RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12549
(336 letters)
>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 = 276 bits (709), Expect = 1e-92
Identities = 50/267 (18%), Positives = 96/267 (35%), Gaps = 41/267 (15%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPS---LRKSGVGNVFIKNLDKSIDNKAMYDTFS 132
D++R LD +G P + + + R + V +KNL KS + +Y F
Sbjct: 11 DSKRPLD-------EGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFK 63
Query: 133 AFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
G I+ VA + + + F + A +I K + + + + V
Sbjct: 64 HCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLT----- 116
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAY 250
+++ NF + ++++ + + + SR F ++
Sbjct: 117 ----------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDV 166
Query: 251 ESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYV 310
S E A V+ NG +++G L ++ E K +G + +
Sbjct: 167 TSKEDARYCVEKLNGLKIEGYTLVT-----------KVSNPLEKSKRTDSATLEGREIMI 215
Query: 311 KNLDDSIDDER-LRKEFTPFGTITSAK 336
+NL + DE LR+ F FG+I
Sbjct: 216 RNLSTELLDENLLRESFEGFGSIEKIN 242
Score = 179 bits (456), Expect = 1e-54
Identities = 38/211 (18%), Positives = 79/211 (37%), Gaps = 17/211 (8%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
A+ + + I + +++ N S + + D
Sbjct: 93 GALAAITKTHKV-VGQNEIIVSHLTEC---------TLWMTNFPPSYTQRNIRDLLQDIN 142
Query: 136 SI-LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
+ LS ++ S+ + ++ ++E A +EK+NG+ + + K E+ K
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT-KVSNPLEKSK 201
Query: 195 ELGEKAKLFTNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNND---GKSRGFGFVAY 250
+ I+N + DE L+E FE +G+I + + F+ +
Sbjct: 202 RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261
Query: 251 ESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
E+ + AE+A+Q N + + + V A KK
Sbjct: 262 ENKDSAERALQM-NRSLLGNREISVSLADKK 291
>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 = 254 bits (651), Expect = 6e-84
Identities = 45/251 (17%), Positives = 83/251 (33%), Gaps = 40/251 (15%)
Query: 89 LKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQG 148
L IR + R + I+ L + N+ ++D S + + C V
Sbjct: 3 LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----D 54
Query: 149 NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYI 208
KG FV E A +I + L + + V + + +
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV--------------QLQPTDALLCV 100
Query: 209 KNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
N ++ +E+ P+G++ ++ G+S+G+GF Y + A +A GK
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
Query: 267 EVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDD-ERLRKE 325
+ + LYV L R L V L +D + L +
Sbjct: 161 PLGPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRA 205
Query: 326 FTPFGTITSAK 336
+ + T +
Sbjct: 206 LSAVHSPTFCQ 216
Score = 227 bits (580), Expect = 3e-73
Identities = 48/228 (21%), Positives = 87/228 (38%), Gaps = 17/228 (7%)
Query: 78 ERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI 137
E A++ + L+ R + + D + + NL S+ + + FGS+
Sbjct: 71 EAAINAFHQSRLRERELSVQLQPTDA--------LLCVANLPPSLTQQQFEELVRPFGSL 122
Query: 138 LSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
C + E+ G SKGYGF + +++A ++ + G L + ++V + L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
Query: 197 GEKAKLFTNVYIKNFGEDFND-EKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPE 254
+ + + FND + L + T ++ DG+ +GF + YE+ E
Sbjct: 183 HSR-----CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAE 237
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
AE+A Q +G + G L V L NR
Sbjct: 238 MAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATAL-NR 284
Score = 118 bits (299), Expect = 1e-31
Identities = 25/123 (20%), Positives = 46/123 (37%), Gaps = 2/123 (1%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQR-DPSLRKSGVGNVFIKNLDKSI-DNKAMYDTFSA 133
RA + L R + + W+ + + + L D A+ SA
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSA 208
Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
S C++A + G KG+ + +ET E A ++ ++ +G+ L + V P
Sbjct: 209 VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 268
Query: 194 KEL 196
L
Sbjct: 269 SML 271
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 247 bits (633), Expect = 3e-82
Identities = 50/192 (26%), Positives = 100/192 (52%), Gaps = 10/192 (5%)
Query: 100 QRDPSLRKSG----VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYG 154
R + ++ G + V++ ++ + + F+ FG I S ++ D KG+
Sbjct: 14 GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73
Query: 155 FVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE---KELGEKAKLFTNVYIKNF 211
FV +E EAA ++E++N ++L + + VG+ + + +L E+A+ F +Y+ +
Sbjct: 74 FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 133
Query: 212 GEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
+D +D+ +K +FE +G I S + GK +G+GF+ YE + ++ AV + N ++
Sbjct: 134 HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG 193
Query: 270 GKILYVGRAQKK 281
G+ L VG+A
Sbjct: 194 GQYLRVGKAVTP 205
Score = 144 bits (366), Expect = 4e-42
Identities = 35/166 (21%), Positives = 69/166 (41%), Gaps = 16/166 (9%)
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
+ + + G R+ + VY+ + + ++ +++ F P+G I S
Sbjct: 5 ASMTGGQQMGRGSAAQRQGALAIMS-------RVYVGSIYYELGEDTIRQAFAPFGPIKS 57
Query: 233 YRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
+ + K +GF FV YE PE A+ A++ N + G+ + VGR + + +
Sbjct: 58 IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ 117
Query: 291 RFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
E + +YV ++ + D+ ++ F FG I SA
Sbjct: 118 LAEEAR-------AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSAT 156
Score = 127 bits (321), Expect = 1e-35
Identities = 30/127 (23%), Positives = 58/127 (45%), Gaps = 10/127 (7%)
Query: 78 ERALDTMNFDALKGRPIRIMWS----QRDPSLRK-----SGVGNVFIKNLDKSIDNKAMY 128
+ AL+ MN L GR I++ Q P + + +++ ++ + + + +
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 129 DTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
F AFG I S +A+D G KGYGF+ +E +++ ++ +N L + + VGK +
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Query: 188 PRKEREK 194
Sbjct: 204 TPPMPLL 210
Score = 32.7 bits (75), Expect = 0.12
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPS 104
++ A+ +MN L G+ +R+ + P
Sbjct: 179 SSQDAVSSMNLFDLGGQYLRVGKAVTPPM 207
>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 = 224 bits (572), Expect = 1e-73
Identities = 41/184 (22%), Positives = 82/184 (44%), Gaps = 10/184 (5%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
S + N+FI NL+ + + S + V G ++ +G+V F
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDE 218
E+ E K++E + G+ + + + K R ++ + KN + ++
Sbjct: 62 ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVR------AARTLLAKNLSFNITED 114
Query: 219 KLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
+LKE+FE I +++ DGKS+G ++ ++S AEK ++ G E+DG+ + +
Sbjct: 115 ELKEVFEDALEIR---LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
Query: 279 QKKA 282
+K
Sbjct: 172 GEKG 175
Score = 126 bits (319), Expect = 1e-35
Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 18/135 (13%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
N++I N + + +LK V++ G +R FG+V +ES E EKA++
Sbjct: 13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 72
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
G +V G + + + + + + L KNL +I ++
Sbjct: 73 L-TGLKVFGNEIKLEKPKGRDSKKVR----------------AARTLLAKNLSFNITEDE 115
Query: 322 LRKEFTPFGTITSAK 336
L++ F I
Sbjct: 116 LKEVFEDALEIRLVS 130
Score = 105 bits (265), Expect = 9e-28
Identities = 24/114 (21%), Positives = 49/114 (42%), Gaps = 5/114 (4%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D E+AL+ + + G I++ + S + + KNL +I + + F
Sbjct: 66 DLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124
Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
I + G SKG ++ F++E A K++E+ G ++ + V + +
Sbjct: 125 EIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 213 bits (544), Expect = 9e-69
Identities = 102/157 (64%), Positives = 119/157 (75%), Gaps = 13/157 (8%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSIDNKA+YDTFSAFG
Sbjct: 69 DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128
Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
+ILSCKV DE SKGYGFVHFET+EAA ++IEK+NGMLLN + VFVG+F RKERE E
Sbjct: 129 NILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187
Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
LG +AK F + ++ G I +
Sbjct: 188 LGARAKEFYPYDVPDY------------AGSSGRIVT 212
Score = 186 bits (475), Expect = 2e-58
Identities = 54/210 (25%), Positives = 106/210 (50%), Gaps = 7/210 (3%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
+PS + ++++ +L + +Y+ FS G ILS +V +D S GY +V+
Sbjct: 4 GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND 217
F+ A ++++ +N ++ K V + K N++IKN + ++
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV------GNIFIKNLDKSIDN 117
Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
+ L + F +G I S +V+ ++ S+G+GFV +E+ E AE+A++ NG ++ + ++VGR
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 278 AQKKAERTQELKRRFEMLKIERLNRYQGVN 307
+ + ER EL R + + Y G +
Sbjct: 178 FKSRKEREAELGARAKEFYPYDVPDYAGSS 207
Score = 105 bits (264), Expect = 3e-27
Identities = 38/135 (28%), Positives = 63/135 (46%), Gaps = 18/135 (13%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
++Y+ + D + L E F P G I S RV + +S G+ +V ++ P AE+A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
N + GK + + +Q+ L + N+++KNLD SID++
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDP----------------SLRKSGVGNIFIKNLDKSIDNKA 119
Query: 322 LRKEFTPFGTITSAK 336
L F+ FG I S K
Sbjct: 120 LYDTFSAFGNILSCK 134
Score = 41.5 bits (98), Expect = 1e-04
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
Y +LYV +L + + L ++F+P G I S +
Sbjct: 12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR 46
>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 = 187 bits (477), Expect = 3e-59
Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 11/178 (6%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN---SKGYGFVHFETEEAA 164
S +F+ + ++ K + + F +G++ V +D N SKG FV F T +AA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMF 224
++ ++ M + + + P + E KLF I + + ++ MF
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMF 116
Query: 225 EPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV---DGKILYVGRA 278
+G I R++ DG SRG FV + + A+ A++A + + + V A
Sbjct: 117 SSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 136 bits (346), Expect = 1e-39
Identities = 24/137 (17%), Positives = 56/137 (40%), Gaps = 18/137 (13%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKA 259
+++ ++++ L+E+FE YG + V+ N +S+G FV + + + A +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDD 319
A + +V + + + + E+ N + L++ + +
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPA--------------DSEKNNAVEDRKLFIGMISKKCTE 109
Query: 320 ERLRKEFTPFGTITSAK 336
+R F+ FG I +
Sbjct: 110 NDIRVMFSSFGQIEECR 126
Score = 98.5 bits (246), Expect = 4e-25
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 4/99 (4%)
Query: 78 ERALDTMN---FDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF 134
A + ++ PI++ + + + +FI + K + FS+F
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR-KLFIGMISKKCTENDIRVMFSSF 119
Query: 135 GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
G I C++ + G S+G FV F T A +I+ ++
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 158
>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 = 190 bits (484), Expect = 3e-59
Identities = 40/259 (15%), Positives = 93/259 (35%), Gaps = 43/259 (16%)
Query: 91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
G I I + + +F+ NL I + F +G + +D
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57
Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKN 210
+G+GF+ E+ A + +++G +L S+ + + A + +KN
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI--------------RFATHGAALTVKN 103
Query: 211 FGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWNGKEV- 268
