39/106 (36%), Gaps = 9/106 (8%)
Query: 176 RIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAF 231
G +K+ V +L ++++D++E F +G + + A
Sbjct: 21 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD 80
Query: 232 VTFELDSVAKSLIGQ--HVNIKDKKVVVMEATPKKKMNERQDNRNN 275
V FE + A + Q V + + + + + + + + ++
Sbjct: 81 VHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI---DLEHHHHH 123
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 75.4 bits (186), Expect = 4e-17
Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 3/90 (3%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S + + V + + LKE F G + A++ DK+ G+S+G G
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGT 60
Query: 150 IRFSSHESALKAMLKKH--KIGNRICDVRI 177
+ F A++A+ + + +R V++
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKM 90
Score = 48.1 bits (115), Expect = 2e-07
Identities = 24/109 (22%), Positives = 34/109 (31%), Gaps = 12/109 (11%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----REFAFVTFELDSVAK 241
+ S VFV +L + L+E F G VV I + R VTFE A
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAV 70
Query: 242 SLIGQ--HVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMS 288
I + D+ + V + F + P S
Sbjct: 71 QAISMFNGQLLFDRPMHVKMDERA------LPKGDFFPPERPQQSGPSS 113
>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 = 76.8 bits (189), Expect = 5e-17
Identities = 21/83 (25%), Positives = 38/83 (45%)
Query: 80 DASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
DA+ + T+ + + T L V + + + + L+ FE++G + + D+
Sbjct: 47 DATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 106
Query: 140 NTGRSKGFGFIRFSSHESALKAM 162
T S+GF F+RF A AM
Sbjct: 107 YTKESRGFAFVRFHDKRDAEDAM 129
Score = 57.9 bits (140), Expect = 2e-10
Identities = 28/141 (19%), Positives = 49/141 (34%), Gaps = 22/141 (15%)
Query: 149 FIRFSSHESALKAMLKKHKIGNRICDVRIPESTKIGTEEPVA------------SKVFVG 196
+ ++ E K + + ++TK T + + + V
Sbjct: 20 AVDAATAEKVFKQYANDNGVDGE---WTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVD 76
Query: 197 SLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAKSLIGQ--HVN 249
+LT + LR FE YG V DV IP+ R FAFV F A+ +
Sbjct: 77 NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV 136
Query: 250 IKDKKVVVMEATPKKKMNERQ 270
+ +++ V A + +
Sbjct: 137 LDGRELRVQMARYGRPPDSHH 157
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 75.5 bits (186), Expect = 6e-17
Identities = 20/81 (24%), Positives = 32/81 (39%)
Query: 82 SGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNT 141
G S T L V + + + + L+ FE++G + + D+ T
Sbjct: 26 GGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 85
Query: 142 GRSKGFGFIRFSSHESALKAM 162
S+GF F+RF A AM
Sbjct: 86 KESRGFAFVRFHDKRDAEDAM 106
Score = 55.5 bits (134), Expect = 7e-10
Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 7/87 (8%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVA 240
+ + + V +LT + LR FE YG V DV IP+ R FAFV F A
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 241 KSLIGQ--HVNIKDKKVVVMEATPKKK 265
+ + + +++ V A +
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRP 129
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 74.3 bits (183), Expect = 7e-17
Identities = 12/59 (20%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV--DKNTGRSKGFGFIRFSSHESALKAM 162
+++ I + + + +L N+++ DK T +++GF F++ SS A + +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Score = 50.0 bits (120), Expect = 2e-08
Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 13/83 (15%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGA--VVDVLIPK-PF----REFAFVTFELDSVAKSL 243
+ + ++ P + Y + V ++ + K R FAFV A L
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 244 I----GQHV--NIKDKKVVVMEA 260
+ H I K + V A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
>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 = 77.8 bits (191), Expect = 7e-17
Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 4/100 (4%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV--D 138
+ + + + L + + W TD DL E G + +K +
Sbjct: 46 PTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN 105
Query: 139 KNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVR 176
+ G+SKGF + S S+ K M L K ++ + V
Sbjct: 106 RANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT 145
Score = 56.6 bits (136), Expect = 1e-09
Identities = 23/162 (14%), Positives = 49/162 (30%), Gaps = 15/162 (9%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGA--VVDVLIPK-----PFREFA 230
+ T +++G+LT T+ DL E G ++++ + + FA
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115
Query: 231 FVTFELDSVAKSLI----GQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSP 286
V ++ +K L+ + ++ + VV + +R
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELH--GQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG- 172
Query: 287 MSNSRQYGGGNGYYDNRQQQQGGYNNKRRRNDYDDWHHGNGG 328
G + + +G + D G GG
Sbjct: 173 -KAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGG 213
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 74.1 bits (183), Expect = 7e-17
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+SG + V +P+ FT LK+ F + G + +A + G+SKG G ++F S E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYA--DIKMENGKSKGCGVVKFESPE 59
Query: 157 SALKA--MLKKHKIGNRICDVRI 177
A +A M+ K+ R DVRI
Sbjct: 60 VAERACRMMNGMKLSGREIDVRI 82
Score = 47.6 bits (114), Expect = 2e-07
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 7/82 (8%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF---REFAFVTFELDSVAKSLIGQ 246
A ++FV +L D T L++ F G V+ I + V FE VA+ +
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERAC-R 66
Query: 247 HVN---IKDKKVVVMEATPKKK 265
+N + +++ V
Sbjct: 67 MMNGMKLSGREIDVRIDRNASG 88
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 74.2 bits (183), Expect = 8e-17
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 89 QSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
S D GP ++ + L V G+ T+ D+ + F ++G ++ ++ +D+ TG K
Sbjct: 6 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 146 GFGFIRFSSHESALKAM--LKKHKIGNRICDV 175
G+ + + +++ A AM L + + V
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
Score = 50.3 bits (121), Expect = 2e-08
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 13/84 (15%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSLI 244
+FV + + TE D+ + F YG + ++ + R + V +E A++ +
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAAM 82
Query: 245 ----GQHVNIKDKKVVVMEATPKK 264
GQ ++ + + V +
Sbjct: 83 EGLNGQ--DLMGQPISVDWCFVRG 104
>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 = 74.3 bits (183), Expect = 8e-17
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 93 SYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
S +SG T + V +P+T + +++ ++F + + + G G + F
Sbjct: 5 SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64
Query: 153 SSHESALKAMLKKHK--IGNR 171
S + A A++ + IG+R
Sbjct: 65 ESRDEATAAVIDLNDRPIGSR 85
Score = 41.9 bits (99), Expect = 2e-05
Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 7/93 (7%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVD-VLIPKP----FREFAFV 232
S+ + +P + + V ++ ++ ++ + F Y + V + A V
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 233 TFELDSVAKSLIGQH--VNIKDKKVVVMEATPK 263
FE A + + I +KV ++ +
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95
>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 = 74.2 bits (183), Expect = 8e-17
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ S+ + L V + ++ D+ F+ FG ++ V + G
Sbjct: 1 GSSGSSGSESRGGRD------RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-G 53
Query: 143 RSKGFGFIRFSSHESALKAMLKKH 166
SKG F++FSSH A A+ H
Sbjct: 54 SSKGCAFVKFSSHTEAQAAIHALH 77
Score = 55.4 bits (134), Expect = 4e-10
Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 12/98 (12%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----REFAFVTFELDSVA 240
+ K+FVG L +E D+ F+ +G + + + + + AFV F + A
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEA 69
Query: 241 KSLI----GQHV-NIKDKKVVVMEATPKKKMNERQDNR 273
++ I G +VV A K E +
Sbjct: 70 QAAIHALHGSQTMPGASSSLVVKFADTDK---ESGPSS 104
>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 = 73.0 bits (180), Expect = 2e-16
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
IP+ T+ + + G + + D TGRSKG+ FI F ES+ A+ L ++
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 168 IGNR 171
+G+R
Sbjct: 69 LGSR 72
Score = 58.8 bits (143), Expect = 2e-11
Identities = 12/96 (12%), Positives = 38/96 (39%), Gaps = 11/96 (11%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFELDSVAKSL 243
+ V++GS+ D TE + + G V+++ + + + +AF+ F + S
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRS-KGYAFIEFRDLESSASA 60
Query: 244 IGQ--HVNIKDKKVVVMEATPKKK--MNERQDNRNN 275
+ + + + ++ ++ + ++
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96
>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 = 73.8 bits (182), Expect = 2e-16
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
T+L + +P + + +L+ + FG + + D +G S+G GF R S E
Sbjct: 24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAV 82
Query: 162 M 162
+
Sbjct: 83 I 83
Score = 44.9 bits (107), Expect = 3e-06
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 8/85 (9%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----REFAFVTFELDSVAK 241
+E + +++ +L + E +L + +G V+ I + R F E +
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 80
Query: 242 SLIGQHVN---IKDKKVVVMEATPK 263
++I H N IK V P
Sbjct: 81 AVI-GHFNGKFIKTPPGVSAPTEPL 104
>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 = 73.1 bits (180), Expect = 2e-16
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG---RSKGFGFIRFSSH 155
G ++ L + + ++ T+ LK F + G ++ + KN S GFGF+ +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 156 ESALKAM 162
E A KA+
Sbjct: 61 EQAQKAL 67
Score = 50.3 bits (121), Expect = 2e-08
Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 10/85 (11%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK--------PFREFAFVTFELDSVAKS 242
S +F+ +L TE L+ F GA+ I K F FV ++ A+
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 243 LIG--QHVNIKDKKVVVMEATPKKK 265
+ Q + K+ V + K
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATK 90
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 75.3 bits (185), Expect = 2e-16
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 91 KRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFI 150
G L+V + + +D D++E F +FGTL+ A V D+ +GRS G +
Sbjct: 76 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 134
Query: 151 RFSSHESALKAM 162
F ALKAM
Sbjct: 135 HFERRADALKAM 146
Score = 44.8 bits (106), Expect = 7e-06
Identities = 15/103 (14%), Positives = 37/103 (35%), Gaps = 6/103 (5%)
Query: 176 RIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAF 231
G +K+ V +L ++++D++E F +G + + A
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD 133
Query: 232 VTFELDSVAKSLIGQH--VNIKDKKVVVMEATPKKKMNERQDN 272
V FE + A + Q+ V + + + + + + +
Sbjct: 134 VHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 176
>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 = 72.1 bits (178), Expect = 3e-16
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ D L+ F+ F + +V D TG S+G+GF+ F+S + A AM
Sbjct: 8 DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Score = 49.4 bits (119), Expect = 3e-08
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 13/82 (15%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSLI- 244
+FVG L ++ + LR F+ + + + + + + FV+F A++ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW-DMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 245 ---GQHVNIKDKKVVVMEATPK 263
GQ +N + + + A
Sbjct: 62 SMQGQDLN--GRPLRINWAAKL 81
>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 = 4e-16
Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S ++ + + + G+P+ + ++ ++F + GRS G F
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 150 IRFSSHESALKAMLK-KHKIGNRICDVRIPESTK 182
++F+S E A KA+ K K +IG+R + I +S++
Sbjct: 62 VQFASQEIAEKALKKHKERIGHRY--IEIFKSSR 93
Score = 37.8 bits (88), Expect = 7e-04
Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 6/77 (7%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVD-VLIPKP----FREFAFVTFE-LDSVAKSLIGQ 246
V + L ++ ++ + F V + + +P AFV F + K+L
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 247 HVNIKDKKVVVMEATPK 263
I + + + +++
Sbjct: 78 KERIGHRYIEIFKSSRA 94
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 72.4 bits (178), Expect = 4e-16
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
SS + S+ + Q L V IP+ F D DL++ F QFG + + ++ S
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGS 68
Query: 145 KGFGFIRFSSHESALKAM 162
KGFGF+ F + A +A
Sbjct: 69 KGFGFVTFENSADADRAR 86
Score = 55.0 bits (133), Expect = 6e-10
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 10/96 (10%)
Query: 176 RIPESTKIGTEEPVAS-KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK---PFREFAF 231
+P + + TE ++ V ++ + DLR+ F +G ++DV I + F F
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGF 73
Query: 232 VTFELDSVAKSLI----GQHVNIKDKKVVVMEATPK 263
VTFE + A G V +K+ V AT +
Sbjct: 74 VTFENSADADRAREKLHGTVVE--GRKIEVNNATAR 107
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 72.3 bits (178), Expect = 5e-16
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK-NTGRSKGFG 148
S S + ++V IP+ +++E F FG L+ + TG +GFG
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 149 FIRFSSHESALKAM 162
F+ F + + A KA
Sbjct: 62 FVDFITKQDAKKAF 75
Score = 60.4 bits (147), Expect = 9e-12
Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 9/99 (9%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVT 233