++E L++ F +G + V+ +D G++ G GFV + + A KA++
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFL 163
Query: 269 ---DGKILYVGRAQKKAERTQELKRRFE-------------------MLKIERLNRYQGV 306
+ + V ++ + ++ + + E +R++ +
Sbjct: 164 LTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKAL 223
Query: 307 NLYVKNLDDSIDDERLRKE 325
+ K + +D +
Sbjct: 224 DEMEKQQREQVDRNIREAK 242
Score = 178 bits (453), Expect = 1e-54
Identities = 46/225 (20%), Positives = 79/225 (35%), Gaps = 37/225 (16%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
E A ++ LK RP+RI ++ + +KNL + N+ + FS FG
Sbjct: 70 LAEIAKAELDGTILKSRPLRIRFATHGA--------ALTVKNLSPVVSNELLEQAFSQFG 121
Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG---MLLNSKIVFVGKFIPRKER 192
+ V D++G + G GFV F + A K++E+ +L + + + + + +
Sbjct: 122 PVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD 181
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
E L EK T Y K F GT
Sbjct: 182 EDGLPEKLMQKTQQYHKERE-------QPPRFAQPGTFEFEYAS---------------- 218
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKI 297
KA+ ++ + + A++K E E R L +
Sbjct: 219 ---RWKALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLML 260
Score = 145 bits (368), Expect = 7e-42
Identities = 37/154 (24%), Positives = 57/154 (37%), Gaps = 28/154 (18%)
Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS 242
+G I K K + +++ N D +E K +FE YG + + +
Sbjct: 2 MGFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN----RD 57
Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
RGFGF+ ES AE A +G + + L + A
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT----------------------- 94
Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
G L VKNL + +E L + F+ FG + A
Sbjct: 95 -HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV 127
>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 = 186 bits (474), Expect = 8e-59
Identities = 50/176 (28%), Positives = 88/176 (50%), Gaps = 13/176 (7%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANK 166
+ N+ + L + + ++ +Y F A G I +C++ +D + G S GY FV F +E + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEP 226
+I+ +NG+ + +K + V P E K+ TN+Y+ N D++L +F
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGK 112
Query: 227 YGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA 278
YG+I ++ G+ RG FV Y E A++A+ A N +G + L V A
Sbjct: 113 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 147 bits (374), Expect = 6e-44
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 20/136 (14%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
TN+ + +D D +L +F G I + R+M + G S G+ FV + S +++A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDE 320
+ NG V K L V A+ E ++ NLYV NL +I D+
Sbjct: 63 KVLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDD 104
Query: 321 RLRKEFTPFGTITSAK 336
+L F +G+I
Sbjct: 105 QLDTIFGKYGSIVQKN 120
Score = 136 bits (346), Expect = 1e-39
Identities = 22/103 (21%), Positives = 54/103 (52%), Gaps = 3/103 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D++RA+ +N ++ + +++ +++ P N+++ NL ++I + + F +G
Sbjct: 57 DSQRAIKVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG 114
Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
SI+ + +D+ G +G FV + E A ++I +N ++
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 157
>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 = 171 bits (436), Expect = 6e-54
Identities = 80/111 (72%), Positives = 90/111 (81%), Gaps = 1/111 (0%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
G GN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV DE SKGYGFVHFET+EAA ++
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERA 61
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDE 218
IEK+NGMLLN + VFVG+F RKERE ELG +AK FTNVYIKNFG
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112
Score = 125 bits (315), Expect = 8e-36
Identities = 34/117 (29%), Positives = 64/117 (54%), Gaps = 10/117 (8%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
N++IKN + +++ L + F +G I S +V+ ++ S+G+GFV +E+ E AE+A++
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65
Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDE 320
NG ++ + ++VGR + + ER EL R + + N+Y+KN
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAK----------EFTNVYIKNFGPGSTRA 112
Score = 51.9 bits (125), Expect = 1e-08
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
N+++KNLD SID++ L F+ FG I S K
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCK 36
Score = 34.1 bits (79), Expect = 0.016
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQR------DPSLRKSGVGNVFIKNLDKSIDNKA 126
ERA++ MN L R + + + + R NV+IKN A
Sbjct: 57 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 113
>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 = 170 bits (432), Expect = 1e-52
Identities = 30/110 (27%), Positives = 60/110 (54%), Gaps = 1/110 (0%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D AL T+N ++ ++I W+ + N+F+ +L+ ++D++ + + F F
Sbjct: 53 DANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFP 112
Query: 136 SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
S LS V D + G+S+GYGFV F +++ A +++ + G LN + + +
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
Score = 159 bits (404), Expect = 2e-48
Identities = 42/170 (24%), Positives = 85/170 (50%), Gaps = 8/170 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+++ NLDK+I + F G I + K+ D+ + Y FV + AN +++ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
G + + IV + ++ + N+++ + + +DE L+ F+ + + S
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDT------FNLFVGDLNVNVDDETLRNAFKDFPSYLS 116
Query: 233 YRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
VM G SRG+GFV++ S + A+ A+ + G++++G+ L + A K
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 118 bits (297), Expect = 1e-32
Identities = 32/132 (24%), Positives = 62/132 (46%), Gaps = 17/132 (12%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
+Y+ N + ++ LK+ F+ G I + ++M + + K+ + FV Y A A+Q N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRK 324
GK+++ I+ + A + ++ + NL+V +L+ ++DDE LR
Sbjct: 63 GKQIENNIVKINWAFQS----------------QQSSSDDTFNLFVGDLNVNVDDETLRN 106
Query: 325 EFTPFGTITSAK 336
F F + S
Sbjct: 107 AFKDFPSYLSGH 118
Score = 32.1 bits (74), Expect = 0.12
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQR 101
D + A+D+M L GRP+RI W+ +
Sbjct: 141 DAQNAMDSMQGQDLNGRPLRINWAAK 166
>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 = 165 bits (420), Expect = 1e-50
Identities = 47/172 (27%), Positives = 88/172 (51%), Gaps = 13/172 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
N+ + L +++ + F + G I SCK+ +D+ G S GYGFV++ + A K+I
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
+NG+ L +K + V P ++ N+Y+ + ++L+++F YG I
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMTQKELEQLFSQYGRI 115
Query: 231 TSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA 278
+ R++ G SRG GF+ ++ AE+A++ NG++ G + + V A
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 150 bits (381), Expect = 6e-45
Identities = 28/103 (27%), Positives = 59/103 (57%), Gaps = 3/103 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D E+A++T+N L+ + I++ +++ PS N+++ L K++ K + FS +G
Sbjct: 56 DAEKAINTLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
I++ ++ D+ G S+G GF+ F+ A ++I+ +NG +
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS 156
Score = 131 bits (331), Expect = 2e-37
Identities = 33/135 (24%), Positives = 61/135 (45%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ E+ + +F G I S +++ G+S G+GFV Y P+ AEKA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG + K + V A+ + + NLYV L ++ +
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASI------------------RDANLYVSGLPKTMTQKE 104
Query: 322 LRKEFTPFGTITSAK 336
L + F+ +G I +++
Sbjct: 105 LEQLFSQYGRIITSR 119
>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 = 164 bits (417), Expect = 7e-50
Identities = 32/191 (16%), Positives = 76/191 (39%), Gaps = 21/191 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ------GNSKGYGFVHFETEEAANK 166
+++ N+ I +AM D F+A + A K + F+ F + + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL------------FTNVYIKNFGED 214
++ +G++ + + + + + + ++I
Sbjct: 67 AMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 215 FNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI 272
ND+++KE+ +G + ++ ++ + G S+G+ F Y ++A+ NG ++ K
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 273 LYVGRAQKKAE 283
L V RA A+
Sbjct: 186 LLVQRASVGAK 196
Score = 121 bits (305), Expect = 2e-33
Identities = 19/140 (13%), Positives = 51/140 (36%), Gaps = 10/140 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
+Y+ N +E + + F + + + + F F+ + S + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 259 AVQAWNGKEVDGKILYVGRAQKKAER--TQELKRRFEMLKIERLNRYQGVNLYVKNLDDS 316
A+ +G G+ L + R E + + + L++ L +
Sbjct: 67 AMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 317 IDDERLRKEFTPFGTITSAK 336
++D+++++ T FG + +
Sbjct: 126 LNDDQVKELLTSFGPLKAFN 145
Score = 93.9 bits (234), Expect = 5e-23
Identities = 23/129 (17%), Positives = 52/129 (40%), Gaps = 20/129 (15%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQ------------------RDPSLRKSGVGNVFIKN 117
+T +A+ + +G+ ++I ++ +FI
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 118 LDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLL 176
L +++ + + ++FG + + + +D G SKGY F + +++I +NGM L
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 177 NSKIVFVGK 185
K + V +
Sbjct: 182 GDKKLLVQR 190
Score = 28.1 bits (63), Expect = 3.1
Identities = 4/25 (16%), Positives = 12/25 (48%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQ 100
T++A+ +N L + + + +
Sbjct: 168 VTDQAIAGLNGMQLGDKKLLVQRAS 192
>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 = 155 bits (393), Expect = 1e-46
Identities = 31/174 (17%), Positives = 73/174 (41%), Gaps = 17/174 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ------GNSKGYGFVHFETEEAANK 166
+++ N+ I +AM D F+A + A K + F+ F + + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEP 226
++ +G++ + + + + + ++I ND+++KE+
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPG--------AHKLFIGGLPNYLNDDQVKELLTS 117
Query: 227 YGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
+G + ++ ++ + G S+G+ F Y ++A+ NG ++ K L V RA
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 123 bits (310), Expect = 2e-34
Identities = 24/111 (21%), Positives = 52/111 (46%), Gaps = 4/111 (3%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
+T +A+ + +G+ ++I L + +FI L +++ + + ++FG
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAH--KLFIGGLPNYLNDDQVKELLTSFG 119
Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK 185
+ + + +D G SKGY F + +++I +NGM L K + V +
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Score = 93.8 bits (234), Expect = 2e-23
Identities = 18/138 (13%), Positives = 47/138 (34%), Gaps = 26/138 (18%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
+Y+ N +E + + F + + + + F F+ + S + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 259 AVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSID 318
A+ +G G+ L + R L++ L + ++
Sbjct: 67 AMAF-DGIIFQGQSLKIRRPHDYQPLPG------------------AHKLFIGGLPNYLN 107
Query: 319 DERLRKEFTPFGTITSAK 336
D+++++ T FG + +
Sbjct: 108 DDQVKELLTSFGPLKAFN 125
>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 = 132 bits (334), Expect = 6e-39
Identities = 37/92 (40%), Positives = 55/92 (59%), Gaps = 2/92 (2%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQD-EQGNSKGYGFVHFETEEAAN 165
SG +FI NLD ID K +YDTFSAFG IL K+ +D + GNSKGY F++F + +A++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKEREKELG 197
+IE +NG L ++ + V + +
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
Score = 87.6 bits (218), Expect = 7e-22
Identities = 20/83 (24%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
++I N + +++ L + F +G I ++M + G S+G+ F+ + S + ++ A++
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
A NG+ + + + V A KK +
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