S+ ++ SK+ V ++ + ++RE F +G + V +PK F FV
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 234 FELDSVAKSLIGQHVNIKD---KKVVVMEATPKKKMNER 269
F AK + +++V+ A + +
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 71.9 bits (177), Expect = 5e-16
Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 3/93 (3%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
+ S ++ L + G+P++ T +L+E + GT++ + ++ G+ KG
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59
Query: 147 FGFIRFSSHESALKAM--LKKHKIGNRICDVRI 177
++ + + A +A+ + I I V I
Sbjct: 60 LAYVEYENESQASQAVMKMDGMTIKENIIKVAI 92
Score = 57.3 bits (139), Expect = 8e-11
Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 6/87 (6%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----PFREFAFVTFELDSVA 240
+ K+F+ L T+ +L E + +G V D+ + + A+V +E +S A
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQA 71
Query: 241 KSLIGQ--HVNIKDKKVVVMEATPKKK 265
+ + + IK+ + V +
Sbjct: 72 SQAVMKMDGMTIKENIIKVAISNSGPS 98
>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 = 72.6 bits (178), Expect = 5e-16
Identities = 22/104 (21%), Positives = 49/104 (47%), Gaps = 4/104 (3%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLV-VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+SG+S + S + + P + V + G+P+ + + ++F++ +E +
Sbjct: 2 SSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61
Query: 140 NTGRSKGFGFIRFSSHESALKAMLK-KHKIGNRICDVRIPESTK 182
G++ G GF+ F + A+ + K +GNR +++ TK
Sbjct: 62 PNGKATGEGFVEFRNEADYKAALCRHKQYMGNRF--IQVHPITK 103
Score = 40.6 bits (95), Expect = 1e-04
Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 6/88 (6%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVD-VLIPKP----FREFAFVTFE-LDSVAKSLIGQ 246
V++ L + + + F+ V D + I FV F +L
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 247 HVNIKDKKVVVMEATPKKKMNERQDNRN 274
+ ++ + V T K + + R
Sbjct: 88 KQYMGNRFIQVHPITKKGMLEKIDMIRK 115
>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 = 72.6 bits (178), Expect = 6e-16
Identities = 20/102 (19%), Positives = 47/102 (46%), Gaps = 3/102 (2%)
Query: 82 SGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNT 141
+ + Q +++ + + + G+P+ T ++ ++F +
Sbjct: 21 MASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPE 80
Query: 142 GRSKGFGFIRFSSHESALKAMLK-KHKIGNRICDVRIPESTK 182
G+ G F++F+S E A KA+ K K +IG+R + + +S++
Sbjct: 81 GKITGEAFVQFASQELAEKALGKHKERIGHRY--IEVFKSSQ 120
Score = 35.6 bits (82), Expect = 0.006
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAV-VDVLIPKP----FREFAFVTFE-LDS 238
+ V + L T+ ++ + F V + +P AFV F +
Sbjct: 37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQEL 96
Query: 239 VAKSLIGQHVNIKDKKVVVMEATPK 263
K+L I + + V +++ +
Sbjct: 97 AEKALGKHKERIGHRYIEVFKSSQE 121
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 72.3 bits (178), Expect = 6e-16
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 1/83 (1%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQ-NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+SG+S K + P + N L + + T+ DL F +F + ++
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61
Query: 140 NTGRSKGFGFIRFSSHESALKAM 162
TGR +G FI F + E A +A+
Sbjct: 62 MTGRMRGQAFITFPNKEIAWQAL 84
Score = 55.0 bits (133), Expect = 7e-10
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 10/97 (10%)
Query: 176 RIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE-----FA 230
+IP + EP +++ +L+P +TE DL F + I A
Sbjct: 12 KIPMFSSYNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70
Query: 231 FVTFELDSVAKSLIGQHVN---IKDKKVVVMEATPKK 264
F+TF +A + VN + K +V+ KK
Sbjct: 71 FITFPNKEIAWQAL-HLVNGYKLYGKILVIEFGKNKK 106
>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 = 71.6 bits (176), Expect = 9e-16
Identities = 22/100 (22%), Positives = 48/100 (48%), Gaps = 5/100 (5%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV 137
A + +++ GP ++ + L V I +++++E F +G ++ ++ +
Sbjct: 1 AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60
Query: 138 DKNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDV 175
D+ TG SKG+ + + +H+ AL A L +I + V
Sbjct: 61 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
Score = 49.2 bits (118), Expect = 8e-08
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 13/85 (15%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSL 243
+FV S+ + E +++E F YG + ++ + R +A V +E A +
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD-RRTGFSKGYALVEYETHKQALAA 84
Query: 244 I----GQHVNIKDKKVVVMEATPKK 264
G I + + V K
Sbjct: 85 KEALNGA--EIMGQTIQVDWCFVKG 107
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 71.1 bits (175), Expect = 1e-15
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
IP+ T+ LK+ F + G + + D+ TG+ KG+GF + E+AL AM L +
Sbjct: 15 NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74
Query: 168 IGNR 171
R
Sbjct: 75 FSGR 78
Score = 53.8 bits (130), Expect = 1e-09
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 187 EPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFELDSVA 240
+ VFVG++ + TE L++ F G VV + KP + + F ++ A
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP-KGYGFCEYQDQETA 63
Query: 241 KSLIG--QHVNIKDKKVVVMEATPKKKMNERQDNRNN 275
S + + + V A +K E +
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100
>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 = 71.1 bits (175), Expect = 1e-15
Identities = 24/113 (21%), Positives = 49/113 (43%), Gaps = 9/113 (7%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
GP+ + ++ + + + + L + F FG + V D SKG+GF+ F + E+A
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAA 58
Query: 159 LKAM--LKKHKIGNRICDV-----RIPESTKIGTEEPVASKVFVGSLTPDLTE 204
+A+ + + +R V R ++G + V++ + P T
Sbjct: 59 ERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111
Score = 53.4 bits (129), Expect = 2e-09
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 8/94 (8%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI---PKPFREFAFVTFELDSVAKSLIGQ 246
+ +F+ +L + L + F +G ++ + + + FV FE A+ I +
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI-E 63
Query: 247 HVN---IKDKKVVVMEATPKK-KMNERQDNRNNF 276
+N + D+KV V +K + E F
Sbjct: 64 KMNGMLLNDRKVFVGRFKSRKEREAELGARAKEF 97
>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 = 70.7 bits (174), Expect = 2e-15
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S PD G L V + + + + L+ FE++G + + + +T +GF F
Sbjct: 3 SGSSGPDVDGM---ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 150 IRFSSHESALKAM 162
+RF A A
Sbjct: 60 VRFHDRRDAQDAE 72
Score = 58.8 bits (143), Expect = 3e-11
Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 7/86 (8%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTFELDSVAKSLIG 245
+ V +LT + LR FE YG V DV IP+ R FAFV F A+
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 246 Q--HVNIKDKKVVVMEATPKKKMNER 269
+ +++ V A ++
Sbjct: 74 AMDGAELDGRELRVQVARYGRRDLSG 99
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 71.7 bits (176), Expect = 2e-15
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 2/84 (2%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVD 138
+ SG T L V G+ D L F FG + + +D
Sbjct: 39 VNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98
Query: 139 KNTGRSKGFGFIRFSSHESALKAM 162
T + +GF F+ F E A A+
Sbjct: 99 YETEKHRGFAFVEFELAEDAAAAI 122
Score = 58.3 bits (141), Expect = 8e-11
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAF 231
S G ++VG L ++ + L F +G + D+ IP E FAF
Sbjct: 51 GGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD-YETEKHRGFAF 109
Query: 232 VTFELDSVAKSLI 244
V FEL A + I
Sbjct: 110 VEFELAEDAAAAI 122
>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 = 70.3 bits (173), Expect = 2e-15
Identities = 15/53 (28%), Positives = 23/53 (43%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 19 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Score = 59.5 bits (145), Expect = 2e-11
Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 13/100 (13%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVT 233
S+ ++VG L ++ + L F +G + D+ IP E FAFV
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD-YETEKHRGFAFVE 60
Query: 234 FELDSVAKSLI----GQHVNIKDKKVVVMEATPKKKMNER 269
FEL A + I + + + V A P +
Sbjct: 61 FELAEDAAAAIDNMNES--ELFGRTIRVNLAKPMRIKESG 98
>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 = 70.4 bits (173), Expect = 3e-15
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
G+ + LK F + G + + D+ T +S+GF FI F + A A +
Sbjct: 14 GLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKS 72
Query: 168 IGNRICDV 175
+ + V
Sbjct: 73 LHGKAIKV 80
Score = 66.2 bits (162), Expect = 8e-14
Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 12/115 (10%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----PFREFAFVTFELDSVAK 241
E K+F+G L + E L+ F +G + +VL+ K R FAF+TFE + AK
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 242 SLIGQHVNIKD---KKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQY 293
+ + +N K K + V +A Q + R+RSP + +
Sbjct: 63 NAA-KDMNGKSLHGKAIKVEQAKKP----SFQSGGRRRPPASSRNRSPSGSLEHH 112
>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 = 70.5 bits (173), Expect = 3e-15
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 89 QSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
S D GP ++ + L V G+ T+ D+ + F ++G ++ ++ +D+ TG K
Sbjct: 5 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 146 GFGFIRFSSHESALKAM--LKKHKIGNRICDV 175
G+ + + +++ A AM L + + V
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
Score = 58.2 bits (141), Expect = 8e-11
Identities = 19/105 (18%), Positives = 40/105 (38%), Gaps = 13/105 (12%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAKSLI 244
+FV + + TE D+ + F YG + ++ + R + V +E A++ +
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAAM 81
Query: 245 ----GQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRS 285
GQ ++ + + V + ++ R DR R
Sbjct: 82 EGLNGQ--DLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR 124
>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 = 70.0 bits (172), Expect = 3e-15
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 108 VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LKKH 166
+ + DL+++F G + + D+N+ RSKG ++ F +S A+ L
Sbjct: 30 CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQ 89
Query: 167 KIGNRICDV 175
++ V
Sbjct: 90 RLLGVPIIV 98
Score = 60.4 bits (147), Expect = 8e-12
Identities = 21/98 (21%), Positives = 32/98 (32%), Gaps = 6/98 (6%)
Query: 181 TKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-----PFREFAFVTFE 235
+ EE A VF L + DL + F G V DV I + A+V F
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 236 LDSVAKSLIGQH-VNIKDKKVVVMEATPKKKMNERQDN 272
IG + ++V + +K +
Sbjct: 76 EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSS 113
>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 = 70.1 bits (172), Expect = 3e-15
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ K+ ++ + V + T D+K F FG + A V D TG
Sbjct: 1 GSSGSSGQKKDTSNH------FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG 54
Query: 143 RSKGFGFIRFSSHESALKAM 162
+SKG+GF+ F + A A+
Sbjct: 55 KSKGYGFVSFFNKWDAENAI 74
Score = 53.9 bits (130), Expect = 2e-09
Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 13/107 (12%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-----PFREFAFV 232
K T VFVG L+P++T D++ F +G + D + K + + FV
Sbjct: 5 SSGQKKDTSNHF--HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 233 TFELDSVAKSLI----GQHVNIKDKKVVVMEATPKKKMNERQDNRNN 275
+F A++ I GQ + +++ AT K + N
Sbjct: 63 SFFNKWDAENAIQQMGGQ--WLGGRQIRTNWATRKPPAPKSTYESNT 107
>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 = 71.4 bits (175), Expect = 4e-15
Identities = 19/86 (22%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 80 DASGNSSATQSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVK 136
+A + +++ GP ++ + L V I +++++E F +G ++ ++
Sbjct: 46 EAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLN 105
Query: 137 VDKNTGRSKGFGFIRFSSHESALKAM 162
+D+ TG SKG+ + + +H+ AL A
Sbjct: 106 LDRRTGFSKGYALVEYETHKQALAAK 131
Score = 52.1 bits (125), Expect = 2e-08
Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 14/98 (14%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFELDSVAKSLI 244
+FV S+ + E +++E F YG + ++ + + +A V +E A +
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS-KGYALVEYETHKQALAAK 131
Query: 245 GQHVN---IKDKKVVVMEATPKKKMNERQDNRNNFDRR 279
+ +N I + + V K ++ ++ RR
Sbjct: 132 -EALNGAEIMGQTIQVDWCFVKG---PKRVKKSEKRRR 165
>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 = 69.1 bits (170), Expect = 4e-15
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
+ T + F FG + A V D TG+SKG+GF+ F + A A+ +
Sbjct: 13 DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72
Query: 168 IGNRICDVRIPESTK 182
+G R R +T+
Sbjct: 73 LGGRQI--RTNWATR 85
Score = 50.2 bits (121), Expect = 2e-08
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-PF----REFAFVTFELDSVAKSLIGQ 246
VFVG L+P++T + + F +G + D + K + + FV+F A++ I Q
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 247 --HVNIKDKKVVVMEATPK 263
+ +++ AT K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 69.6 bits (171), Expect = 4e-15
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S ++ L V IP+ F D DL++ F QFG + +V++ N SKGFGF
Sbjct: 2 SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGF 59
Query: 150 IRFSSHESALKAM 162
+ F + A +A
Sbjct: 60 VTFENSADADRAR 72
Score = 55.8 bits (135), Expect = 3e-10
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 7/96 (7%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE----FAFVTFE 235
S+ + ++ V ++ + DLR+ F +G ++DV I F FVTFE
Sbjct: 5 SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFE 63
Query: 236 LDSVAKSLIGQ--HVNIKDKKVVVMEATPKKKMNER 269
+ A + ++ +K+ V AT + N
Sbjct: 64 NSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99
>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 = 68.7 bits (169), Expect = 4e-15
Identities = 15/53 (28%), Positives = 23/53 (43%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 14 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Score = 58.7 bits (143), Expect = 2e-11
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELD 237
G+ ++VG L ++ + L F +G + D+ IP E FAFV FEL
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD-YETEKHRGFAFVEFELA 59
Query: 238 SVAKSLI 244
A + I
Sbjct: 60 EDAAAAI 66
>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 = 69.6 bits (171), Expect = 4e-15
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LKKHKI 168
+ + +LK + V VD TG ++ FG++ F S E KA+ L K+
Sbjct: 24 NLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALELTGLKV 82
Query: 169 GNRICDVRIPES 180
+ P+
Sbjct: 83 FGNEIKLEKPKG 94
Score = 53.0 bits (128), Expect = 3e-09
Identities = 17/92 (18%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 179 ESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTF 234
E G+E +F+G+L P+ + ++L+ A D+ + R+F +V F
Sbjct: 6 EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 65
Query: 235 E-LDSVAKSLIGQHVNIKDKKVVVMEATPKKK 265
E + + K+L + + ++ + + +
Sbjct: 66 ESAEDLEKALELTGLKVFGNEIKLEKPKGRDG 97
>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 = 69.4 bits (170), Expect = 6e-15
Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 4/103 (3%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S + + + IP++ T D+ ++ E E A + N G+ G
Sbjct: 3 SGSSGEGDVNSAKVC-AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61
Query: 150 IRFSSHESALKAMLK-KHKIGNRICDVRIPESTKIGTEEPVAS 191
++F + + A K+ + K+ R + + T E +
Sbjct: 62 VQFKNEDDARKSERLHRKKLNGR--EAFVHVVTLEDMREIEKN 102
Score = 44.0 bits (104), Expect = 5e-06
Identities = 16/114 (14%), Positives = 35/114 (30%), Gaps = 10/114 (8%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVD-VLIPKP----FREFAFV 232
S+ G + ++ +T+ D+ + E + V + A V
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62
Query: 233 TFE-LDSVAKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRS 285
F+ D KS + ++ V T + + ++ N + S
Sbjct: 63 QFKNEDDARKSERLHRKKLNGREAFVHVVTLE----DMREIEKNPPAQGKSGPS 112
>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 = 68.4 bits (168), Expect = 8e-15
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 9/82 (10%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+SG+S ++ + + V + + L E F Q G L + D+
Sbjct: 2 SSGSSGMFPAQEE--------ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR- 52
Query: 141 TGRSKGFGFIRFSSHESALKAM 162
G+ K FGF+ F ES A+
Sbjct: 53 EGKPKSFGFVCFKHPESVSYAI 74
Score = 49.9 bits (120), Expect = 3e-08
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----PFREFAFVT 233
S +E VFVG+L + E L E F G + V I K + F FV
Sbjct: 4 GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVC 63
Query: 234 FE 235
F+
Sbjct: 64 FK 65
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--L 163
L+ + + T+++LKE FE +++ G+SKG +I F S A K +
Sbjct: 19 LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 164 KKHKIGNRICDV 175
+ +I R +
Sbjct: 74 QGAEIDGRSVSL 85
Score = 50.3 bits (121), Expect = 2e-08
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 2/91 (2%)
Query: 179 ESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDS 238
E + A + +L+ ++TE +L+E FE + V + A++ F+ ++
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64
Query: 239 VAKSLIG--QHVNIKDKKVVVMEATPKKKMN 267
A+ + Q I + V + K
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 67.7 bits (166), Expect = 2e-14
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S T LV+ + ++ T+ L+E FE+ ++ G+SKG+ F
Sbjct: 3 SGSSGNSTWSGESKT-LVLSNLSYSATEETLQEVFEKATFIKV----PQNQNGKSKGYAF 57
Query: 150 IRFSSHESALKAM--LKKHKIGNR 171
I F+S E A +A+ K +I R
Sbjct: 58 IEFASFEDAKEALNSCNKREIEGR 81
Score = 49.2 bits (118), Expect = 6e-08
Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 9/91 (9%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF----REFAFVTFELDSVA 240
T + + + +L+ TE L+E FE + +P+ + +AF+ F A
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDA 66
Query: 241 KSLIGQ--HVNIKDKKVVVMEATPKKKMNER 269
K + I+ + + + P+ N
Sbjct: 67 KEALNSCNKREIEGRAIRLELQGPRGSPNSG 97
>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 = 67.2 bits (165), Expect = 2e-14
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ + T +L+ +F G++ + DK +G KGF +I FS ES ++
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Score = 53.7 bits (130), Expect = 1e-09
Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 12/84 (14%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFELDSVAKSL 243
A ++VG++ T +L HF G+V V I P + FA++ F ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP-KGFAYIEFSDKESVRTS 64
Query: 244 I---GQHVNIKDKKVVVMEATPKK 264
+ + +++ V+ +
Sbjct: 65 LALDES--LFRGRQIKVIPKRTNR 86
>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 = 67.2 bits (165), Expect = 2e-14
Identities = 13/60 (21%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN-TGRSKGFGFIRFSSHESALKAM 162
T + + + T + + E F +G ++ ++ V++ SKG+ ++ F + + A KA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Score = 60.2 bits (147), Expect = 5e-12
Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 10/86 (11%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK------PFREFAFVTFELDSVAK 241
+KV +G LT ++T+ + E F YG + + +P + +A+V FE A+
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 242 SLIGQHVN---IKDKKVVVMEATPKK 264
+ +H++ I +++
Sbjct: 62 KAL-KHMDGGQIDGQEITATAVLAPW 86
>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 = 66.9 bits (164), Expect = 3e-14
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S + P + L V G T L+ F FG + +D + + F
Sbjct: 2 SSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAF 53
Query: 150 IRFSSHESALKAMLKKHKIGNRICDVRI 177
+ + ESA +A+ + + G ++ V++
Sbjct: 54 VTYEKMESADQAVAELN--GTQVESVQL 79
Score = 55.4 bits (134), Expect = 3e-10
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN--- 249
++V D+T + LR F +G ++D+ + P R AFVT+E A + +N
Sbjct: 18 LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-RNCAFVTYEKMESADQAV-AELNGTQ 73
Query: 250 IKDKKVVVMEATPKKKMNE 268
++ ++ V A + ++
Sbjct: 74 VESVQLKVNIARKQPMLDS 92
>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 = 67.5 bits (165), Expect = 3e-14
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
+ + S+P+ P + L V G T L+ F FG + ++ +D
Sbjct: 19 SHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNII--DLSMDPP-- 72
Query: 143 RSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRI 177
+ F+ + ESA +A+ + + G ++ V++
Sbjct: 73 --RNCAFVTYEKMESADQAVAELN--GTQVESVQL 103
Score = 58.2 bits (141), Expect = 7e-11
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN--- 249
++V D+T + LR F +G ++D+ + P R AFVT+E A + +N
Sbjct: 42 LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-RNCAFVTYEKMESADQAV-AELNGTQ 97
Query: 250 IKDKKVVVMEATPKKKMNERQDN 272
++ ++ V A + ++
Sbjct: 98 VESVQLKVNIARKQPMLDAATGK 120
>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 = 66.5 bits (163), Expect = 5e-14
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ + + Q +L V + D L++ F FGT+ A V ++ G
Sbjct: 1 GSSGSSGDRITRY------QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GG 52
Query: 143 RSKGFGFIRFSSHESALKAM 162
RSKGFGF+ FSS E A KA+
Sbjct: 53 RSKGFGFVCFSSPEEATKAV 72
Score = 46.4 bits (111), Expect = 7e-07
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 15/88 (17%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSV 239
++V +L + + LR+ F +G + K E F FV F
Sbjct: 11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSA---KVMMEGGRSKGFGFVCFSSPEE 67
Query: 240 AKSLI----GQHVNIKDKKVVVMEATPK 263
A + G+ V K + V A K
Sbjct: 68 ATKAVTEMNGRIVA--TKPLYVALAQRK 93
>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 = 67.1 bits (164), Expect = 6e-14
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ + T DL+ +F G++ + DK +G KG+ +I F+ S A+
Sbjct: 43 NVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Score = 52.8 bits (127), Expect = 6e-09
Identities = 15/93 (16%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 179 ESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFV 232
+ +E V+VG++ T DL HF G++ + I P + +A++
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHP-KGYAYI 83
Query: 233 TFELDSVAKSLIGQH-VNIKDKKVVVMEATPKK 264
F + + + + + + V+
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLPKRTNM 116
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 66.2 bits (162), Expect = 6e-14
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 10/88 (11%)
Query: 88 TQSKRSYPD--NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
+ ++ S P + T + IP T+ DL F+ FG + + K K
Sbjct: 10 QVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFIL--DFKH----YPEK 63
Query: 146 GFGFIRFSSHESALKAM--LKKHKIGNR 171
G FI++ +HE A + L R
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPFQGR 91
Score = 57.7 bits (140), Expect = 6e-11
Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQH 247
P + ++G++ TE+DL F+ +G ++D + F+ ++ A I
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-KGCCFIKYDTHEQAAVCI-VA 82
Query: 248 VN---IKDKKVVVMEATPK 263
+ + + + +
Sbjct: 83 LANFPFQGRNLRTGWGKER 101
>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 = 67.2 bits (164), Expect = 7e-14
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 80 DASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+G + + + G+P+ T+ND+ +F + V ++
Sbjct: 23 SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV---RVHIEI 79
Query: 140 NT-GRSKGFGFIRFSSHESALKAMLK-KHKIGNR 171
GR G + F++HE A+ AM K + + +R
Sbjct: 80 GPDGRVTGEADVEFATHEEAVAAMSKDRANMQHR 113
Score = 37.1 bits (86), Expect = 0.002
Identities = 16/103 (15%), Positives = 33/103 (32%), Gaps = 6/103 (5%)
Query: 176 RIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAF 231
R ++ + V + L TE+D+ F V V I A
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEAD 90
Query: 232 VTFELDSVAKSLIGQH-VNIKDKKVVVMEATPKKKMNERQDNR 273
V F A + + + N++ + + + + N ++
Sbjct: 91 VEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSSQ 133
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 65.7 bits (161), Expect = 8e-14
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HV 248
S++FVG+L PD+TE ++R+ FE YG +V I K + F F+ E ++A+ + ++
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNM 74
Query: 249 NIKDKKVVVMEATPKKKMNERQD 271
++ K++ V A +
Sbjct: 75 PLRGKQLRVRFACHSASLTSGPS 97
Score = 63.0 bits (154), Expect = 8e-13
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S Q + L V +P T+ ++++ FE++G + + KGFGF
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGF 55
Query: 150 IRFSSHESALKAM 162
IR + A A
Sbjct: 56 IRLETRTLAEIAK 68
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 66.5 bits (162), Expect = 8e-14
Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 4/98 (4%)
Query: 82 SGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV---D 138
S SS + + + G+P+T T ++ +F Q + +
Sbjct: 2 SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61
Query: 139 KNTGRSKGFGFIRFSSHESALKAMLK-KHKIGNRICDV 175
GR G F+ F+ E A A+ K K +G R ++
Sbjct: 62 YPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL 99
Score = 35.2 bits (81), Expect = 0.006
Identities = 11/80 (13%), Positives = 24/80 (30%), Gaps = 9/80 (11%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVD----VLIPKP----FREFAFVTFE-LDSVAKSL 243
V + L T ++ F + + +L AFV F + +L
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 244 IGQHVNIKDKKVVVMEATPK 263
+ + + + +T
Sbjct: 86 RKHKDLLGKRYIELFRSTAA 105
>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 = 65.3 bits (160), Expect = 9e-14
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ ++ T +KE F QFG + + D+ T + KGFGF+ ES +A+
Sbjct: 8 NLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Score = 51.4 bits (124), Expect = 9e-09
Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 12/90 (13%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDSVAK---S 242
++VG+L T ++E F +G V +V + RE F FV + +SV++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD-RETKKPKGFGFVEMQEESVSEAIAK 61
Query: 243 LIGQHVNIKDKKVVVMEATPKKKMNERQDN 272
L + + + V EA PKK + +
Sbjct: 62 LDNT--DFMGRTIRVTEANPKKSLEHHHHH 89
>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 = 65.7 bits (161), Expect = 1e-13
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S N+ + L V G+ T+ LKE F+ A + D+ TG SKGFGF
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVR---ARIVTDRETGSSKGFGF 58
Query: 150 IRFSSHESALKAM 162
+ F+S E A A
Sbjct: 59 VDFNSEEDAKAAK 71
Score = 45.7 bits (109), Expect = 1e-06
Identities = 25/93 (26%), Positives = 33/93 (35%), Gaps = 12/93 (12%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDS 238
+ +FV L+ D TE L+E F V I RE F FV F +
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTD-RETGSSKGFGFVDFNSEE 65
Query: 239 VAKSLIGQH--VNIKDKKVVVMEATPKKKMNER 269
AK+ I KV + A PK +
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSG 98
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 8/88 (9%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S D L V + + ++ +++ F VK + + + F
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAF 55
Query: 150 IRFSSHESALKAM--LKKHKIGNRICDV 175
+ FS+ E A++AM L + +V
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDGSPIEV 83