Score = 44.9 bits (107), Expect = 2e-06
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+++ NLD ID++ L F+ FG I
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTP 36
Score = 29.1 bits (66), Expect = 0.54
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
++ A++ MN L RPI + ++ + S + SG +
Sbjct: 60 ASDAAIEAMNGQYLCNRPITVSYAFKKDS-KGSGPSS 95
>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 = 132 bits (335), Expect = 5e-38
Identities = 42/174 (24%), Positives = 88/174 (50%), Gaps = 14/174 (8%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
+FI L+ + + F +G++ K+ +D G S+G+GF+ FE + ++ ++
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 170 KVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT 229
+ +L+ K++ + IPR E++K +++ G D ++ +E F +GT
Sbjct: 64 TQH--ILDGKVIDPKRAIPRDEQDKT--------GKIFVGGIGPDVRPKEFEEFFSQWGT 113
Query: 230 ITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
I ++M + G+SRGFGFV Y+S + ++ Q + + + + RA+ +
Sbjct: 114 IIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166
Score = 91.1 bits (227), Expect = 2e-22
Identities = 36/141 (25%), Positives = 65/141 (46%), Gaps = 26/141 (18%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEF 255
E K+F I D ++ L+E F YGT+T ++M G+SRGFGF+++E P
Sbjct: 2 ESCKMF----IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS 57
Query: 256 AEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDD 315
++ V+ +DGK++ RA + E+ + K ++V +
Sbjct: 58 VDEVVKT--QHILDGKVIDPKRAIPRDEQDKTGK------------------IFVGGIGP 97
Query: 316 SIDDERLRKEFTPFGTITSAK 336
+ + + F+ +GTI A+
Sbjct: 98 DVRPKEFEEFFSQWGTIIDAQ 118
Score = 69.5 bits (171), Expect = 2e-14
Identities = 23/116 (19%), Positives = 53/116 (45%), Gaps = 8/116 (6%)
Query: 76 DTERALDTMNFDALKGRPIRI-MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF 134
+ + T + L G+ I RD + G +F+ + + K + FS +
Sbjct: 57 SVDEVVKTQHI--LDGKVIDPKRAIPRDEQDK---TGKIFVGGIGPDVRPKEFEEFFSQW 111
Query: 135 GSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
G+I+ ++ D + G S+G+GFV +++ +A ++ + + + + + + PR
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166
>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 = 131 bits (331), Expect = 6e-37
Identities = 32/211 (15%), Positives = 72/211 (34%), Gaps = 35/211 (16%)
Query: 100 QRDPSLRKSGVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
P L +G + + NL+ + + ++++ F +G + K+ + K V
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQM 79
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVG----KFIPRKEREKELGEKAKLFTN--------- 205
A ++ +NG L+ K + + + + +E K + N
Sbjct: 80 ADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 139
Query: 206 --------------VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYE 251
+++ N ++E LK +F G + K R +
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--KDRKMALIQMG 197
Query: 252 SPEFAEKAVQAWNGKEV-DGKILYVGRAQKK 281
S E A +A+ + ++ + L V ++
Sbjct: 198 SVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
Score = 97.8 bits (243), Expect = 3e-24
Identities = 24/151 (15%), Positives = 56/151 (37%), Gaps = 21/151 (13%)
Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ + + N E + L +F YG + +++ + V A+ A+
Sbjct: 35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSH 91
Query: 263 WNGKEVDGKILYVGRAQKKA-------ERTQELKRRFEMLKIERLNRYQGVN-------- 307
NG ++ GK + + ++ + + Q L + + + R + N
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 308 --LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++ N+ S+ +E L+ F+ G +
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182
>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 = 126 bits (317), Expect = 3e-35
Identities = 30/202 (14%), Positives = 69/202 (34%), Gaps = 35/202 (17%)
Query: 109 GVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
G + + NL+ + + ++++ F +G + K+ + K V A +
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLA 57
Query: 168 IEKVNGMLLNSKIVFVG----KFIPRKEREKELGEKAKLFTN------------------ 205
+ +NG L+ K + + + + +E K + N
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 206 -----VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAV 260
+++ N ++E LK +F G + K R + S E A +A+
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--KDRKMALIQMGSVEEAVQAL 175
Query: 261 QAWNGKEV-DGKILYVGRAQKK 281
+ ++ + L V ++
Sbjct: 176 IDLHNHDLGENHHLRVSFSKST 197
Score = 102 bits (255), Expect = 4e-26
Identities = 24/151 (15%), Positives = 56/151 (37%), Gaps = 21/151 (13%)
Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ + + N E + L +F YG + +++ + V A+ A+
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSH 60
Query: 263 WNGKEVDGKILYVGRA-------QKKAERTQELKRRFEMLKIERLNRYQGVN-------- 307
NG ++ GK + + + ++ + Q L + + + R + N
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 308 --LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++ N+ S+ +E L+ F+ G +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 151
>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 = 122 bits (308), Expect = 5e-35
Identities = 44/105 (41%), Positives = 59/105 (56%), Gaps = 5/105 (4%)
Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
G +R N+Y+KN + +DE+L++ F P+GTITS +VM G+S+
Sbjct: 1 GSSGSSGDRITRYQ-----VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK 55
Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQEL 288
GFGFV + SPE A KAV NG+ V K LYV AQ+K ER
Sbjct: 56 GFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100
Score = 98.8 bits (247), Expect = 4e-26
Identities = 33/89 (37%), Positives = 57/89 (64%), Gaps = 1/89 (1%)
Query: 105 LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAA 164
+ + V N+++KNLD ID++ + FS FG+I S KV + G SKG+GFV F + E A
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEA 68
Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
K++ ++NG ++ +K ++V ++ER+
Sbjct: 69 TKAVTEMNGRIVATKPLYVALAQRKEERQ 97
Score = 73.0 bits (180), Expect = 2e-16
Identities = 32/39 (82%), Positives = 35/39 (89%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+R+ RYQ VNLYVKNLDD IDDERLRK F+PFGTITSAK
Sbjct: 8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK 46
Score = 27.9 bits (63), Expect = 1.5
Identities = 9/37 (24%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
+ +A+ MN + +P+ + +QR R+SG +
Sbjct: 67 EATKAVTEMNGRIVATKPLYVALAQRKEE-RQSGPSS 102
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 120 bits (304), Expect = 2e-34
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 6/103 (5%)
Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
+PR E T ++++ F D + +L E+F P+G + +++
Sbjct: 12 SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------N 65
Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
GF FV +E E A KA++ +GK + L V ++ A+R +
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 81.6 bits (202), Expect = 1e-19
Identities = 11/62 (17%), Positives = 22/62 (35%)
Query: 275 VGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITS 334
+G + + L R + + L+V+ + + L + F PFG +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60
Query: 335 AK 336
K
Sbjct: 61 VK 62
Score = 74.6 bits (184), Expect = 5e-17
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 7/96 (7%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
+ +F++ + + + F FG + K+ G+ FV F
Sbjct: 20 HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEF 72
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
E E+A K+IE+V+G ++ + V +R +
Sbjct: 73 EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 25.7 bits (57), Expect = 9.5
Identities = 3/32 (9%), Positives = 16/32 (50%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRK 107
+A++ ++ + +P+ +++S+ +
Sbjct: 77 SAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 119 bits (301), Expect = 4e-34
Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 104 SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEA 163
S SG +F++NL K + D F+ G +L + + G SKG G V FE+ E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEV 60
Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
A ++ +NGM L+ + + V R +R
Sbjct: 61 AERACRMMNGMKLSGREIDV-----RIDRNAS 87
Score = 101 bits (253), Expect = 5e-27
Identities = 24/81 (29%), Positives = 43/81 (53%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
++++N DF + LK+ F G + + +GKS+G G V +ESPE AE+A +
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 264 NGKEVDGKILYVGRAQKKAER 284
NG ++ G+ + V + +
Sbjct: 69 NGMKLSGREIDVRIDRNASGP 89
Score = 46.4 bits (111), Expect = 5e-07
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V+NL + L+ +F G + A
Sbjct: 7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD 39
>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 = 120 bits (304), Expect = 3e-33
Identities = 44/198 (22%), Positives = 85/198 (42%), Gaps = 11/198 (5%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
S+ + + +FI L ++++ F +G++ C V +D S+G+GFV
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA--KLFTNVYIKNFGEDF 215
+ T E + ++ ++ ++V + + R++ ++ K+F + ED
Sbjct: 62 YATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIF----VGGIKEDT 116
Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
+ L++ FE YG I +M GK RGF FV ++ + +K V V+G
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNC 175
Query: 274 YVGRAQKKAERTQELKRR 291
V +A K E +
Sbjct: 176 EVRKALSKQEMASASSSQ 193
Score = 97.0 bits (242), Expect = 3e-24
Identities = 43/152 (28%), Positives = 68/152 (44%), Gaps = 19/152 (12%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRG 244
+ + E KE + KLF I + DE L+ FE +GT+T VM N +SRG
Sbjct: 1 MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
FGFV Y + E + A+ A +VDG+++ RA + + Q + KI
Sbjct: 57 FGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDS-QRPGAHLTVKKI------- 107
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+V + + ++ LR F +G I +
Sbjct: 108 ----FVGGIKEDTEEHHLRDYFEQYGKIEVIE 135
>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 = 117 bits (295), Expect = 6e-33
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
+ V++ N +KLKE+F G + ++ + DGKSRG G V +E A +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
+NG+ + + ++V ++ +
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGDFFPPERP 106
Score = 97.4 bits (243), Expect = 2e-25
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 1/99 (1%)
Query: 99 SQRDPSLRKSGVG-NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
S +L+ +G VF+ NLD + K + + FS G ++ + +D+ G S+G G V
Sbjct: 3 SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVT 62
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
FE A ++I NG LL + + V +
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFF 101
Score = 58.5 bits (142), Expect = 4e-11
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
G ++V NLD + ++L++ F+ G + A
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD 46
>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 = 115 bits (290), Expect = 3e-32
Identities = 27/105 (25%), Positives = 48/105 (45%), Gaps = 11/105 (10%)
Query: 191 EREKEL---GEKAKL-------FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NND 239
L G +A++ TN+YI N ++++L+ M +P+G + S R++ ++
Sbjct: 3 SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS 62
Query: 240 GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
G SRG GF ES E E + +NGK + + +
Sbjct: 63 GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107
Score = 103 bits (260), Expect = 8e-28
Identities = 21/92 (22%), Positives = 40/92 (43%)
Query: 101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET 160
+ ++ N++I NL S+D + + + FG ++S ++ +D G S+G GF E+
Sbjct: 16 QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 75
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
E I NG + + P +
Sbjct: 76 TEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107
Score = 86.2 bits (214), Expect = 3e-21
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 282 AERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ + LK ++ + NLY+ NL S+D++ L PFG + S +
Sbjct: 2 SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR 56