Score = 52.7 bits (127), Expect = 4e-09
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI----GQH 247
++V +L +E + + F + K R++AFV F A + G+
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-RDYAFVHFSNREDAVEAMKALNGKV 75
Query: 248 VNIKDKKVVVMEATPKKK 265
++ + V A P K
Sbjct: 76 LD--GSPIEVTLAKPVDK 91
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ---H 247
+K+++G+L+P +T DLR+ F + + +AFV + + A I
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-SGYAFVDYPDQNWAIRAIETLSGK 67
Query: 248 VNIKDKKVVVMEATPKKK 265
V + K + V + KK
Sbjct: 68 VELHGKIMEVDYSVSKKL 85
Score = 60.0 bits (146), Expect = 8e-12
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 6/65 (9%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
SG L + + T +DL++ F + G+ F+ +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNW 56
Query: 158 ALKAM 162
A++A+
Sbjct: 57 AIRAI 61
>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 = 64.2 bits (157), Expect = 2e-13
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 93 SYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFA------NVKV--DKNTGRS 144
+ + N + V G+ T + +YF+Q G ++ + + D+ TG+
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 145 KGFGFIRFSSHESALKAM 162
KG + F SA A+
Sbjct: 63 KGEATVSFDDPPSAKAAI 80
Score = 44.2 bits (105), Expect = 3e-06
Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 17/92 (18%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAV-VDVLIPKP------------FREFAFV 232
+ +FV L ++T + ++F+ G + + +P + A V
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 233 TFELDSVAKSLIGQHVN---IKDKKVVVMEAT 261
+F+ AK+ I + + V AT
Sbjct: 69 SFDDPPSAKAAI-DWFDGKEFSGNPIKVSFAT 99
>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 = 66.0 bits (161), Expect = 3e-13
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
++ L V + + T+ + E F + G ++ + +DK + GF F+ + S A A
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 162 M--LKKHKIGNRICDV 175
M + ++ +RI
Sbjct: 98 MRYINGTRLDDRIIRT 113
Score = 60.2 bits (146), Expect = 3e-11
Identities = 23/124 (18%), Positives = 46/124 (37%), Gaps = 14/124 (11%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFELDSVAKSLIG 245
++VG+L+ TE + E F G + +++ K F FV + + A++ +
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 246 --QHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGYYDNR 303
+ D+ + K+ + R+ R++ + Y G G Y
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY-------RQDYDAGRGGYGKL 152
Query: 304 QQQQ 307
Q Q
Sbjct: 153 AQNQ 156
>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 = 66.7 bits (162), Expect = 4e-13
Identities = 12/65 (18%), Positives = 23/65 (35%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
+ L P T+ + E ++ G +VKV G + + S AL+
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 162 MLKKH 166
+ +
Sbjct: 182 LGFLN 186
Score = 58.2 bits (140), Expect = 4e-10
Identities = 16/165 (9%), Positives = 43/165 (26%), Gaps = 46/165 (27%)
Query: 112 PWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHKIG 169
+ + F +G +E VK K+ G + + + +A+ L + +
Sbjct: 14 QSKMNCDRVFNVFCLYGNVE--KVKFMKS---KPGAAMVEMADGYAVDRAITHLNNNFMF 68
Query: 170 NRICDV----------------------------------RIPESTKIGTEEPVASKVFV 195
+ +V PE + ++ +
Sbjct: 69 GQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHF 128
Query: 196 GSLTPDLTESDLREHFEYYGAVVDVLIPKP-----FREFAFVTFE 235
+ ++TE + E + G + + ++
Sbjct: 129 FNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173
Score = 42.0 bits (98), Expect = 1e-04
Identities = 21/120 (17%), Positives = 34/120 (28%), Gaps = 7/120 (5%)
Query: 193 VFVGSLTPD-LTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN-- 249
+ V L + + F YG V V K A V I H+N
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAI-THLNNN 65
Query: 250 -IKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGYYDNRQQQQG 308
+ +K+ V + K+ + D S + ++ NR Q
Sbjct: 66 FMFGQKMNVCVS--KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPS 123
>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 = 64.3 bits (157), Expect = 4e-13
Identities = 26/100 (26%), Positives = 41/100 (41%), Gaps = 10/100 (10%)
Query: 81 ASGNSSATQSKRSYPD--NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVD 138
S SS + + D N +N + GI TD +++ F FG + V +
Sbjct: 1 GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
Query: 139 KNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVR 176
KG+ F+RFS+HESA A+ + I +
Sbjct: 61 ------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94
Score = 61.2 bits (149), Expect = 5e-12
Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 3/84 (3%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI--GQHV 248
V+ G + LT+ +R+ F +G ++++ + + ++FV F A I
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGT 84
Query: 249 NIKDKKVVVMEATPKKKMNERQDN 272
I+ V M +
Sbjct: 85 TIEGHVVKCYWGKESPDMTSGPSS 108
>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 = 64.4 bits (157), Expect = 4e-13
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTL------EFANVKV--DKNT 141
S S D N+ + V G+ + T +DL ++F+Q G + + + DK T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 142 GRSKGFGFIRFSSHESALKAM 162
G+ KG + + +A A+
Sbjct: 62 GKPKGDATVSYEDPPTAKAAV 82
Score = 46.2 bits (110), Expect = 8e-07
Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 17/100 (17%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAV-VDVLIPKP------------FREFAFV 232
E+ S ++V L +T DL + F+ G V ++ +P + A V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 233 TFELDSVAKSLIGQHVN---IKDKKVVVMEATPKKKMNER 269
++E AK+ + + + + K+ V A K MN
Sbjct: 71 SYEDPPTAKAAV-EWFDGKDFQGSKLKVSLARKKPPMNSG 109
>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 = 63.8 bits (156), Expect = 4e-13
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
+ S+ D + + V G+ ++ L E F Q G + ++ D+ TG
Sbjct: 2 SSGSSGPISERNQDAT-------VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTG 54
Query: 143 RSKGFGFIRFSSHESALKAM 162
+ +G+GF+ F S E A A+
Sbjct: 55 QHQGYGFVEFLSEEDADYAI 74
Score = 56.5 bits (137), Expect = 2e-10
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 9/93 (9%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFELDS 238
+E + V+VG L ++E L E F G VV+ +PK R + FV F +
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD-RVTGQHQGYGFVEFLSEE 68
Query: 239 VAKSLIGQ--HVNIKDKKVVVMEATPKKKMNER 269
A I + + K + V +A+ K
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
>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 = 63.6 bits (155), Expect = 6e-13
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN-TGRSKGFG 148
S S + + + G+P+ T+ND+ +F V ++ GR G
Sbjct: 2 SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP---MRVHIEIGPDGRVTGEA 58
Query: 149 FIRFSSHESALKAMLK-KHKIGNR 171
+ F++HE A+ AM K K + +R
Sbjct: 59 DVEFATHEDAVAAMAKDKANMQHR 82
Score = 33.9 bits (78), Expect = 0.015
Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 5/47 (10%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTFE 235
V + L TE+D+ F + V I A V F
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFA 63
>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 = 63.0 bits (154), Expect = 6e-13
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSL 243
G+ ++K+ VG+++P T +LR FE YG V++ I K +AFV E A
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEA 60
Query: 244 I----GQHVNIKDKKVVVMEATPKKK 265
I + K++ V +T + +
Sbjct: 61 IRGLDNT--EFQGKRMHVQLSTSRLR 84
Score = 49.5 bits (119), Expect = 3e-08
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
S +T L V I T T+ +L+ FE++G + ++ K + F+ E
Sbjct: 5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAED 56
Query: 158 ALKAM 162
A++A+
Sbjct: 57 AVEAI 61
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 62.3 bits (152), Expect = 1e-12
Identities = 28/110 (25%), Positives = 41/110 (37%), Gaps = 17/110 (15%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI----GQH 247
KV+VG+L + +L F YYG + V I + FAFV FE A+ + G+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK- 60
Query: 248 VNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGN 297
I +V V +T + R DR + G
Sbjct: 61 -VICGSRVRVELSTGMPRR-----------SRFDRPPARRKLLEVLFNGP 98
Score = 45.7 bits (109), Expect = 1e-06
Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 7/68 (10%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIG 169
+ +L+ F +G L + GF F+ F A A+ G
Sbjct: 7 NLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGLD--G 59
Query: 170 NRICDVRI 177
IC R+
Sbjct: 60 KVICGSRV 67
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 62.4 bits (152), Expect = 1e-12
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
V+N + + G P T +D+KE+ E G + ++ + KG F+ F S ESA K
Sbjct: 9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKK 67
Query: 161 AM-LKKHKIGNRICDV 175
+ K +
Sbjct: 68 FVETPGQKYKETDLLI 83
Score = 58.2 bits (141), Expect = 4e-11
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 7/95 (7%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIP----KPFREFAFVTFE-LDSVA 240
+ V++ D T D++E E G V+++ + K F+ FV F+ ++S
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 241 KSLIGQHVNIKDKKVVVMEATP--KKKMNERQDNR 273
K + K+ ++++ KK ER+ N+
Sbjct: 67 KFVETPGQKYKETDLLILFKDDYFAKKNEERKQNK 101
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 96 DNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH 155
+SG + L V + T T+ L++ F QFG LE VK K + FI F
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLE--RVKK------LKDYAFIHFDER 55
Query: 156 ESALKAM 162
+ A+KAM
Sbjct: 56 DGAVKAM 62
Score = 56.1 bits (136), Expect = 2e-10
Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN-- 249
+FV +L +TE L + F +G + V K +++AF+ F+ A + + +N
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERV---KKLKDYAFIHFDERDGAVKAM-EEMNGK 68
Query: 250 -IKDKKVVVMEATPKKKMNERQDNR 273
++ + + ++ A P + + + +
Sbjct: 69 DLEGENIEIVFAKPPDQKRKERKAQ 93
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 62.3 bits (151), Expect = 2e-12
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-------PFREFAFVTFEL- 236
+ + KVFVG L PD+ E ++ F +G +V K P + +AF+ F+
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 237 DSVAKSLIGQHVNIKDKKVVVMEATPKKKM 266
SV + + V T K K
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKDKP 92
Score = 57.3 bits (138), Expect = 1e-10
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 3/73 (4%)
Query: 110 GIPWTFTDNDLKEYFEQFGTL--EFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK-H 166
G+P ++++ F +FG L ++ + K+ KG+ F+ F S +
Sbjct: 15 GLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE 74
Query: 167 KIGNRICDVRIPE 179
+ G V P
Sbjct: 75 EDGKLYLCVSSPT 87
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 62.1 bits (151), Expect = 2e-12
Identities = 22/92 (23%), Positives = 45/92 (48%), Gaps = 9/92 (9%)
Query: 95 PDNSGPVQNTDLVVL--GIPWTFTDNDLKEYFEQFGTLEFANVKVDKN-TGRSKGFGFIR 151
P+ DL V G+P++ +ND++++F L V + K+ GR+ G G ++
Sbjct: 6 SGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHG---LRVDAVHLLKDHVGRNNGNGLVK 62
Query: 152 FSSHESALKAMLK-KHKIGNRICDVRIPESTK 182
F S + +A+ + + + R V + +T+
Sbjct: 63 FLSPQDTFEALKRNRMLMIQRY--VEVSPATE 92
Score = 37.8 bits (88), Expect = 6e-04
Identities = 19/102 (18%), Positives = 33/102 (32%), Gaps = 6/102 (5%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVT 233
S K P V V + E+D+R+ F V V + K V
Sbjct: 4 GSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVK 62
Query: 234 FE-LDSVAKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRN 274
F ++L + + + V V AT ++ + +
Sbjct: 63 FLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITS 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 = 61.1 bits (149), Expect = 3e-12
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--H 247
K+FVG+++ T +LR FE G V++ + K ++AFV E ++ AK+ I Q
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNG 65
Query: 248 VNIKDKKVVVMEATPKKK 265
+K K++ V +T +K
Sbjct: 66 KEVKGKRINVELSTKGQK 83
Score = 49.5 bits (119), Expect = 3e-08
Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 8/53 (15%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ T +L+ FE+ G + +V K + F+ A A+
Sbjct: 16 NVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAI 60
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 63.0 bits (153), Expect = 3e-12
Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 15/115 (13%)
Query: 136 KVDKNTGRSKGFGFIRF---SSHESALKAMLKKHKI-GNRICDVRIPESTKIGTEE---- 187
K+ N KG ++ E K + + G D T
Sbjct: 4 KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63
Query: 188 -------PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
P+ KV+VG+L + +++L F YYG + V + + FAFV FE
Sbjct: 64 HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFE 118
Score = 46.4 bits (110), Expect = 2e-06
Identities = 15/92 (16%), Positives = 27/92 (29%), Gaps = 11/92 (11%)
Query: 71 QDRVYYCTFDASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTL 130
+ + S + + S P + + V + +L+ F +G L
Sbjct: 47 DATKTFTVTEGSHHHHHHMHRDSCPLD------CKVYVGNLGNNGNKTELERAFGYYGPL 100
Query: 131 EFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
V GF F+ F A A+
Sbjct: 101 RSVWVA-----RNPPGFAFVEFEDPRDAADAV 127
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 62.0 bits (151), Expect = 3e-12
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFA------NVKV--DKNTGRSKGFGFIR 151
N + V G+ T + +YF+Q G ++ + + D+ TG+ KG +
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 152 FSSHESALKAM 162
F SA A+
Sbjct: 64 FDDPPSAKAAI 74
Score = 50.5 bits (121), Expect = 3e-08
Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 19/112 (16%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAV-VDVLIPKP------------FREFAFV 232
+ + +FV L ++T + ++F+ G + + +P + A V
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 233 TFELDSVAKSLI----GQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRN 280
+F+ AK+ I G+ + V AT + N N +
Sbjct: 63 SFDDPPSAKAAIDWFDGKE--FSGNPIKVSFATRRADFNRGGGNGRGGLEHH 112
>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 = 61.5 bits (150), Expect = 3e-12
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 4/90 (4%)
Query: 90 SKRSYPDNSGPVQNTDLVVLG-IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFG 148
+ + P LG +P+ T+ +KE+F + N R KGFG
Sbjct: 5 HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 64
Query: 149 FIRFSSHESALKAM-LKKHKIGNRICDVRI 177
+ F +S L A+ L + +GNR +R+
Sbjct: 65 YAEFEDLDSLLSALSLNEESLGNR--RIRV 92
Score = 51.9 bits (125), Expect = 6e-09
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFE-LDSVAKSLI 244
F+G+L D+TE ++E F + V +P+ F + FE LDS+ +L
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 245 GQHVNIKDKKVVVMEATPKK 264
++ ++++ V A +
Sbjct: 80 LNEESLGNRRIRVDVADQAQ 99
>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 = 61.3 bits (149), Expect = 4e-12
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 7/99 (7%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGT--LEFANVKVDKNTGRSKGFGFIRFSSHESA 158
N L + GIP ++ E + L+ + +++GF F+ + SH +A
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 159 LKAMLK----KHKIGNRICDVRIPESTKIGTEEPVASKV 193
A K + ++ V E +I +E V V
Sbjct: 66 AMARRKLMPGRIQLWGHQIAVDWAE-PEIDVDEDVMETV 103
Score = 57.5 bits (139), Expect = 1e-10
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVV-DVLIPK------PFREFAFVTFELDSVA---- 240
++F+G + ++ E V DV++ R FAFV +E A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 241 KSLIGQHVNIKDKKVVVMEATPKKKMNER 269
+ L+ + + ++ V A P+ ++E
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEIDVDED 98
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 60.4 bits (147), Expect = 4e-12
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA--- 158
T L V G+ T T+ DL+ +F QFG + + V + + FI+F++ ++A
Sbjct: 11 TITTLYVGGLGDTITETDLRNHFYQFGEIR--TITVVQR----QQCAFIQFATRQAAEVA 64
Query: 159 LKAMLKKHKIGNRICDVR 176
+ K + R +V+
Sbjct: 65 AEKSFNKLIVNGRRLNVK 82
Score = 58.1 bits (141), Expect = 4e-11
Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSV 239
S+ E+ + ++VG L +TE+DLR HF +G + + + + ++ AF+ F
Sbjct: 2 SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-QQCAFIQFATRQA 60
Query: 240 AKSLIGQHVN---IKDKKVVVM 258
A+ + N + +++ V
Sbjct: 61 AEVAAEKSFNKLIVNGRRLNVK 82
>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 = 60.3 bits (147), Expect = 6e-12
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HV 248
K+F+G+L + TE ++R FE YG V++ I K + FV E + A+ I H
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---NYGFVHIEDKTAAEDAIRNLHHY 65
Query: 249 NIKDKKVVVMEATPKKK 265
+ + V + K K
Sbjct: 66 KLHGVNINVEASKNKSK 82
Score = 50.7 bits (122), Expect = 1e-08
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
SG L + +P T+ +++ FEQ+G + ++ K +GF+ +
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54
Query: 158 ALKAM 162
A A+
Sbjct: 55 AEDAI 59
>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 = 60.7 bits (148), Expect = 6e-12
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LKKHKIG 169
+P+ T+ +KE+F + N R KGFG+ F +S L A+ L + +G
Sbjct: 23 LPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLG 82
Query: 170 NR 171
N+
Sbjct: 83 NK 84
Score = 55.7 bits (135), Expect = 3e-10
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE------FAFVTFE-LDSVAKSLI 244
F+G+L D+TE ++E F + V +P+ F + FE LDS+ +L
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 245 GQHVNIKDKKVVVMEATPKKKMNERQDN 272
++ +K++ V A + + +
Sbjct: 76 LNEESLGNKRIRVDVADQAQDKDSGPSS 103
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 63.5 bits (154), Expect = 7e-12
Identities = 30/187 (16%), Positives = 61/187 (32%), Gaps = 42/187 (22%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGI-PWTFTDNDLKEYFEQFGTLEFANVKVDKNTGR 143
+ + + P +G + L+V + P T L F +G ++ VK+ N
Sbjct: 17 RGSHMGRIAIPGLAGAGNSV-LLVSNLNPERVTPQSLFILFGVYGDVQ--RVKILFN--- 70
Query: 144 SKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRIPESTKIGTEE-------------- 187
K ++ + A AM L HK+ + + + + +
Sbjct: 71 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 130
Query: 188 ------------------PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-RE 228
P ++ + + ++ P ++E DL+ F G VV R+
Sbjct: 131 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK 190
Query: 229 FAFVTFE 235
A +
Sbjct: 191 MALIQMG 197
Score = 60.0 bits (145), Expect = 1e-10
Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 5/102 (4%)
Query: 65 APLDGWQDRVYYCTFDASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYF 124
P +G +D+ + S + N P T L + IP + ++ DLK F
Sbjct: 114 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT-LHLSNIPPSVSEEDLKVLF 172
Query: 125 EQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKH 166
G VK K + + I+ S E A++A++ H
Sbjct: 173 SSNG----GVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 210
Score = 45.8 bits (108), Expect = 6e-06
Identities = 25/127 (19%), Positives = 44/127 (34%), Gaps = 8/127 (6%)
Query: 184 GTEEPVASKVFVGSLTPD-LTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKS 242
G S + V +L P+ +T L F YG V V I +E A V + A+
Sbjct: 28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQL 87
Query: 243 LIGQHVN---IKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGY 299
+ H+N + K + + + + R+ D+ + R G+
Sbjct: 88 AM-SHLNGHKLHGKPIRITLSKHQNVQLPREGQE---DQGLTKDYGNSPLHRFKKPGSKN 143
Query: 300 YDNRQQQ 306
+ N
Sbjct: 144 FQNIFPP 150
>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 = 59.9 bits (146), Expect = 9e-12
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 110 GIPWTFTDNDLKEYFEQFGT-LEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ + L + F FG L+ + D +TG SKG+ FI F+S +++ A+
Sbjct: 12 NLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Score = 46.8 bits (112), Expect = 4e-07
Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 12/92 (13%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVD--VLIPKPF----REFAFVTFELDSVAKSLI 244
S +F+G+L P++ E L + F +G ++ ++ P + +AF+ F + + I
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 245 ----GQHVNIKDKKVVVMEATPKKKMNERQDN 272
GQ++ ++ + V A K +
Sbjct: 66 EAMNGQYLC--NRPITVSYAFKKDSKGSGPSS 95
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 60.0 bits (146), Expect = 1e-11
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 92 RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
+ G + NT L V P +++L E F FG ++ + GF F+
Sbjct: 20 HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVE 71
Query: 152 FSSHESALKAM 162
F ESA KA+
Sbjct: 72 FEEAESAAKAI 82
Score = 58.5 bits (142), Expect = 4e-11
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN- 249
+++FV D+ ES+L E F +G + +V I FAFV FE A I + V+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAI-EEVHG 87
Query: 250 --IKDKKVVVMEATPKKK 265
++ + V+ + K
Sbjct: 88 KSFANQPLEVVYSKLPAK 105
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 58.8 bits (143), Expect = 2e-11
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 180 STKIGTEEPVASK-VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
S KIG + + ++VG L P+ + + L F+ +G++ + K FA++ +E
Sbjct: 6 SGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYE 61
Score = 50.7 bits (122), Expect = 2e-08
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T L V G+ + L F++FG++ + + F +I++ S ++A A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIR--TIDHV----KGDSFAYIQYESLDAAQAAC 70
Query: 163 LK 164
K
Sbjct: 71 AK 72
>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 = 58.5 bits (142), Expect = 2e-11
Identities = 15/68 (22%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNT-GRSKGFGFIRFSSHESALKAMLK 164
+ + G P+ T+ ++ E+ L+ +++ +N G G+ F+ FS+ E +A+
Sbjct: 13 VKLRGAPFNVTEKNVMEFL---APLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC 69
Query: 165 -KHKIGNR 171
+ +G R
Sbjct: 70 NREYMGGR 77
Score = 35.4 bits (82), Expect = 0.003
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 5/62 (8%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTFELDSV 239
G+ V + ++TE ++ E V + I + + FV F +
Sbjct: 4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEE 62
Query: 240 AK 241
K
Sbjct: 63 VK 64
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 58.1 bits (141), Expect = 4e-11
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKV--DKNTGRSKGFGFIRFSSHESALKAMLKKH- 166
+ +N + F G +VK+ ++ TG G+ F+ F+ +A K + K +
Sbjct: 16 DLEPYMDENFISRAFATMGE-TVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKING 74
Query: 167 -KIGNRICDVRI 177
+ R
Sbjct: 75 KPLPGATPAKRF 86
Score = 39.2 bits (92), Expect = 2e-04
Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 12/91 (13%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYG-AVVDVLIPKPF-----REFAFVTFELDSV 239
+A+ +++G L P + E+ + F G V+ V I + + FV F +
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 240 AKSLI----GQHVN--IKDKKVVVMEATPKK 264
A+ + G+ + K+ + AT
Sbjct: 65 AEKCLHKINGKPLPGATPAKRFKLNYATYSG 95
>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 = 58.2 bits (141), Expect = 6e-11
Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P N L + +P+ T ++ + F ++G + ++V NT ++G ++ + A
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIR--QIRV-GNTPETRGTAYVVYEDIFDAK 61
Query: 160 KAM 162
A+
Sbjct: 62 NAV 64
Score = 57.0 bits (138), Expect = 2e-10
Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF--REFAFVTFELDSVAKSLIG--QHV 248
+++ +L +T ++ + F YG + + + R A+V +E AK+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 249 NIKDKKVVVMEATPKKKMNERQDNRN 274
N+ ++ +VV+ + + +
Sbjct: 71 NVSNRYLVVLYYNANRAFQKMDTKKK 96
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 57.7 bits (139), Expect = 7e-11
Identities = 20/110 (18%), Positives = 36/110 (32%), Gaps = 15/110 (13%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+SG + V G+P D L YFE V + R G + F
Sbjct: 2 SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLTFREPA 58
Query: 157 SALKAMLKK-HKIGNRICDVR--IPESTKIGTEEPVASKVFVGSLTPDLT 203
A + + + H++ +R P + ++ + L P +
Sbjct: 59 DAERVLAQADHELHGAQLSLRPAPPRAPA---------RLLLQGLPPGTS 99
Score = 46.9 bits (111), Expect = 5e-07
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 11/86 (12%)
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYY-----GAVVDVLIPKPFREFAFVTFELDSV 239
+ V V L P + + L +FE G V+ +TF +
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL---GCGGVLTFREPAD 59
Query: 240 AKSLI--GQHVNIKDKKVVVMEATPK 263
A+ ++ H + ++ + A P+
Sbjct: 60 AERVLAQADHE-LHGAQLSLRPAPPR 84
>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 = 57.3 bits (139), Expect = 7e-11
Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 187 EPVASKVFVGSL-TPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIG 245
+ S++F+G+L ++++ DL F YG ++ + I F F+ F+ + I
Sbjct: 19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA---FGFIQFDNPQSVRDAIE 75
Query: 246 --QHVNIKDKKVVVMEATPKKK 265
KK+++ ++ +
Sbjct: 76 XESQEMNFGKKLILEVSSSNAR 97
Score = 41.5 bits (98), Expect = 3e-05
Identities = 19/96 (19%), Positives = 34/96 (35%), Gaps = 11/96 (11%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPW-TFTDNDLKEYFEQFGTLEFANVKVDKNT 141
G+S S G + L + +P + DL F +G + N+K
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----- 56
Query: 142 GRSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRI 177
FGFI+F + +S A+ + ++
Sbjct: 57 ---NAFGFIQFDNPQSVRDAIEXES--QEMNFGKKL 87
>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 = 59.5 bits (144), Expect = 9e-11
Identities = 28/159 (17%), Positives = 51/159 (32%), Gaps = 40/159 (25%)
Query: 112 PWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHKIG 169
P T L F +G ++ VK+ N K ++ + A AM L HK+
Sbjct: 13 PERVTPQSLFILFGVYGDVQ--RVKILFN---KKENALVQMADGNQAQLAMSHLNGHKLH 67
Query: 170 NRICDVRI--------------------------------PESTKIGTEEPVASKVFVGS 197
+ + + P S P ++ + + +
Sbjct: 68 GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSN 127
Query: 198 LTPDLTESDLREHFEYYGAVVD-VLIPKPFREFAFVTFE 235
+ P ++E DL+ F G VV + R+ A +
Sbjct: 128 IPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMG 166
Score = 58.8 bits (142), Expect = 2e-10
Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 5/89 (5%)
Query: 78 TFDASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKV 137
+ S + N P T L + IP + ++ DLK F G VK
Sbjct: 96 DYGNSPLHRFKKPGSKNFQNIFPPSAT-LHLSNIPPSVSEEDLKVLFSSNG----GVVKG 150
Query: 138 DKNTGRSKGFGFIRFSSHESALKAMLKKH 166
K + + I+ S E A++A++ H
Sbjct: 151 FKFFQKDRKMALIQMGSVEEAVQALIDLH 179
Score = 43.7 bits (103), Expect = 2e-05
Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 6/110 (5%)
Query: 193 VFVGSLTPD-LTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN-- 249
+ V +L P+ +T L F YG V V I +E A V + A+ + H+N
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAM-SHLNGH 64
Query: 250 -IKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNG 298
+ K + + + + R+ + D SP+ ++ G N
Sbjct: 65 KLHGKPIRITLSKHQNVQLPREGQEDQ-GLTKDYGNSPLHRFKKPGSKNF 113
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 57.1 bits (138), Expect = 1e-10
Identities = 16/88 (18%), Positives = 28/88 (31%), Gaps = 5/88 (5%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S + L + IP L Q+G +E +
Sbjct: 2 SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVN 58
Query: 150 IRFSSHESALKAM--LKKHKIGNRICDV 175
+ +SS + A +A+ L ++ N V