>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 = 113 bits (286), Expect = 1e-31
Identities = 27/96 (28%), Positives = 52/96 (54%), Gaps = 1/96 (1%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAE 257
+A ++I + N++ LK +F +G I+ ++ + KSRGF F+ +E+P A+
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 258 KAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
A + NGK + GK + V +A+K + ++ +R
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPA 98
Score = 86.2 bits (214), Expect = 3e-21
Identities = 20/87 (22%), Positives = 37/87 (42%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
G +FI L++ + K + F G I + +D S+G+ F+ FE A + +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELG 197
+NG L+ K + V + +
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQSGGRR 94
Score = 44.6 bits (106), Expect = 3e-06
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++ L+ +++ L+ F G I+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVL 38
Score = 26.1 bits (58), Expect = 9.2
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG 109
D + A MN +L G+ I++ +++ PS + G
Sbjct: 60 DAKNAAKDMNGKSLHGKAIKVEQAKK-PSFQSGG 92
>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 = 118 bits (296), Expect = 3e-31
Identities = 34/230 (14%), Positives = 67/230 (29%), Gaps = 7/230 (3%)
Query: 112 NVFIKNLDKSID----NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
++I NL++ I K++Y FS FG IL V++ +G FV F+ +A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 68
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
+ + G K + + + ++ K + K+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128
Query: 228 GTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
G + + + L G+ A Q
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188
Query: 287 ELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+L L++ NL + ++ L F F +
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVR 238
Score = 86.9 bits (214), Expect = 7e-20
Identities = 31/221 (14%), Positives = 69/221 (31%), Gaps = 22/221 (9%)
Query: 78 ERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI 137
AL +M +P+RI +++ D S + + F++ K K A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTD-SDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124
Query: 138 LSCKVAQDEQGNSKGYGFVHFETEEAANKS-----------------IEKVNGMLLNSKI 180
+ A G +G +A + +
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184
Query: 181 VFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG 240
+ + +P + + + +++ N E+ N+ L +F + R++
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--- 241
Query: 241 KSRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQK 280
FV +++ A A A G ++ + + A+K
Sbjct: 242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>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 = 112 bits (281), Expect = 6e-31
Identities = 29/105 (27%), Positives = 50/105 (47%), Gaps = 4/105 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+YI+N E++ ++F YG I RV N ++RG +V YE A+ AV
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 264 NGKEVDGKILYVG-RAQKKAERTQELKRRFEMLKIERLNRYQGVN 307
+G V + L V +A + + K++ E +++ L G+N
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKKEE--QLKLLKEKYGIN 110
Score = 77.4 bits (191), Expect = 6e-18
Identities = 21/108 (19%), Positives = 51/108 (47%), Gaps = 2/108 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
++I+NL I + MYD F +G I +V ++G +V +E A +++ +
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHL 67
Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
+G ++++ + V + + +K +K + + + +G + + K
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 115
Score = 39.3 bits (92), Expect = 2e-04
Identities = 11/38 (28%), Positives = 16/38 (42%)
Query: 299 RLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
RL LY++NL I E + F +G I +
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR 39
Score = 27.0 bits (60), Expect = 4.3
Identities = 5/33 (15%), Positives = 17/33 (51%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKS 108
D + A+D ++ + R + +++ + + +K
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKM 91
>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 = 111 bits (280), Expect = 7e-31
Identities = 16/91 (17%), Positives = 47/91 (51%), Gaps = 6/91 (6%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
++++N +E L++ F +G + + + + + F+ ++ + A KA++
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------KDYAFIHFDERDGAVKAMEE 64
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
NGK+++G+ + + A+ ++ +E K + +
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95
Score = 78.5 bits (194), Expect = 2e-18
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 7/92 (7%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
+ V +F++NL ++ + + FS FG + K K Y F+HF+ + A K+
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKA 61
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEK 199
+E++NG L + + + P ++ KE +
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ 93
Score = 53.1 bits (128), Expect = 3e-09
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+V+NL +++ +E L K F+ FG + K
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK 42
Score = 26.1 bits (58), Expect = 8.4
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKS 108
+A++ MN L+G I I++++ RK
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKE 89
>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 = 111 bits (280), Expect = 9e-31
Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
N++I + ++F D+ L +MF P+G + S +V S+ FGFV+Y++P A+ A+Q
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQEL 288
+ NG ++ K L V + K +
Sbjct: 86 SMNGFQIGMKRLKVQLKRSKNDSKSGP 112
Score = 92.0 bits (229), Expect = 3e-23
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
N+FI +L + ++ + F FG+++S KV D+Q SK +GFV ++ +A +I+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGE 198
+NG + K + V + + +
Sbjct: 87 MNGFQIGMKRLKVQLKRSKNDSKSGPSS 114
Score = 65.8 bits (161), Expect = 1e-13
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 288 LKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L ++ + +G NL++ +L D+ L + F PFG + SAK
Sbjct: 8 LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK 56
>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 = 112 bits (280), Expect = 8e-30
Identities = 24/192 (12%), Positives = 61/192 (31%), Gaps = 36/192 (18%)
Query: 112 NVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
+ + LD+S ++ +++ F +G++ K + G V A +++I
Sbjct: 6 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITH 61
Query: 171 VNGMLLNSKIVFVG-----KFIPRKEREKELGEKAKLFT--------------------- 204
+N + + + V +P + E G +
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 205 ---NVYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKA 259
++ N + +E E+ + G V + + G + ++S A +
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 260 VQAWNGKEVDGK 271
+ N ++
Sbjct: 182 LGFLNHYQMKNP 193
Score = 84.4 bits (208), Expect = 2e-19
Identities = 18/153 (11%), Positives = 47/153 (30%), Gaps = 23/153 (15%)
Query: 204 TNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ + + N +++ +F YG + + M + G V ++A+
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS---KPGAAMVEMADGYAVDRAITH 61
Query: 263 WNGKEVDGKILYVGRAQ------KKAERTQELKRRFEMLKIERLNRYQ------------ 304
N + G+ + V ++ ++ ++ ++ R NR+
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 305 -GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+ N + +E + G
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTS 154
Score = 35.8 bits (82), Expect = 0.011
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 304 QGVNLYVKNLD-DSIDDERLRKEFTPFGTITSAK 336
L V LD ++ +R+ F +G + K
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVK 36
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 107 bits (270), Expect = 2e-29
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 2/98 (2%)
Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
+PR E +++ N F D L++MF +G I ++ N+ S+
Sbjct: 12 SGLVPRGSHMN--TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 69
Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
GFGFV +E+ A++A + +G V+G+ + V A +
Sbjct: 70 GFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 79.7 bits (197), Expect = 8e-19
Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 1/91 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
+ KS + + N+ + + F FG IL ++ +E+G SKG+GFV F
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTF 76
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
E A+++ EK++G ++ + + V R
Sbjct: 77 ENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 70.8 bits (174), Expect = 1e-15
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 275 VGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITS 334
+G + + L R + N+ Q L+V N+ D LR+ F FG I
Sbjct: 1 MGSSHHHHHHSSGLVPRGS--HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58
Query: 335 AK 336
+
Sbjct: 59 VE 60
>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 = 107 bits (268), Expect = 6e-29
Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 1/103 (0%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFG 246
+ GE + + + N +D ++E+F +GT+ V + G+S G
Sbjct: 20 DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 79
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELK 289
V +E A KA++ + G +DG+ + + + +
Sbjct: 80 DVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122
Score = 87.4 bits (217), Expect = 2e-21
Identities = 20/87 (22%), Positives = 40/87 (45%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+ + NLD + + + + F+ FG++ V D G S G VHFE A K++++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGE 198
G+ L+ + + + + + E
Sbjct: 97 KGVPLDGRPMDIQLVASQIDLEHHHHH 123
Score = 62.8 bits (153), Expect = 2e-12
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 276 GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
G Q + + F+ G L V NLD + D +++ F FGT+ A
Sbjct: 6 GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65
Query: 336 K 336
Sbjct: 66 A 66
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 104 bits (262), Expect = 5e-28
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
N++I + ++F D L F P+G + S +V S+ FGFV++++P+ A+ A++
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 262 AWNGKEVDGKILYVGRAQ 279
A NG +V K L V +
Sbjct: 101 AMNGFQVGTKRLKVQLKK 118
Score = 93.6 bits (233), Expect = 7e-24
Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 2/106 (1%)
Query: 80 ALDTMNFDALKGRPIRIMWSQRDPSLRKSGVG-NVFIKNLDKSIDNKAMYDTFSAFGSIL 138
+ ++ L + + + G N+FI +L + + + TF FG+++
Sbjct: 9 SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68
Query: 139 SCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
S KV D+Q SK +GFV F+ ++A +I+ +NG + +K + V
Sbjct: 69 SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114
Score = 76.6 bits (189), Expect = 1e-17
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 285 TQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ L +++ +G NL++ +L D L F PFG + SAK
Sbjct: 20 SVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAK 71
>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 = 103 bits (259), Expect = 8e-28
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-----NNDGKSRGFGFVAYESPEFAEK 258
+ ++IKN +E LK +F G I S + S GFGFV Y+ PE A+K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 259 AVQAWNGKEVDGKILYVGRAQKKAER 284
A++ G VDG L V +++ +
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATKP 91
Score = 86.9 bits (216), Expect = 1e-21
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN----SKGYGFVHFETEEA 163
SG +FIKNL+ S + + FS G+I SC +++ + S G+GFV ++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
A K+++++ G ++ + V +
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRISERATKPA 92
Score = 54.2 bits (131), Expect = 9e-10
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++KNL+ S +E L+ F+ G I S
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT 36
Score = 26.4 bits (59), Expect = 5.4
Identities = 5/28 (17%), Positives = 12/28 (42%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDP 103
++AL + + G + + S+R
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERAT 89
>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 = 102 bits (256), Expect = 3e-27
Identities = 18/89 (20%), Positives = 42/89 (47%), Gaps = 3/89 (3%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
V++ ++ +++ F YG++ +++ G S+G+GFV++ + +K V+
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKR 290
+ GK L +G A +K + +
Sbjct: 69 --SQINFHGKKLKLGPAIRKQNLSTYHVQ 95
Score = 99.6 bits (249), Expect = 2e-26
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 2/99 (2%)
Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
K VF+ +D +D + F+ +GS+ K+ D G SKGYGFV F + K
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTN 205
+E + + + K + +G I ++ + L N
Sbjct: 66 IVE--SQINFHGKKLKLGPAIRKQNLSTYHVQPRPLIFN 102
Score = 44.9 bits (107), Expect = 2e-06
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V +D +D+ +R F +G++ K
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVK 40
>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 = 100 bits (250), Expect = 2e-26
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGF 247
+ G + + + N +D ++E+F +GT+ V + G+S G
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD 74
Query: 248 VAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ 279
V +E A KA++ +NG +DG+ + +
Sbjct: 75 VHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
Score = 82.3 bits (204), Expect = 7e-20
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
+ ++G + + NLD + + + + F+ FG++ V D G S G VHF
Sbjct: 19 GFGGGAGVETGG-KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHF 77
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFV 183
E + A K++++ NG+ L+ + + +
Sbjct: 78 ERKADALKAMKQYNGVPLDGRPMNI 102
Score = 65.8 bits (161), Expect = 8e-14
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 283 ERTQELKR-----RFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
R ++L F+ G L V NLD + D +++ F FGT+ A
Sbjct: 2 SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 60
>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 = 98.9 bits (247), Expect = 5e-26
Identities = 23/83 (27%), Positives = 43/83 (51%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+++ N F D L++MF +G I ++ N+ S+GFGFV +E+ A++A +
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74
Query: 263 WNGKEVDGKILYVGRAQKKAERT 285
+G V+G+ + V A +
Sbjct: 75 LHGTVVEGRKIEVNNATARVMTN 97
Score = 81.6 bits (202), Expect = 1e-19
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 1/94 (1%)
Query: 101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET 160
S KS + + N+ + + F FG IL ++ +E+G SKG+GFV FE
Sbjct: 6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFEN 64
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
A+++ EK++G ++ + + V R
Sbjct: 65 SADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98
Score = 45.4 bits (108), Expect = 1e-06
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++ L+V N+ D LR+ F FG I +
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 46
>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 = 98.5 bits (246), Expect = 6e-26
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
V++ N +E L E+F G +T + +GK + FGFV ++ PE A+
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Query: 262 AWNGKEVDGKILYVGRAQ 279
NG + G+ + V
Sbjct: 76 LLNGIRLYGRPINVSGPS 93
Score = 81.9 bits (203), Expect = 9e-20
Identities = 20/74 (27%), Positives = 39/74 (52%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
VF+ NL+ + + +Y+ F G + + +D +G K +GFV F+ E+ + +I +
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77
Query: 172 NGMLLNSKIVFVGK 185
NG+ L + + V
Sbjct: 78 NGIRLYGRPINVSG 91
Score = 52.6 bits (127), Expect = 3e-09
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V NL+ + +E L + F G +T
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVT 47
Score = 25.7 bits (57), Expect = 9.7
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 76 DTERALDTMNFDALKGRPIRI 96
A+ +N L GRPI +
Sbjct: 69 SVSYAIALLNGIRLYGRPINV 89
>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 = 98.1 bits (245), Expect = 9e-26
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 4/88 (4%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ + ++E + +F+P+G I V+ DG S+G FV + S A+ A+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 262 AWNGKEV---DGKILYVGRAQKKAERTQ 286
A +G + L V A E
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
Score = 81.2 bits (201), Expect = 2e-19
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+F+ L+K + + F FG I C V + G+SKG FV F + A +I +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 172 NG---MLLNSKIVFVGKFIPRKER 192
+G M S + V KE
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKES 100
Score = 51.9 bits (125), Expect = 6e-09
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ L+V L+ +E + + F PFG I
Sbjct: 14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT 46
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 99.5 bits (248), Expect = 2e-25
Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 1/103 (0%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFG 246
+ GE + + + N +D ++E+F +GT+ V + G+S G
Sbjct: 73 DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 132
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELK 289
V +E A KA++ + G +DG+ + + + +
Sbjct: 133 DVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175
Score = 82.2 bits (203), Expect = 5e-19
Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 6/113 (5%)
Query: 90 KGRPIRIMWSQRDPSLRKSGVG------NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVA 143
+ +P+ W G + + NLD + + + + F+ FG++ V
Sbjct: 62 RPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVD 121
Query: 144 QDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
D G S G VHFE A K++++ G+ L+ + + + + + E
Sbjct: 122 YDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 174
Score = 71.4 bits (175), Expect = 4e-15
Identities = 15/73 (20%), Positives = 25/73 (34%)
Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLR 323
G+ ++ K + F+ G L V NLD + D ++
Sbjct: 47 PAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQ 106
Query: 324 KEFTPFGTITSAK 336
+ F FGT+ A
Sbjct: 107 ELFAEFGTLKKAA 119
>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 = 98.0 bits (244), Expect = 4e-25
Identities = 22/141 (15%), Positives = 56/141 (39%), Gaps = 10/141 (7%)
Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL---GEKAKLFTNVYIKNFGEDFNDEK 219
+++ ++ + + G+ + + E + +Y+KN + ++
Sbjct: 2 PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKD 61
Query: 220 LKEMFEPYGTITSYR-------VMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI 272
LK +F Y +S + +G+ +G F+ + + A KA++ NG + GK
Sbjct: 62 LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121
Query: 273 LYVGRAQKKAERTQELKRRFE 293
+ V A+ + + + +
Sbjct: 122 MVVQFARSARPKQDPKEGKRK 142
Score = 76.8 bits (189), Expect = 2e-17
Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 7/82 (8%)
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLD 314
+ + + L GR ++ T + R +E + +YVKNL
Sbjct: 2 PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGE-------PNCRIYVKNLA 54
Query: 315 DSIDDERLRKEFTPFGTITSAK 336
+ ++ L+ F + +S
Sbjct: 55 KHVQEKDLKYIFGRYVDFSSET 76
Score = 69.5 bits (170), Expect = 1e-14
Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 6/96 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCK------VAQDEQGNSKGYGFVHFETEEAAN 165
+++KNL K + K + F + S + ++G KG F+ E+AA
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
K++++ NG +L K + V + ++ K K
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK 142
>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 = 94.5 bits (236), Expect = 1e-24
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
+ +YI+ D+ L ++ +PYG I S + + K +G+GFV ++SP A+KAV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 262 AWNGKEVDGKILYVGRAQ 279
A V ++
Sbjct: 66 ALKASGVQAQMAKQSGPS 83
Score = 74.5 bits (184), Expect = 3e-17
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 3/83 (3%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANK 166
SG ++I+ L ++ + +G I+S K D KGYGFV F++ AA K
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 167 SIEKVNGMLLNSKIVFVGKFIPR 189
++ + + +++ P
Sbjct: 63 AVTALKASGVQAQMAKQSG--PS 83
Score = 47.5 bits (114), Expect = 2e-07
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LY++ L D+ L K P+G I S K
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTK 36
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 94.3 bits (235), Expect = 2e-24
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMF-EPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
++++ + D +D L E F + Y + +V+ + G S+G+GFV + ++A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 263 WNGK-EVDGKILYVGRAQKKAERTQELK 289
G + K + + A KA R + ++
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPVE 98
Score = 90.4 bits (225), Expect = 8e-23
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
++F+ +L +D+ +Y+ F + S KV D+ G SKGYGFV F E +++ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 171 VNG-MLLNSKIVFVGKFIPRKEREKEL 196
G + L SK V + IP+ R K +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPV 97
Score = 50.4 bits (121), Expect = 3e-08
Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFT-PFGTITSAK 336
+ +L+V +L +DD L + F + + K
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK 41
Score = 29.2 bits (66), Expect = 0.73
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 76 DTERALDTMN-FDALKGRPIRIMWSQRDPSLRKSG 109
+ +RAL L +P+R+ + S K
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPV 97
>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 = 92.6 bits (231), Expect = 7e-24
Identities = 23/80 (28%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
N+++ + + +DE L+ F+ + + S VM G SRG+GFV++ S + A+ A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 262 AWNGKEVDGKILYVGRAQKK 281
+ G++++G+ L + A K
Sbjct: 62 SMQGQDLNGRPLRINWAAKL 81
Score = 77.5 bits (192), Expect = 2e-18
Identities = 23/79 (29%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+F+ +L+ ++D++ + + F F S LS V D + G+S+GYGFV F +++ A +++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 171 VNGMLLNSKIVFVGKFIPR 189
+ G LN + + +
Sbjct: 63 MQGQDLNGRPLRINWAAKL 81
Score = 46.3 bits (111), Expect = 4e-07
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
NL+V +L+ ++DDE LR F F + S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGH 32
Score = 30.9 bits (71), Expect = 0.11
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDP 103
D + A+D+M L GRP+RI W+ +
Sbjct: 55 DAQNAMDSMQGQDLNGRPLRINWAAKLE 82
>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 = 92.7 bits (231), Expect = 9e-24
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+Y++N ++E +++ F RV K R + FV + + E A +A++A
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK----KIRDYAFVHFSNREDAVEAMKA 70
Query: 263 WNGKEVDGKILYVGRAQKKAERTQ 286
NGK +DG + V A+ + +
Sbjct: 71 LNGKVLDGSPIEVTLAKPVDKDSS 94
Score = 70.4 bits (173), Expect = 2e-15
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
S V ++++NL S + + F+ +V + + Y FVHF E A ++
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEA 67
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKER 192
++ +NG +L+ + V P +
Sbjct: 68 MKALNGKVLDGSPIEVTLAKPVDKD 92
Score = 46.5 bits (111), Expect = 5e-07
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV+NL S +E + KEF +
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVER 46
Score = 31.5 bits (72), Expect = 0.096
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQ---RDPSLRKSG 109
D A+ +N L G PI + ++ +D S SG
Sbjct: 63 DAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 92.8 bits (231), Expect = 1e-23
Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 6/94 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
V ++ + LK+M YG + ++ + K G V + S A++ V+