Sbjct: 59 VTYSSKDQARQALDKLNGFQLENFTLKV 86
Score = 44.4 bits (105), Expect = 3e-06
Identities = 10/58 (17%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAV--VDVLIPKPFREFAFVTFE 235
S+ + K+ + ++ P L L YG V + + VT+
Sbjct: 5 SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS 62
>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 = 57.3 bits (139), Expect = 1e-10
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE--FAFVTFE 235
+++VG+L PD+ D+ + F YGA+ D+ + FAFV FE
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFE 69
Score = 53.5 bits (129), Expect = 2e-09
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 5/82 (6%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+SG+S + + + V +P D+++ F ++G + ++K +
Sbjct: 2 SSGSSGMSGGGVIRGPAGNN--DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR- 58
Query: 141 TGRSKGFGFIRFSSHESALKAM 162
F F+ F A A+
Sbjct: 59 --GGPPFAFVEFEDPRDAEDAV 78
>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 = 56.8 bits (137), Expect = 1e-10
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 5/85 (5%)
Query: 96 DNSGPVQNTDLVVL--GIPWTFTDNDLKEYFEQFGTLEFANV--KVDKNTGRSKGFGFIR 151
+ ++ G+PW+ T D+ +F N + G+ +G I
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61
Query: 152 FSSHESALKAMLK-KHKIGNRICDV 175
S + KA+ K + +G R +V
Sbjct: 62 MESEQDVQKALEKHRMYMGQRYVEV 86
Score = 33.7 bits (77), Expect = 0.020
Identities = 13/102 (12%), Positives = 28/102 (27%), Gaps = 8/102 (7%)
Query: 182 KIGTEEPVASKVFVGSLTPDLTESDLREHFEYY---GAVVDVLIPKP----FREFAFVTF 234
K+ E + L T D+ F + R A +
Sbjct: 3 KLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEM 62
Query: 235 ELDSVAKSLIGQH-VNIKDKKVVVMEATPKKKMNERQDNRNN 275
E + + + +H + + + V V E + + +
Sbjct: 63 ESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVK 104
>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 = 57.2 bits (138), Expect = 2e-10
Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 7/96 (7%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANV--KVDKN 140
G+S ++ G V + + G+PW+ + D++ + + +
Sbjct: 1 GSSGSSGMMLGPEGGEGYV----VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR 56
Query: 141 TGRSKGFGFIRFSSHESALKAMLK-KHKIGNRICDV 175
GR G F+ S + A+ K + +G+R +V
Sbjct: 57 EGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV 92
Score = 35.7 bits (82), Expect = 0.005
Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 8/94 (8%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHF---EYYGAVVDVLIPKPFRE----FA 230
+G E V + L + D++ + V V A
Sbjct: 5 SSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEA 64
Query: 231 FVTFELDSVAKSLIGQH-VNIKDKKVVVMEATPK 263
FV E + K + + ++ + + V ++
Sbjct: 65 FVELESEDDVKLALKKDRESMGHRYIEVFKSHRT 98
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 56.1 bits (136), Expect = 2e-10
Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKV--DKNTGRSKGFGFIRFSSHESALKAM 162
+P+ D+ F+ +V++ DK+T + KGF ++ F +S +A+
Sbjct: 22 NLPFNTVQGDIDAIFKDLSI---RSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Score = 50.7 bits (122), Expect = 2e-08
Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-----PFREFAFVTFE-LDSVAKSLIG 245
+VG+L + + D+ F+ + V + + F+ F +V F+ +DS+ ++L
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 246 QHVNIKDKKVVVMEATPKKKMNERQDN 272
+ D+ + V A +K+ +
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDKSGPSS 102
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 56.6 bits (137), Expect = 2e-10
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 187 EPVASKVFVGSLTPDL-TESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIG 245
+ + S+VF+G+L L +SD+ F YG V + K +AFV + + A++ +
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG---YAFVQYSNERHARAAVL 80
Query: 246 --QHVNIKDKKVVVMEATPKKK 265
+ + + + A K
Sbjct: 81 GENGRVLAGQTLDINMAGEPKP 102
Score = 42.0 bits (99), Expect = 3e-05
Identities = 18/105 (17%), Positives = 41/105 (39%), Gaps = 11/105 (10%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTF-TDNDLKEYFEQFGTLEFANVKVDK 139
+SG S Q+ N N+ + + + +D++ F ++G + +V
Sbjct: 5 SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--- 61
Query: 140 NTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRIPESTK 182
KG+ F+++S+ A A+ + + D+ + K
Sbjct: 62 -----KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK 101
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 56.1 bits (136), Expect = 2e-10
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 111 IPWTFTDNDLKEYF-EQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK---KH 166
+ D L E+F + + + V +D+ TG SKG+GF++F+ +A+ +
Sbjct: 17 LTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAV 75
Query: 167 KIGNR 171
+G++
Sbjct: 76 GLGSK 80
Score = 34.2 bits (79), Expect = 0.012
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 8/88 (9%)
Query: 193 VFVGSLTPDLTESDLREHF-EYYGAVVDVLIPKPF----REFAFVTFELDSVAKSLIGQ- 246
+FVG LTPD+ + L E F + Y + + + + FV F + K + +
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 247 --HVNIKDKKVVVMEATPKKKMNERQDN 272
V + K V + A PK + ++
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASRVKPVES 99
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 56.1 bits (136), Expect = 2e-10
Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 6/94 (6%)
Query: 185 TEEPVASKVFVGSL-TPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSL 243
P S++F+G+L ++++ DL F YG ++ + I F F+ F+ +
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA---FGFIQFDNPQSVRDA 61
Query: 244 IG--QHVNIKDKKVVVMEATPKKKMNERQDNRNN 275
I KK+++ ++ + +
Sbjct: 62 IECESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95
Score = 41.0 bits (97), Expect = 4e-05
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 10/66 (15%)
Query: 112 PWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNR 171
+ DL F +G + N+K FGFI+F + +S A+ +
Sbjct: 20 LKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECES--QEM 69
Query: 172 ICDVRI 177
++
Sbjct: 70 NFGKKL 75
>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 = 56.9 bits (137), Expect = 3e-10
Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 5/97 (5%)
Query: 89 QSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANV--KVDKNTGRSKG 146
+ S + + + G+PW+ + D++ + + A + GR G
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG 89
Query: 147 FGFIRFSSHESALKAMLK-KHKIGNRICDVRIPESTK 182
F+ S + A+ K + +G+R + + +S +
Sbjct: 90 EAFVELGSEDDVKMALKKDRESMGHRY--IEVFKSHR 124
Score = 34.6 bits (79), Expect = 0.015
Identities = 9/80 (11%), Positives = 22/80 (27%), Gaps = 8/80 (10%)
Query: 192 KVFVGSLTPDLTESDLREHFEYY---GAVVDVLIPKPFRE----FAFVTFELDSVAKSLI 244
V + L + D++ V AFV + K +
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 245 GQH-VNIKDKKVVVMEATPK 263
+ ++ + + V ++
Sbjct: 106 KKDRESMGHRYIEVFKSHRT 125
>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 = 55.7 bits (135), Expect = 3e-10
Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 5/100 (5%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF---REFAFVTF 234
S+ + ++ ++VG+L+ D+TE + + F G + + FV F
Sbjct: 3 SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF 62
Query: 235 ELDSVAKSLIGQ--HVNIKDKKVVVMEATPKKKMNERQDN 272
A + + I K+V V AT +
Sbjct: 63 YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
Score = 55.3 bits (134), Expect = 4e-10
Identities = 22/105 (20%), Positives = 36/105 (34%), Gaps = 11/105 (10%)
Query: 86 SATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
S+ S D Q L V + T+ + + F Q G + + + +
Sbjct: 2 SSGSSGMMEDDG----QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP- 56
Query: 146 GFGFIRFSSHESALKAM--LKKHKIGNRICDV---RIPESTKIGT 185
+ F+ F H A A+ + KI + V P S K G
Sbjct: 57 -YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 55.2 bits (133), Expect = 5e-10
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE----LDSV 239
G P+A+ V+VG+L D SDL+ G+V L + R AF+ +
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQA 72
Query: 240 AKSLIGQHVNIKDKKVVVMEATPKK 264
L G + + + V A ++
Sbjct: 73 VSCLQG--LRLGTDTLRVALARQQR 95
Score = 49.4 bits (118), Expect = 5e-08
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 7/88 (7%)
Query: 86 SATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
S+ S P G D+ V +P +DLK + G+ V + +
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGS-----VPLRLTWQGPR 56
Query: 146 GFGFIRFSSHESALKAM--LKKHKIGNR 171
F+ + +A +A+ L+ ++G
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTD 84
>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 = 59.1 bits (142), Expect = 7e-10
Identities = 28/230 (12%), Positives = 68/230 (29%), Gaps = 3/230 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L V + + T++ L+ FE +G ++ ++ K +G+ +G+ FI + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 166 HKI---GNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI 222
G R+ T G G+ + + +
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224
Query: 223 PKPFREFAFVTFELDSVAKSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDR 282
P P + + + ++ + + + ++++ R + +R D+
Sbjct: 225 PSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDK 284
Query: 283 SRSPMSNSRQYGGGNGYYDNRQQQQGGYNNKRRRNDYDDWHHGNGGNSNN 332
R S + R+++ G + G
Sbjct: 285 DRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGE 334
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 54.0 bits (130), Expect = 1e-09
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 99 GPVQ-NTDLVVLGIP------WTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
GP+ + +VV G P L F + G + +D+ TG++KGF F+
Sbjct: 1 GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60
Query: 152 FSSHESALKAM 162
S A K +
Sbjct: 61 CGSMNDAKKII 71
Score = 35.5 bits (82), Expect = 0.004
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 194 FVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE-----FAFVTFELDSVAKSLI 244
+ S + + L F G VV++ P F FV + AK +I
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
>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 = 13/57 (22%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVK-----VDKNTGRSKGFGFIRFSSHESALKAM 162
+ + DLK F ++ + GR KG FI + ++A KA+
Sbjct: 53 LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
Score = 44.8 bits (106), Expect = 4e-06
Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 12/95 (12%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAV--------VDVLIPK--PFREFAFVTFELDSVA 240
+++V +L + E DL+ F Y D+ + K + AF+ + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 241 KSLIG--QHVNIKDKKVVVMEATPKKKMNERQDNR 273
+ + K +VV A + + ++ +
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSARPKQDPKEGK 140
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 52.9 bits (127), Expect = 5e-09
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 11/90 (12%)
Query: 92 RSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
P + ++ +VV G+P + + DLK++ + G + +A+V G G
Sbjct: 3 APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGV 55
Query: 150 IRFSSHESALKA--MLKKHKIGNRICDVRI 177
+ F E A L K + +
Sbjct: 56 VEFVRKEDMTYAVRKLDNTKFRSHEGETAY 85
Score = 46.7 bits (111), Expect = 6e-07
Identities = 17/97 (17%), Positives = 29/97 (29%), Gaps = 4/97 (4%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HVN 249
+V V L P + DL++H G V + + V F + + +
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDNTK 75
Query: 250 IKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSP 286
+ + K + R RSRS
Sbjct: 76 FRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSR 112
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 53.0 bits (127), Expect = 5e-09
Identities = 11/109 (10%), Positives = 37/109 (33%), Gaps = 8/109 (7%)
Query: 178 PESTKIGTEEPVASKVFVGSLTPDLTESDLREH----FEYYGAVVDVLIPKP--FREFAF 231
P+ + V + ++ P++ + L+ G ++D+++ A+
Sbjct: 17 PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76
Query: 232 VTFELDSVAKSLIG--QHVNIKDKKVVVMEATPKKKMNERQDNRNNFDR 278
+ F A++ + Q + +V+ + + + +
Sbjct: 77 IVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHHHH 125
Score = 46.0 bits (109), Expect = 1e-06
Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 9/80 (11%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKE----YFEQFGTLEFANVKVDKNTG 142
+ S P ++ P + +++ I L+ G + ++ VD +
Sbjct: 15 DSPDLGSTPPHTEP--SQVVLITNINPEVPKEKLQALLYALASSQG--DILDIVVDL-SD 69
Query: 143 RSKGFGFIRFSSHESALKAM 162
+ G +I F++ ESA +
Sbjct: 70 DNSGKAYIVFATQESAQAFV 89
>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 = 5e-09
Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 8/72 (11%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T ++ +P +++E F +FG+L + + F A KA
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAF 63
Query: 163 --LKKHKIGNRI 172
L K +
Sbjct: 64 RHLAYSKFHHVP 75
Score = 46.7 bits (111), Expect = 5e-07
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK 241
+ +L ++++E F +G++ VL+P A V F A+
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEAR 60
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 52.5 bits (126), Expect = 5e-09
Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 11/90 (12%)
Query: 92 RSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S P + ++ +VV G+P + + DLK++ + G + +A+V G G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGV 54
Query: 150 IRFSSHESALKA--MLKKHKIGNRICDVRI 177
+ F E A L K + +
Sbjct: 55 VEFVRKEDMTYAVRKLDNTKFRSHEGETAY 84
Score = 45.9 bits (109), Expect = 9e-07
Identities = 16/99 (16%), Positives = 29/99 (29%), Gaps = 10/99 (10%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HVN 249
+V V L P + DL++H G V + + V F + + +