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEML 295
+ V G I++ K +R + +E++
Sbjct: 67 NLHLTSVMGNIIHAQLDIKGQQR----MKYYELI 96
Score = 79.0 bits (195), Expect = 1e-18
Identities = 12/86 (13%), Positives = 32/86 (37%), Gaps = 1/86 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
V L+ ++ + D +G + ++ + G V F + A ++++
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKEL 196
++ + I+ I ++R K
Sbjct: 68 LHLTSVMGNIIHAQLDIKGQQRMKYY 93
Score = 41.2 bits (97), Expect = 4e-05
Identities = 4/30 (13%), Positives = 13/30 (43%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ L+D++ + L+ +G + +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVE 37
Score = 25.8 bits (57), Expect = 9.3
Identities = 4/32 (12%), Positives = 12/32 (37%), Gaps = 3/32 (9%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRK 107
+ + ++ ++ G I Q D ++
Sbjct: 60 GAKETVKNLHLTSVMGNIIHA---QLDIKGQQ 88
>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 = 92.3 bits (230), Expect = 1e-23
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ +++ N D +E+++++FE YG + K +GFGF+ E+ AE A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH----KDKGFGFIRLETRTLAEIAKVE 70
Query: 263 WNGKEVDGKILYVGRAQKKAERTQ 286
+ + GK L V A A T
Sbjct: 71 LDNMPLRGKQLRVRFACHSASLTS 94
Score = 66.1 bits (162), Expect = 5e-14
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAAN 165
+ +F+ NL I + M F +G + +D KG+GF+ ET A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65
Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKERE 193
+ +++ M L K + V
Sbjct: 66 IAKVELDNMPLRGKQLRVRFACHSASLT 93
Score = 42.6 bits (101), Expect = 1e-05
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
Q L+V NL I +E +RK F +G
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF 46
Score = 29.1 bits (66), Expect = 0.55
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 78 ERALDTMNFDALKGRPIRIMWSQRDPSLR 106
E A ++ L+G+ +R+ ++ SL
Sbjct: 65 EIAKVELDNMPLRGKQLRVRFACHSASLT 93
>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 = 94.1 bits (234), Expect = 1e-23
Identities = 29/140 (20%), Positives = 61/140 (43%), Gaps = 5/140 (3%)
Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELG---EKAKLFTNVYIKNFGE 213
+E A + G N++ R E + EL +++ +++ + E
Sbjct: 23 IVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHE 82
Query: 214 DFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
+ +++++E F YG I + + + G S+G+ V YE+ + A A +A NG E+ G+
Sbjct: 83 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 142
Query: 272 ILYVGRAQKKAERTQELKRR 291
+ V K + + +
Sbjct: 143 TIQVDWCFVKGPKRVKKSEK 162
Score = 68.7 bits (168), Expect = 3e-14
Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 1/91 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+F+ ++ + + + F +G I + + D G SKGY V +ET + A + E
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
+NG + + + V + + + EK +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164
Score = 35.2 bits (81), Expect = 0.012
Identities = 16/95 (16%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ----- 304
+E E ++ + K K GR T+E +E ++ E + +
Sbjct: 13 FEVDEDGDQGIVRLKEKAKHRK----GRGFGSDSNTREAIHSYERVRNEDDDELEPGPQR 68
Query: 305 ---GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
G L+V ++ + ++ ++++F +G I +
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 103
>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 = 89.7 bits (223), Expect = 1e-22
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 6/83 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ GED L+ F P+G I + R FV YE E A++AV
Sbjct: 16 NTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMD----PPRNCAFVTYEKMESADQAVAEL 69
Query: 264 NGKEVDGKILYVGRAQKKAERTQ 286
NG +V+ L V A+K+
Sbjct: 70 NGTQVESVQLKVNIARKQPMLDS 92
Score = 68.9 bits (169), Expect = 6e-15
Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+++ D + + FS FG+I+ + + FV +E E+A++++ ++
Sbjct: 17 TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAEL 69
Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
NG + S + V + +
Sbjct: 70 NGTQVESVQLKVNIARKQPMLD 91
Score = 48.4 bits (116), Expect = 9e-08
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
ER +G LYV D + LR F+PFG I
Sbjct: 8 ERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLS 44
Score = 30.7 bits (70), Expect = 0.16
Identities = 4/34 (11%), Positives = 16/34 (47%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG 109
++A+ +N ++ +++ +++ P L
Sbjct: 61 SADQAVAELNGTQVESVQLKVNIARKQPMLDSGP 94
>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 = 89.1 bits (222), Expect = 1e-22
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKA 259
T V+I + + + E+F YG I + S+G+ +V +E+P+ AEKA
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 260 VQAWNGKEVDGKILYVGRAQKKAER 284
++ +G ++DG+ + R
Sbjct: 64 LKHMDGGQIDGQEITATAVLAPWPR 88
Score = 70.6 bits (174), Expect = 9e-16
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
V I L +++ + + FS +G I + + SKGY +V FE + A K+++
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
++G ++ + + + R
Sbjct: 66 HMDGGQIDGQEITATAVLAPWPR 88
Score = 37.5 bits (88), Expect = 5e-04
Identities = 4/31 (12%), Positives = 14/31 (45%)
Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+++ L ++ + + + F+ +G I
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMID 35
>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 = 89.7 bits (223), Expect = 2e-22
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
+Y+KN + L +F + + G+ RG F+ + + E A +A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
NG ++ GKIL + + K +R+
Sbjct: 86 LVNGYKLYGKILVIEFGKNKKQRSS 110
Score = 75.4 bits (186), Expect = 3e-17
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 1/83 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
+++KNL + + + F+ F + G +G F+ F +E A +++
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 171 VNGMLLNSKIVFVGKFIPRKERE 193
VNG L KI+ + +K+R
Sbjct: 87 VNGYKLYGKILVIEFGKNKKQRS 109
Score = 45.4 bits (108), Expect = 2e-06
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 293 EMLKIERLNRYQ----GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
E+ KI + Y LY+KNL + + L F F
Sbjct: 9 EIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP 56
Score = 27.6 bits (62), Expect = 2.2
Identities = 6/27 (22%), Positives = 12/27 (44%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRD 102
+AL +N L G+ + I + +
Sbjct: 79 IAWQALHLVNGYKLYGKILVIEFGKNK 105
>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 = 88.1 bits (219), Expect = 4e-22
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 205 NVYIKNFGEDFNDEKLKE----MFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAV 260
+YI N E ++LK+ +F +G I V K RG FV ++ A A+
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNAL 68
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELK 289
++ G K + + A+ ++ ++K
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 66.1 bits (162), Expect = 5e-14
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 112 NVFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
++I NL++ I K+++ FS FG IL V++ +G FV F+ +A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 67
Query: 168 IEKVNGMLLNSKIVFV 183
+ + G K + +
Sbjct: 68 LRSMQGFPFYDKPMRI 83
Score = 42.6 bits (101), Expect = 1e-05
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 307 NLYVKNLDDSIDDERLRKE----FTPFGTITSAK 336
+Y+ NL++ I + L+K F+ FG I
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDIL 43
Score = 27.2 bits (61), Expect = 2.8
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRD 102
AL +M +P+RI +++ D
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYAKTD 89
>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 = 89.0 bits (221), Expect = 6e-22
Identities = 27/110 (24%), Positives = 48/110 (43%), Gaps = 16/110 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
N+ + ++ +L+++FE YG I S +++ D +SRG+GFV ++S A++A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC-DRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYV 310
NG + K L V A +R N Y+
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQRP------------GIAGAVGDGNGYL 139
Score = 74.0 bits (182), Expect = 2e-16
Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 3/98 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+ + + ++D + F +G I S K+ D E S+GYGFV F++ +A ++I
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYI 208
+NG + +K + V +R G N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGD--GNGYL 139
Score = 40.5 bits (95), Expect = 1e-04
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
NL V + ++D+ +LR+ F +G I S K
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVK 73
>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 = 87.3 bits (217), Expect = 1e-21
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYE 251
+ G ++ N++I N + + +LK V++ G +R FG+V +E
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66
Query: 252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
S E EKA++ G +V G + + + + +
Sbjct: 67 SAEDLEKALEL-TGLKVFGNEIKLEKPKGRDGT 98
Score = 75.4 bits (186), Expect = 2e-17
Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 1/97 (1%)
Query: 97 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFV 156
M + N+FI NL+ + + S + V G ++ +G+V
Sbjct: 4 MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63
Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
FE+ E K++E G+ + + + K R
Sbjct: 64 DFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDGTR 99
Score = 39.5 bits (93), Expect = 1e-04
Identities = 5/30 (16%), Positives = 11/30 (36%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
NL++ NL+ + L+ +
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLA 48
>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 = 86.3 bits (214), Expect = 4e-21
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 10/114 (8%)
Query: 177 NSKIVFVGKFIPRKEREKELGEKA--KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR 234
+S +V G + R E+ + +Y+ D L+ F P+G I
Sbjct: 11 SSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS 68
Query: 235 VMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV--GRAQKKAERTQ 286
+ R FV YE E A++AV NG +V+ L V R Q +
Sbjct: 69 MD----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAAT 118
Score = 67.5 bits (165), Expect = 3e-14
Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 7/87 (8%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+++ D + + FS FG+I+ + + FV +E E+A++++ ++
Sbjct: 41 TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAEL 93
Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGE 198
NG + S + V + + G+
Sbjct: 94 NGTQVESVQLKVNIARKQPMLDAATGK 120
Score = 39.3 bits (92), Expect = 3e-04
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+G LYV D + LR F+PFG I
Sbjct: 38 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLS 68
Score = 33.2 bits (76), Expect = 0.030
Identities = 4/33 (12%), Positives = 17/33 (51%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKS 108
++A+ +N ++ +++ +++ P L +
Sbjct: 85 SADQAVAELNGTQVESVQLKVNIARKQPMLDAA 117
>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 = 85.4 bits (212), Expect = 6e-21
Identities = 28/83 (33%), Positives = 49/83 (59%), Gaps = 2/83 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
+++ D N++ L+++F YG I+ V+ +SRGFGFV +E+ + A+ A+ A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 263 WNGKEVDGKILYVGRAQKKAERT 285
NGK VDG+ + V +A K ++
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNR 96
Score = 71.1 bits (175), Expect = 9e-16
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
G +F+ L + +++ FS +G I V +D E S+G+GFV FE + A ++
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
+NG ++ + + V + +
Sbjct: 73 AMNGKSVDGRQIRVDQAGKSSDN 95
Score = 36.5 bits (85), Expect = 0.002
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+V L +++ L + F+ +G I+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVV 43
Score = 26.1 bits (58), Expect = 8.2
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQ-RDPSLRKSGVG 111
D + A+ MN ++ GR IR+ + + G
Sbjct: 66 DAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102
>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 = 85.1 bits (211), Expect = 7e-21
Identities = 25/94 (26%), Positives = 53/94 (56%), Gaps = 2/94 (2%)
Query: 192 REKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVA 249
L + + +Y+ + + ++ L+ +FEP+G I S ++M + G+S+G+GF+
Sbjct: 15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE 283
+ E A+KA++ NG E+ G+ + VG ++ +
Sbjct: 75 FSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 66.6 bits (163), Expect = 4e-14
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+++ +L +I + F FG I S ++ D E G SKGYGF+ F E A K++E+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
+NG L + + VG R +
Sbjct: 88 LNGFELAGRPMKVGHVTERTD 108
Score = 39.6 bits (93), Expect = 2e-04
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV +L +I ++ LR F PFG I S +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQ 57
>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 = 84.2 bits (209), Expect = 1e-20
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
+ + N ED + L+E+F P+G+I+ + + G+S+GF F+++ E A +A+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 262 AWNGKEVDGKILYVGRAQKKAERT 285
+G D IL V A+
Sbjct: 76 GVSGFGYDHLILNVEWAKPSTNSG 99
Score = 73.8 bits (182), Expect = 9e-17
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 1/91 (1%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETE 161
P+ R + + NL + + + F FGSI +A+D G SKG+ F+ F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
E A ++I V+G + I+ V P
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 38.0 bits (89), Expect = 6e-04
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ V NL + + L++ F PFG+I+
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIY 46
Score = 25.6 bits (57), Expect = 9.7
Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQ-RDPSLRKSG 109
D RA+ ++ + + W++ S SG
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
>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 = 84.7 bits (210), Expect = 1e-20
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
+V++ + + E +K F P+G I+ RV+ GKS+G+GFV++ + AE A+Q
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
G+ + G+ + A +K +
Sbjct: 76 QMGGQWLGGRQIRTNWATRKPPAPK 100
Score = 74.3 bits (183), Expect = 1e-16
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+VF+ +L I + + F+ FG I +V +D G SKGYGFV F + A +I++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 171 VNGMLLNSKIVFVGKFIPRKEREK 194
+ G L + + + K
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPK 100
Score = 44.3 bits (105), Expect = 4e-06
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++ + +++V +L I E ++ F PFG I+ A+
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDAR 46
Score = 43.1 bits (102), Expect = 9e-06
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
D E A+ M L GR IR W+ R P KS +
Sbjct: 69 DAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>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 = 84.2 bits (209), Expect = 2e-20
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
N E+ G+ + V A+ +
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIK 95
Score = 71.9 bits (177), Expect = 5e-16
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELG 197
+N L + + V P + +E
Sbjct: 74 MNESELFGRTIRVNLAKPMRIKESGPS 100
Score = 41.8 bits (99), Expect = 2e-05
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV L + +DD+ L F PFG IT +
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 43
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 82.9 bits (205), Expect = 4e-20
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 1/99 (1%)
Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYES 252
+ + + +VYIK F D + +KE E G + + ++ +G FV ++S
Sbjct: 2 RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 61
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
E A+K V+ K + +L + + A++ +E K+
Sbjct: 62 IESAKKFVETPGQKYKETDLLILFKDDYFAKKNEERKQN 100
Score = 65.1 bits (159), Expect = 1e-13
Identities = 16/88 (18%), Positives = 37/88 (42%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+V+IK + + G +L+ ++ + KG FV F++ E+A K +E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEK 199
+ ++ + K ++ +E +
Sbjct: 73 GQKYKETDLLILFKDDYFAKKNEERKQN 100
Score = 35.5 bits (82), Expect = 0.003
Identities = 3/30 (10%), Positives = 13/30 (43%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++Y+K + +++ G + + +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ 42
>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 = 82.3 bits (204), Expect = 5e-20
Identities = 24/92 (26%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
+ +K + + KN + +++LKE+FE I R+++ DGKS+G ++ ++S
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGKSKGIAYIEFKS 62
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
AEK ++ G E+DG+ + + +K
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94
Score = 58.4 bits (142), Expect = 3e-11
Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 4/81 (4%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+ KNL +I + + F I + G SKG ++ F++E A K++E+
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 172 NGMLLNSKIVFVGKFIPRKER 192
G ++ + V + +
Sbjct: 74 QGAEIDGRSVSLYYTGEKGGT 94
Score = 33.8 bits (78), Expect = 0.014
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
L KNL +I ++ L++ F I
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEI 43
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 81.8 bits (203), Expect = 7e-20
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
+V++ + + + F P+G I+ RV+ GKS+G+GFV++ + AE A+Q
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 263 WNGKEVDGKILYVGRAQKK 281
G+ + G+ + A +K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 70.3 bits (173), Expect = 1e-15
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
+VF+ +L I A+ F+ FG I +V +D G SKGYGFV F + A +I++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 171 VNGMLLNSKIVFVGKFIPR 189
+ G L + + +
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 48.3 bits (116), Expect = 9e-08
Identities = 12/28 (42%), Positives = 14/28 (50%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDP 103
D E A+ M L GR IR W+ R P
Sbjct: 60 DAENAIQQMGGQWLGGRQIRTNWATRKP 87
Score = 41.0 bits (97), Expect = 3e-05
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+++V +L I + F PFG I+ A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDAR 37
>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 = 81.8 bits (203), Expect = 8e-20
Identities = 23/84 (27%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
+ +Y+ + + ++ L+ +FEP+G I + +M D G+S+G+GF+ + E A +A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK-DSDTGRSKGYGFITFSDSECARRAL 64
Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
+ NG E+ G+ + VG ++ +
Sbjct: 65 EQLNGFELAGRPMRVGHVTERLDG 88
Score = 68.7 bits (169), Expect = 6e-15
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+++ +L +I + F FG I + + +D + G SKGYGF+ F E A +++E+
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
+NG L + + VG R +
Sbjct: 67 LNGFELAGRPMRVGHVTERLDG 88
Score = 37.5 bits (88), Expect = 6e-04
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV +L +I ++ LR F PFG I +
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIV 36
>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 = 83.4 bits (206), Expect = 1e-19
Identities = 31/137 (22%), Positives = 50/137 (36%), Gaps = 4/137 (2%)
Query: 155 FVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL--FTNVYIKNFG 212
V T E K NG+ K E + T++ + N
Sbjct: 20 AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+ + L+ +FE YG + + + +SRGF FV + AE A+ A +G +DG
Sbjct: 80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139
Query: 271 KILYVGRAQKKAERTQE 287
+ L V A+
Sbjct: 140 RELRVQMARYGRPPDSH 156
Score = 66.0 bits (161), Expect = 2e-13
Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 1/98 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
+ G+ ++ + NL + F +G + + +D S+G+ FV
Sbjct: 59 HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
F + A +++ ++G +L+ + + V + +
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156
Score = 43.7 bits (103), Expect = 2e-05
Identities = 13/94 (13%), Positives = 23/94 (24%)
Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
G + E + A K+ G ++
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+L V NL + LR+ F +G +
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY 101
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 81.6 bits (202), Expect = 1e-19
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFAEKAVQA 262
++I E+L+E+ + +GT+ R V N GK +G +V YE+ A +AV
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
+G + I+ V +
Sbjct: 78 MDGMTIKENIIKVAISNSGPSS 99
Score = 69.6 bits (171), Expect = 3e-15
Identities = 18/81 (22%), Positives = 37/81 (45%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+FI L S + + + A G++ ++ + G KG +V +E E A++++ K+
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 172 NGMLLNSKIVFVGKFIPRKER 192
+GM + I+ V
Sbjct: 79 DGMTIKENIIKVAISNSGPSS 99
Score = 35.7 bits (83), Expect = 0.003
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++ L S E L + GT+ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLR 48
>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 = 81.1 bits (201), Expect = 2e-19
Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 2/90 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
VY+ + D +E++ ++ G + + ++M + G+S+G+ F+ + E + AV+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
NG ++ + L G + L+
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92
Score = 64.6 bits (158), Expect = 2e-13
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
V++ ++ + + D S G +++ K+ D + G SKGY F+ F E++ ++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
+NG L S+ + G
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDIS 85
Score = 32.6 bits (75), Expect = 0.033
Identities = 4/30 (13%), Positives = 14/30 (46%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+Y+ ++ +E++ + G + + K
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLK 33
>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 = 81.2 bits (201), Expect = 2e-19
Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 4/94 (4%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
E + + + VY D+ +++ F P+G I RV +G+ FV + +
Sbjct: 15 EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----PEKGYSFVRFST 70
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
E A A+ + NG ++G ++ ++ + T
Sbjct: 71 HESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104
Score = 65.0 bits (159), Expect = 2e-13
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
V+ + + ++ M TFS FG I+ +V + KGY FV F T E+A +I V
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81
Query: 172 NGMLLNSKIVFVG 184
NG + +V
Sbjct: 82 NGTTIEGHVVKCY 94
Score = 45.8 bits (109), Expect = 1e-06
Identities = 5/34 (14%), Positives = 14/34 (41%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG 109
A+ ++N ++G ++ W + P +
Sbjct: 73 SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106
Score = 40.8 bits (96), Expect = 5e-05
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+Y + + D+ +R+ F+PFG I +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIR 56
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 80.2 bits (198), Expect = 4e-19
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 1/81 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+ I+N E L + YG + S +N D V Y S + A +A+
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKL 74
Query: 264 NGKEVDGKILYVGRAQKKAER 284
NG +++ L V +
Sbjct: 75 NGFQLENFTLKVAYIPDEMAA 95
Score = 63.2 bits (154), Expect = 6e-13
Identities = 14/86 (16%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAAN 165
++ + + I+N+ + + + +G + SC+ + + V + +++ A
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD--SETAVVNVTYSSKDQAR 68
Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKE 191