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 250 IKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMS 288
+ + + D + RS P S
Sbjct: 75 FRSHEGETAYI------RVKVDGPRSPSYGRSRSSGPSS 107
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 51.6 bits (124), Expect = 6e-09
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 103 NTDLVVLGIPWTFTD------NDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
++ +VV +P D N + + F +FG + N + G++KG+ F+ ++S
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPA 58
Query: 157 SALKAM 162
A+ A+
Sbjct: 59 HAVDAV 64
Score = 30.4 bits (69), Expect = 0.14
Identities = 7/63 (11%), Positives = 25/63 (39%), Gaps = 9/63 (14%)
Query: 191 SKVFVGSL------TPDLTESDLREHFEYYGAVVDVLIPKP---FREFAFVTFELDSVAK 241
S + V ++ + ++ + + F +G + + P+ + + F+ + + A
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 242 SLI 244
+
Sbjct: 62 DAV 64
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.0 bits (125), Expect = 6e-09
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 103 NTDLVVLGIPWTFTD------NDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
++ +VV +P D N + + F +FG + N + G++KG+ F+ ++S
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPA 72
Query: 157 SALKAM 162
A+ A+
Sbjct: 73 HAVDAV 78
Score = 34.7 bits (80), Expect = 0.008
Identities = 7/68 (10%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 186 EEPVASKVFVGSL------TPDLTESDLREHFEYYGAVVDVLIPKP---FREFAFVTFEL 236
+ + S + V ++ + ++ + + F +G + + P+ + + F+ +
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYAS 70
Query: 237 DSVAKSLI 244
+ A +
Sbjct: 71 PAHAVDAV 78
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 51.8 bits (124), Expect = 9e-09
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 5/87 (5%)
Query: 92 RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
R + P + + + +P + DLK+ + NT G G +
Sbjct: 17 RGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALE 73
Query: 152 FSSHESALKA--MLKKHKIGNRICDVR 176
F S E ++A L + + V
Sbjct: 74 FPSEEILVEALERLNNIEFRGSVITVE 100
Score = 34.4 bits (79), Expect = 0.010
Identities = 5/46 (10%), Positives = 15/46 (32%), Gaps = 2/46 (4%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDV--LIPKPFREFAFVTFE 235
++ + +L + DL++ + + F + F
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFP 75
>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 = 17/95 (17%), Positives = 42/95 (44%), Gaps = 8/95 (8%)
Query: 184 GTEEPVASKV-FVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKS 242
G+ P S+V + L D+TE ++ +G V ++L+ K + AF+ + A +
Sbjct: 11 GSGVP--SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANT 67
Query: 243 LI----GQHVNIKDKKVVVMEATPKKKMNERQDNR 273
++ ++ + + + + K+ + N+
Sbjct: 68 MVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102
Score = 47.2 bits (112), Expect = 4e-07
Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 10/78 (12%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
+ V + + +P T+ ++ FG + N+ + +
Sbjct: 2 RGSHHHHHHGSGVPSRV----IHIRKLPIDVTEGEVISLGLPFGKVT--NLLM----LKG 51
Query: 145 KGFGFIRFSSHESALKAM 162
K FI ++ E+A +
Sbjct: 52 KNQAFIEMNTEEAANTMV 69
>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 = 50.7 bits (121), Expect = 3e-08
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
S Q+ + G+ + N L E+ G ++ + + N K + F R+ + E
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPPN----KPYSFARYRTTEE 75
Query: 158 ALKAMLKKHKIGNRICDVR 176
+ +A + + G + D
Sbjct: 76 SKRAYVTLN--GKEVVDDL 92
Score = 46.8 bits (111), Expect = 6e-07
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
V G L ++ + L E G V +L+P P + ++F +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYR 71
>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 = 49.7 bits (119), Expect = 3e-08
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 110 GIPWTFTDNDLKEYFEQFG-----TLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-L 163
IP+ T+ + ++F T N + + K F F+ F S + +AM
Sbjct: 13 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 72
Query: 164 KKHKIGNRICDVRIP 178
+ +R P
Sbjct: 73 DGIIFQGQSLKIRRP 87
Score = 39.7 bits (93), Expect = 9e-05
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 12/66 (18%)
Query: 190 ASKVFVGSLTPDLTESDLREHF-----------EYYGAVVDVLIPKPFREFAFVTFELDS 238
A +++VG++ +TE + + F V+ V I + + FAF+ F
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVD 64
Query: 239 VAKSLI 244
+
Sbjct: 65 ETTQAM 70
>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 = 4e-08
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 7/87 (8%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQH----V 248
V V L + E+DL E E +G + V++ + A V FE AK + V
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF-KRQALVEFENIDSAKECVTFAADVPV 76
Query: 249 NIKDKKVVVMEATPKK--KMNERQDNR 273
I ++ +T K+ + +
Sbjct: 77 YIAGQQAFFNYSTSKRITRPGNSGPSS 103
Score = 46.7 bits (111), Expect = 4e-07
Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 16/107 (14%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G+S ++ S + PV + V G+ + + DL E E+FGT+ V +
Sbjct: 1 GSSGSSGSHHKVSVS--PV----VHVRGLCESVVEADLVEALEKFGTIC--YVMMMPF-- 50
Query: 143 RSKGFGFIRFSSHESALKAM----LKKHKIGNRICDVRIPESTKIGT 185
K + F + +SA + + I + S +I
Sbjct: 51 --KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITR 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 = 49.9 bits (119), Expect = 4e-08
Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 101 VQNTDLVVLGIPWTFTDNDL---KEYFEQFGTLEFANVKVDKNTGRSK---GFGFIRFSS 154
VQ + V+G+ D ++ EYF +FG + + + S+ ++ +
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72
Query: 155 HESALKAMLKKH--KIGNRI 172
E AL+A+ + + R
Sbjct: 73 SEDALRAIQCVNNVVVDGRT 92
Score = 42.5 bits (100), Expect = 2e-05
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 15/87 (17%)
Query: 191 SKVFVGSLTPDLTESDL---REHFEYYGAVVDVLIPKP--------FREFAFVTFELDSV 239
+ VFV L+ L + ++ E+F +G + V+I A+VT+
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 240 AKSLIGQHVN---IKDKKVVVMEATPK 263
A I Q VN + + + T K
Sbjct: 76 ALRAI-QCVNNVVVDGRTLKASLGTTK 101
>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 = 49.3 bits (118), Expect = 4e-08
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HV 248
S + V +L D ++ + + Y + + + + AFVT A++ I
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRN-KRTAFVTLLNGEQAQNAIQMFHQY 63
Query: 249 NIKDKKVVVMEATPKKKM 266
+ + K ++V +
Sbjct: 64 SFRGKDLIVQLQPTDALL 81
Score = 48.6 bits (116), Expect = 9e-08
Identities = 11/92 (11%), Positives = 32/92 (34%), Gaps = 9/92 (9%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ ++V +P ++ + + + R+K F+ + E A
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQA 53
Query: 159 LKAM--LKKHKIGNRICDVRIPESTKIGTEEP 188
A+ ++ + V++ + + P
Sbjct: 54 QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGP 85
>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 = 49.1 bits (118), Expect = 6e-08
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 103 NTDLVVLGIPWTFTDNDLKE----YFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
N + + + ++LK+ F +FG + ++ V + + + +G F+ F SA
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL--DILVSR-SLKMRGQAFVIFKEVSSA 64
Query: 159 LKAM 162
A+
Sbjct: 65 TNAL 68
Score = 43.8 bits (104), Expect = 4e-06
Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREH----FEYYGAVVDVLIPKP--FREFAFVTFELDSV 239
E +++ +L + + +L++ F +G ++D+L+ + R AFV F+ S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 240 AKSLIG--QHVNIKDKKVVVMEATPKKK 265
A + + Q DK + + A
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 51.0 bits (121), Expect = 2e-07
Identities = 26/153 (16%), Positives = 51/153 (33%), Gaps = 12/153 (7%)
Query: 193 VFVGSLTPDLTESDLREH----FEYYGAVVDVLIPK--PFREFAFVTFELDSVAKSLIG- 245
+++ +L + + +L++ F +G ++D+L+ + R AFV F+ S A + +
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 246 -QHVNIKDKKVVVMEATPKK----KMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGYY 300
Q DK + + A KM R+ + +++ G G
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGAT 131
Query: 301 DNRQQQQGGYNNKRRRNDYDDWHHGNGGNSNNA 333
QG H G
Sbjct: 132 PVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM 164
Score = 49.9 bits (118), Expect = 4e-07
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 103 NTDLVVLGIPWTFTDNDLKE----YFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
N + + + ++LK+ F QFG + ++ V + + + +G F+ F SA
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQIL--DILVSR-SLKMRGQAFVIFKEVSSA 65
Query: 159 LKAM 162
A+
Sbjct: 66 TNAL 69
Score = 45.6 bits (107), Expect = 9e-06
Identities = 12/64 (18%), Positives = 20/64 (31%), Gaps = 7/64 (10%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHK 167
+P + L F QF + + + F+ F + A A L+ K
Sbjct: 214 NLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFK 268
Query: 168 IGNR 171
I
Sbjct: 269 ITQN 272
Score = 36.0 bits (82), Expect = 0.013
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 194 FVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
F+ +L + E L F + +V + + AFV F+
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFD 252
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 48.0 bits (114), Expect = 3e-07
Identities = 13/85 (15%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQH----V 248
+ + L D+TE ++ +G V ++L+ K + AF+ + A +++ +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTP 92
Query: 249 NIKDKKVVVMEATPKKKMNERQDNR 273
++ + + + + K+ + N+
Sbjct: 93 VLRGQPIYIQFSNHKELKTDSSPNQ 117
Score = 46.8 bits (111), Expect = 6e-07
Identities = 14/96 (14%), Positives = 35/96 (36%), Gaps = 12/96 (12%)
Query: 82 SGNSSATQSKRSYPDNSGPVQ--NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+SS + S+ +S + + + +P T+ ++ FG + N+ +
Sbjct: 8 HHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVT--NLLM-- 63
Query: 140 NTGRSKGFGFIRFSSHESALKAM----LKKHKIGNR 171
+ K FI ++ E+A + + +
Sbjct: 64 --LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ 97
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 47.4 bits (113), Expect = 3e-07
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQH----V 248
V + L + E+DL E + +G + V++ P + A V FE A + + +
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQI 82
Query: 249 NIKDKKVVVMEATPKK 264
I V +T +K
Sbjct: 83 YIAGHPAFVNYSTSQK 98
Score = 45.9 bits (109), Expect = 1e-06
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
+Y D + + + G+ + DL E ++FG + + V K
Sbjct: 8 HMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV------MPKKRQAL 61
Query: 150 IRFSSHESALKAM 162
+ F A A+
Sbjct: 62 VEFEDVLGACNAV 74
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 46.7 bits (111), Expect = 4e-07
Identities = 17/108 (15%), Positives = 40/108 (37%), Gaps = 15/108 (13%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
SS + + S V L + +P T+ ++ FG + N+ + +
Sbjct: 2 SSGSSGDKMDGAPS-RV----LHIRKLPGEVTETEVIALGLPFGKVT--NILM----LKG 50
Query: 145 KGFGFIRFSSHESALKAM----LKKHKIGNRICDVRIPESTKIGTEEP 188
K F+ ++ E+A+ + + N+ ++ ++ T P
Sbjct: 51 KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGP 98
Score = 46.0 bits (109), Expect = 8e-07
Identities = 11/76 (14%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI----GQHV 248
+ + L ++TE+++ +G V ++L+ K + AF+ + A +++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTP 76
Query: 249 NIKDKKVVVMEATPKK 264
+++++ + + + K+
Sbjct: 77 HLRNQPIYIQYSNHKE 92
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 48.7 bits (115), Expect = 5e-07
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 94 YPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFS 153
+ V+N + + G P T +D+KE+ E G + ++ + KG F+ F
Sbjct: 100 TDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFD 158
Query: 154 SHESALKAM 162
S ESA K +
Sbjct: 159 SIESAKKFV 167
Score = 42.1 bits (98), Expect = 9e-05
Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP----FREFAFVTFE-LDSVAKSLIGQH 247
V++ D T D++E E G V+++ + + F+ FV F+ ++S K +
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG 171
Query: 248 VNIKDKKVVVMEATPKKKMNERQD 271
K+ ++++ K +++
Sbjct: 172 QKYKETDLLIL---FKDDYFAKKN 192
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 45.6 bits (107), Expect = 2e-05
Identities = 40/322 (12%), Positives = 92/322 (28%), Gaps = 63/322 (19%)
Query: 8 YIYVTNNLEEDGMEIPSEDDGTILLSTLQAQYPSAIGLKYKVES-RYRAVKLADGHLYAP 66
++ + N + + + + ++ + +K ++ S + +L Y
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 67 ----LDGWQDRVYYCTFDASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKE 122
L Q+ + F+ S T + D T + + T T +++K
Sbjct: 246 CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 123 YFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE---------SALKAMLKKHKIGNRIC 173
L++ + + E S + ++
Sbjct: 306 LL-----LKYLDCRPQD-------------LPREVLTTNPRRLSIIAESIRDGL--ATWD 345
Query: 174 DVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAV--VDVLIP-------- 223
+ + K+ T + + L P + R+ F+ +V IP
Sbjct: 346 NWKHVNCDKLTT----IIESSLNVLEPA----EYRKMFDRL-SVFPPSAHIPTILLSLIW 396
Query: 224 --KPFREFAFVTFELDSVAKSLIGQHVNIKDKKVVVME---ATPKKKMNERQDNRNNFDR 278
+ V +L SL+ + K+ + + K NE +R+ D
Sbjct: 397 FDVIKSDVMVVVNKL--HKYSLVEKQP--KESTISIPSIYLELKVKLENEYALHRSIVDH 452
Query: 279 RNDRSRSPMSNSRQYGGGNGYY 300
N S+ + Y+
Sbjct: 453 YNIPKTFD-SDDLIPPYLDQYF 473
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 39.9 bits (93), Expect = 1e-04
Identities = 14/93 (15%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 186 EEPVASKV-FVGSL-TPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSL 243
++ +V + +L ++S + + E YG + + ++ + AF+ E A ++
Sbjct: 20 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAM 78
Query: 244 IGQH----VNIKDKKVVVMEATPKKKMNERQDN 272
+ + + + V V + KK+ +
Sbjct: 79 VDHCLKKALWFQGRCVKVDLSEKYKKLVSGPSS 111
Score = 39.5 bits (92), Expect = 2e-04
Identities = 21/115 (18%), Positives = 42/115 (36%), Gaps = 15/115 (13%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTD----LVVLGIPW-TFTDNDLKEYFEQFGTLEFANVKV 137
G+S ++ K + Q + + + +P ++D+ + + E +G ++ N +
Sbjct: 1 GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIK--NYIL 58
Query: 138 DKNTGRSKGFGFIRFSSHESALKAM----LKKHKIGNRICDVRIPESTKIGTEEP 188
R K FI + E A+ + K R V + E K P
Sbjct: 59 ----MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGP 109
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 41.7 bits (97), Expect = 2e-04
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 10/67 (14%)
Query: 184 GTEEPVASKVFVGSLTPDLT---------ESDLREHFEYYGAVVDVLIPKPFREFAFVTF 234
G+ ++VG + L ES +R F G + + + FV F
Sbjct: 128 GSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKF 186
Query: 235 ELDSVAK 241
+ + A+
Sbjct: 187 KYQANAE 193
Score = 39.8 bits (92), Expect = 7e-04
Identities = 16/98 (16%), Positives = 32/98 (32%), Gaps = 20/98 (20%)
Query: 79 FDASGNSSATQSKRSYPDNSGPV-----QNTDLVVLGIP---------WTFTDNDLKEYF 124
+ + Y ++ G + +N L V GI ++ ++ F
Sbjct: 105 RTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVF 164
Query: 125 EQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+ G ++ SK GF++F +A A
Sbjct: 165 SRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAK 196
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 39.2 bits (91), Expect = 3e-04
Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 9/101 (8%)
Query: 82 SGNSSATQSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVD 138
SGN + S + + ++V + + T + L + F +FGT+ K+
Sbjct: 4 SGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL----KII 59
Query: 139 KNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRI 177
T ++ ++++ SA A L I N C +RI
Sbjct: 60 TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100
>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 = 38.2 bits (88), Expect = 0.001
Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 9/107 (8%)
Query: 76 YCTFDASGNSSATQSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEF 132
SGN + S + + ++V + + T + L + F +FGT+
Sbjct: 16 AVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL- 74
Query: 133 ANVKVDKNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRI 177
K+ T ++ ++++ SA A L I N C +RI
Sbjct: 75 ---KIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 118
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 36.2 bits (83), Expect = 0.003
Identities = 19/100 (19%), Positives = 33/100 (33%), Gaps = 8/100 (8%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLV-VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK 139
+SG+S ++ D+ L+ + + T + L G V+
Sbjct: 2 SSGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGK-----VQRIV 56
Query: 140 NTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRI 177
R+ + F S A KA L I C ++I
Sbjct: 57 IFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI 96
Score = 34.3 bits (78), Expect = 0.016
Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 13/96 (13%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK----SLIGQHV 248
+ + + +T L G V ++I K A V FE A+ +L G +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI 87
Query: 249 NIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSR 284
+ + A P + N R ++ S
Sbjct: 88 YAGCCTLKIEYARPTRL---------NVIRNDNDSW 114
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 34.6 bits (80), Expect = 0.010
Identities = 11/45 (24%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 118 NDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+D+ E + G + ++ VDKN+ + G +++ S +A+ A+
Sbjct: 32 DDVIEECNKHGGVI--HIYVDKNSAQ--GNVYVKCPSIAAAIAAV 72
Score = 27.7 bits (62), Expect = 2.5
Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 14/62 (22%)
Query: 187 EPVASKVFV------------GSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE-FAFVT 233
+P+A++ F ++ + D+ E +G V+ + + K + +V
Sbjct: 3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKD-DVIEECNKHGGVIHIYVDKNSAQGNVYVK 61
Query: 234 FE 235
Sbjct: 62 CP 63
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 32.9 bits (75), Expect = 0.034
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 11/72 (15%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFA----------NVKVDKNTGR-SKGFGFI 150
QN+ G+ +D +++E++++F F + V N G G ++
Sbjct: 14 QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYV 73
Query: 151 RFSSHESALKAM 162
+F E A KA+
Sbjct: 74 KFRREEDAEKAV 85
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 31.6 bits (71), Expect = 0.13
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 89 QSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFG 148
++ + + +T + V G P + + F Q+G + + + +
Sbjct: 10 YTQGDSLTSEDHLDDTWVTVFGFPQASA-SYILLQFAQYGNI------LKHVMSNTGNWM 62
Query: 149 FIRFSSHESALKAMLKKHKI 168
IR+ S A KA+ K +I
Sbjct: 63 HIRYQSKLQARKALSKDGRI 82
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 31.2 bits (71), Expect = 0.15
Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 4/45 (8%)
Query: 118 NDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
DL+ +FG + + + G + F E A +
Sbjct: 41 EDLRVECSKFGQIR--KLLLFDRH--PDGVASVSFRDPEEADYCI 81
Score = 26.2 bits (58), Expect = 7.8
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 204 ESDLREHFEYYGAVVDVLIPKPFRE-FAFVTFE 235
DLR +G + +L+ + A V+F
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFR 72
>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 = 31.0 bits (70), Expect = 0.16
Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 12/79 (15%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPW-TFTDNDLKEYFEQFGTLEFANVKVDKNTGR 143
SS + ++ + V + ++ L + E FG + N +
Sbjct: 2 SSGSSGQKGRVETR-RV----VHIMDFQRGKNLRYQLLQLVEPFGVIS--NHLI----LN 50
Query: 144 SKGFGFIRFSSHESALKAM 162
FI ++ E A A+
Sbjct: 51 KINEAFIEMATTEDAQAAV 69
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.5 bits (70), Expect = 0.23
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 10/24 (41%)
Query: 45 LKYKVESRYRAVKLADGHLYAPLD 68
LK K+++ + LYA D
Sbjct: 22 LK-KLQASLK--------LYAD-D 35
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 32.5 bits (74), Expect = 0.25
Identities = 27/199 (13%), Positives = 62/199 (31%), Gaps = 11/199 (5%)
Query: 141 TGR--SKGFGFIRFSSHESALKAMLK--KHKIGNRICDVRIPESTKIGTEEPVASKVFVG 196
T R +G + E ++ + I E ++ E + +
Sbjct: 382 TARSGKEGSSVLFICKDE---LPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEP 438
Query: 197 SLTPDLTESDL---REHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVNIKDK 253
D+ S + R + Y ++P+ + + + +
Sbjct: 439 EDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLS 498
Query: 254 KVVVMEATPKKKMNERQDNRNNFDRRNDRSRSPMSNSRQYGGGNGYYDNRQQQQGGYNNK 313
+ + +A + + +D N +D S ++ Y + D + NN
Sbjct: 499 RSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDYDDEPFRRSNNN 558
Query: 314 RRR-NDYDDWHHGNGGNSN 331
RR + +D ++ + NSN
Sbjct: 559 RRSFSRSNDKNNYSSRNSN 577
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 30.1 bits (68), Expect = 0.32
Identities = 9/49 (18%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 118 NDLKEYFEQFGTLEFANVKVDKNTG----RSKGFGFIRFSSHESALKAM 162
D+++ ++G ++ ++++ + G F+ F+S KAM
Sbjct: 30 EDVRDECSKYGLVK--SIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAM 76
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 31.2 bits (70), Expect = 0.35
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 112 PWTFTDNDLKEYFEQF 127
TF D K Y+ QF
Sbjct: 204 KCTFWDAISKLYYVQF 219
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.7 bits (66), Expect = 0.45
Identities = 10/63 (15%), Positives = 25/63 (39%)
Query: 203 TESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVNIKDKKVVVMEATP 262
++ L + YG V+++++ A V F A+ + V + D + +
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEG 89
Query: 263 KKK 265
+ +
Sbjct: 90 QPQ 92
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 31.3 bits (70), Expect = 0.46
Identities = 9/51 (17%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKH 166
+ N L E+ G ++ + +K + F R+ + E + +A + +
Sbjct: 33 SRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYVTLN 77
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 29.3 bits (66), Expect = 0.69
Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 8/50 (16%)
Query: 119 DLKEYFEQFGTLEFANVKVDKNTGRSK------GFGFIRFSSHESALKAM 162
++ E +FG + V + + + F+ FS KA+
Sbjct: 41 EVTEECGKFGAVN--RVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAI 88
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 29.2 bits (65), Expect = 0.85
Identities = 14/74 (18%), Positives = 23/74 (31%), Gaps = 15/74 (20%)
Query: 119 DLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK-----KHKIGNRIC 173
DL F G +++ +D G + G I F K ++ N+
Sbjct: 35 DLHILFSNHGEIKW----IDFVRGAKE--GIILFKEKAKEALGKAKDANNGNLQLRNKEV 88
Query: 174 DVRIPESTKIGTEE 187
+ E G E
Sbjct: 89 TWEVLE----GEVE 98
>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 = 30.4 bits (68), Expect = 1.3
Identities = 60/304 (19%), Positives = 92/304 (30%), Gaps = 113/304 (37%)
Query: 32 LSTLQAQYPSAIGLKYKVESRYRAVKLADGHLY----APLDGWQDRVYYCTFDASG---N 84
L L Y +G +K + L LD ++V+ + N
Sbjct: 173 LRDLYQTYHVLVG---------DLIKFSAETLSELIRTTLD--AEKVFTQGLNILEWLEN 221
Query: 85 SSATQSKRSYPDN--------SGP----VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEF 132
S T PD S P +Q VV FT +L+ Y + G
Sbjct: 222 PSNT------PDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLK--GA--- 270
Query: 133 ANVKVDKNTGRSKGF---GFIRFS-SHESALKAMLKKHK----IGNRIC-----DVRIPE 179
TG S+G I + S ES ++ K IG R C + +P
Sbjct: 271 --------TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVR-CYEAYPNTSLPP 321
Query: 180 ST-------KIGTEEPVASKVFVGSLTPDLTESDLRE---HFEYYGAVVDVLI--PKPFR 227
S G P+ S + +LT + + + + H V L+ K
Sbjct: 322 SILEDSLENNEGVPSPMLS---ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK--- 375
Query: 228 EFAFVTFELDSVA---KSLIGQHVNIKDKKVVVMEATPKKKMNERQDNRNNFDRRNDRSR 284
V V+ +SL G ++ ++ K A D+SR
Sbjct: 376 --NLV------VSGPPQSLYGLNLTLRKAK-----APSGL----------------DQSR 406
Query: 285 SPMS 288
P S
Sbjct: 407 IPFS 410
Score = 30.0 bits (67), Expect = 1.5
Identities = 22/142 (15%), Positives = 41/142 (28%), Gaps = 56/142 (39%)
Query: 120 LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRIPE 179
+K Y A + + + SAL + GN
Sbjct: 123 IKNYIT-------ARIMAKRPFDKK----------SNSAL---FRAVGEGN--------- 153
Query: 180 STKIGTEEPVASKVFV-----GSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTF 234
+++ G+ E LR+ ++ Y +V LI +F+ T
Sbjct: 154 -----------AQLVAIFGGQGNTDDYFEE--LRDLYQTYHVLVGDLI-----KFSAETL 195
Query: 235 E----LDSVAKSLIGQHVNIKD 252
A+ + Q +NI +
Sbjct: 196 SELIRTTLDAEKVFTQGLNILE 217
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 27.7 bits (61), Expect = 1.9
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 9/82 (10%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA-- 161
T L V +P + + ++ K + +RF + +SA +A
Sbjct: 10 TLLYVYNLPANKDGKSVSNRLRRL-----SDNCGGKVLSITGCSAILRFINQDSAERAQK 64
Query: 162 -MLKKHKIGNRICDVRIPESTK 182
M + GNRI V +
Sbjct: 65 RMENEDVFGNRI-IVSFTPKNR 85
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 27.5 bits (61), Expect = 2.4
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 119 DLKEYFEQFGTLEFANVKVDKNTGRSK---GFGFIRFSSHESALKAMLKKHK 167
+ KE E++G + + + G F+ F ESA+KA++ +
Sbjct: 29 ETKEECEKYGKVG--KCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG 78
>3a5v_A Alpha-galactosidase; beta/alpha barrel, N-glycosylation, hydrolase;
HET: MAN NAG BMA 1PG; 2.00A {Umbelopsis vinacea}
Length = 397
Score = 28.6 bits (63), Expect = 3.2
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 2/65 (3%)
Query: 270 QDNRNNFDRRNDRSRSPMSNSRQYGGGNGYYD--NRQQQQGGYNNKRRRNDYDDWHHGNG 327
D +NF+R + + G + N+ ND D GNG
Sbjct: 188 GDVYDNFNRPDPACPCTTYDCVLAGFRCSVMNIINKAVAVSQKARSGGWNDLDMLEVGNG 247
Query: 328 GNSNN 332
G +
Sbjct: 248 GMNQE 252
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 26.9 bits (59), Expect = 3.5
Identities = 10/65 (15%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE-LDSVAKS 242
G +S + + +LT + LR +G +V + A + + K+
Sbjct: 1 GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKA 59
Query: 243 LIGQH 247
+ +
Sbjct: 60 QMALN 64
>2f1m_A Acriflavine resistance protein A; helical hairpin, lipoyl domain,
beta barrel, transport prote; 2.71A {Escherichia coli}
Length = 277
Score = 27.2 bits (61), Expect = 8.1
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 124 FEQFGTLEFANVKVDKNTG 142
F Q GTLEF++V VD+ TG
Sbjct: 211 FPQDGTLEFSDVTVDQTTG 229
>3qcw_A Neurexin-1-alpha; synaptic adhesion molecule, cell adhesion; HET:
NAG; 2.65A {Bos taurus} PDB: 3r05_A* 3poy_A*
Length = 1245
Score = 27.5 bits (60), Expect = 8.9
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 23 PSEDDGTILLSTLQAQYPSAIGLKYKVESRYRAVKLADGHLYAPLD 68
+E +G IL S + ++ ++ + A+++ DGHLY LD
Sbjct: 452 TTEPNGLILFSHGKPRHQKDAKHPQMIKVDFFAIEMLDGHLYLLLD 497
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
0.314 0.132 0.383
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,559,563
Number of extensions: 335091
Number of successful extensions: 1317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1047
Number of HSP's successfully gapped: 387
Length of query: 363
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 268
Effective length of database: 4,049,298
Effective search space: 1085211864
Effective search space used: 1085211864
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)