++++K+NG L + + V +IP +
Sbjct: 69 QALDKLNGFQLENFTLKV-AYIPDEM 93
Score = 38.6 bits (90), Expect = 3e-04
Identities = 7/35 (20%), Positives = 15/35 (42%)
Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
R + L ++N+ + E L +G + S +
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCE 46
>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 = 83.6 bits (206), Expect = 5e-19
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 4/92 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKA 259
+YI N DE L E G I + N +G+S+GF V S ++K
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
+ +E+ G+ V K+ E++ R
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160
Score = 73.6 bits (180), Expect = 2e-15
Identities = 17/91 (18%), Positives = 39/91 (42%), Gaps = 3/91 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
++I NL ++ + + + G IL K ++ G SKG+ V +E ++ K +
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEK 199
+ + L+ + V + + E+ +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160
Score = 38.2 bits (88), Expect = 0.002
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGT--ITSAK 336
+ + LY+ NL DE L + G I K
Sbjct: 67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK 101
>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 = 79.6 bits (197), Expect = 7e-19
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 2/84 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
+ + N + + L+ +FE YG + + RGF FV + A+ A
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 262 AWNGKEVDGKILYVGRAQKKAERT 285
A +G E+DG+ L V A+
Sbjct: 74 AMDGAELDGRELRVQVARYGRRDL 97
Score = 65.7 bits (161), Expect = 9e-14
Identities = 14/95 (14%), Positives = 33/95 (34%), Gaps = 1/95 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
S G+ + + NL ++ F +G + + ++ +G+ FV
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
F A + ++G L+ + + V +
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96
Score = 36.8 bits (86), Expect = 0.001
Identities = 8/36 (22%), Positives = 14/36 (38%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ + L V NL + LR+ F +G +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVY 44
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 80.2 bits (198), Expect = 1e-18
Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 2/99 (2%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
+ T++ + N + + L+ +FE YG + + + +SRGF
Sbjct: 32 RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91
Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
FV + AE A+ A +G +DG+ L V A+
Sbjct: 92 AFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130
Score = 64.8 bits (158), Expect = 4e-13
Identities = 17/96 (17%), Positives = 40/96 (41%), Gaps = 1/96 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
S P G+ ++ + NL + F +G + + +D S+G+ FV
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
F + A +++ ++G +L+ + + V + +
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131
Score = 39.3 bits (92), Expect = 3e-04
Identities = 11/61 (18%), Positives = 19/61 (31%)
Query: 276 GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
G Q++ R + +L V NL + LR+ F +G +
Sbjct: 18 GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77
Query: 336 K 336
Sbjct: 78 Y 78
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 78.9 bits (195), Expect = 1e-18
Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQ 261
+ + N +E L+E+FE I +V N GKS+G+ F+ + S E A++A+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
+ N +E++G+ + + +
Sbjct: 72 SCNKREIEGRAIRLELQGPRGSP 94
Score = 65.4 bits (160), Expect = 1e-13
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NL S + + + F I KV Q++ G SKGY F+ F + E A +++ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 173 GMLLNSKIVFVGKFIPRKERE 193
+ + + + PR
Sbjct: 75 KREIEGRAIRLELQGPRGSPN 95
Score = 33.0 bits (76), Expect = 0.029
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTI 332
L + NL S +E L++ F I
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI 42
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 79.3 bits (196), Expect = 1e-18
Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 4/91 (4%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPE 254
K + + + ++N N +++E+F +G + + R+ G RGFGFV + + +
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 255 FAEKAVQA-WNGKEVDGKILYVGRAQKKAER 284
A+KA A + + G+ L + A +
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100
Score = 60.0 bits (146), Expect = 1e-11
Identities = 15/86 (17%), Positives = 39/86 (45%), Gaps = 3/86 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
+ ++N+ + + + + FS FG + + ++ + G +G+GFV F T++ A K+
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 170 KV-NGMLLNSKIVFVGKFIPRKEREK 194
+ + L + + + +
Sbjct: 77 ALCHSTHLYGRRLVLEWADSEVTVQS 102
Score = 36.5 bits (85), Expect = 0.002
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ V+N+ + +R+ F+ FG + + +
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVR 46
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 78.3 bits (194), Expect = 1e-18
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPE 254
G A +Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQ 279
A A+ N E+ G+ + V A+
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLAK 85
Score = 62.9 bits (154), Expect = 4e-13
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 171 VNGMLLNSKIVFVGK 185
+N L + + V
Sbjct: 69 MNESELFGRTIRVNL 83
Score = 38.7 bits (91), Expect = 2e-04
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV L + +DD+ L F PFG IT +
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 38
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
++++N ++E L+++F YG ++ + K +GF FV + PE A KA
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
+G+ G++L+V + K E +Q
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
Score = 64.9 bits (159), Expect = 1e-13
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAA 164
SG G +F++NL + + + FSA+G + D KG+ FV F E A
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
K+ +V+G + +++ V +KE +
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIKKEASQ 93
Score = 34.1 bits (79), Expect = 0.010
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+V+NL + +E L K F+ +G ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELH 39
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 79.4 bits (196), Expect = 2e-18
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPE 254
G A +Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E
Sbjct: 57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 255 FAEKAVQAWNGKEVDGKILYVGRA 278
A A+ N E+ G+ + V A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140
Score = 67.9 bits (166), Expect = 3e-14
Identities = 25/121 (20%), Positives = 49/121 (40%), Gaps = 16/121 (13%)
Query: 81 LDTMNFDALKGRPIRIMWSQRDPSLRKSGVG---------------NVFIKNLDKSIDNK 125
L ++ L P + ++ + + R G +++ L + +D+K
Sbjct: 19 LSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDK 78
Query: 126 AMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
++ F FG I ++ D E +G+ FV FE E A +I+ +N L + + V
Sbjct: 79 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
Query: 185 K 185
Sbjct: 139 L 139
Score = 40.9 bits (96), Expect = 1e-04
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV L + +DD+ L F PFG IT +
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 94
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 78.0 bits (193), Expect = 2e-18
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
+ VY+ N + L +F YG + +M + KS+G F+ + + A+ +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 262 AWNGKEVDGKILYVGRA 278
A N K++ G+++ A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 64.2 bits (157), Expect = 2e-13
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 97 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGF 155
M PS V++ NL S+ N +Y FS +G ++ + +D + SKG F
Sbjct: 8 MSGGLAPSKST-----VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62
Query: 156 VHFETEEAANKSIEKVNG 173
+ F +++A +N
Sbjct: 63 ILFLDKDSAQNCTRAINN 80
Score = 34.9 bits (81), Expect = 0.004
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+YV NL S+ + L + F+ +G +
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVT 47
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 78.2 bits (193), Expect = 5e-18
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 2/96 (2%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
R R + + + L+E+F YG I ++ + +SRGF
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90
Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
FV +E+ + A++A + NG E+DG+ + V + K
Sbjct: 91 AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
Score = 68.2 bits (167), Expect = 2e-14
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+ + L + + + FS +G I + D + S+G+ FV+FE + A ++ E+
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 171 VNGMLLNSKIVFVGKFIPRK 190
NGM L+ + + V I ++
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127
Score = 38.9 bits (91), Expect = 3e-04
Identities = 13/74 (17%), Positives = 19/74 (25%), Gaps = 4/74 (5%)
Query: 264 NGKEVDGK-ILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERL 322
+ G A + R R N L V L + L
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSRHVG---NRANPDPNCCLGVFGLSLYTTERDL 63
Query: 323 RKEFTPFGTITSAK 336
R+ F+ +G I
Sbjct: 64 REVFSKYGPIADVS 77
>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 = 76.9 bits (190), Expect = 6e-18
Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
+V++ N + +E+LK++F G + S+R++ + GK +G+GF Y+ E A A++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
NG+E G+ L V A + +
Sbjct: 69 NLNGREFSGRALRVDNAASEKNK 91
Score = 64.6 bits (158), Expect = 2e-13
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFET 160
DP++ +S +VF+ N+ + + D FS G ++S ++ D E G KGYGF ++
Sbjct: 1 DPAVDRSLR-SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
+E A ++ +NG + + + V K +E
Sbjct: 60 QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92
Score = 31.1 bits (71), Expect = 0.14
Identities = 7/30 (23%), Positives = 17/30 (56%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+++V N+ +E+L+ F+ G + S +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFR 39
>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 = 77.0 bits (190), Expect = 7e-18
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 8/91 (8%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
V+I+N D +E L E+ + +G + RV+ + S+G F + + E A+K +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 262 AWN------GKEVDGKILYVGRAQKKAERTQ 286
A + G ++DG+ L V A + E
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
Score = 67.0 bits (164), Expect = 3e-14
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
VFI+NL + +A+ + FG + +V + +SKG F F T+EAA K +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 171 VN------GMLLNSKIVFVGKFIPRKEREK 194
+ G+ L+ + + V + R E
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
Score = 38.1 bits (89), Expect = 5e-04
Identities = 7/36 (19%), Positives = 18/36 (50%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ +G ++++NL ++E L + FG + +
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVR 46
>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 = 76.7 bits (189), Expect = 9e-18
Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 10/91 (10%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
+ +Y++ + + L + F+ G + + GK +G V+YE P
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
A+ AV+ ++GK+ G L V A+KK
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
Score = 57.0 bits (138), Expect = 1e-10
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 9/92 (9%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNSKGYGFVHFETEE 162
++++ L+ S+ + D F G + + D E G KG V +E
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
A ++E +G + V +
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108
Score = 33.1 bits (76), Expect = 0.035
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+YV+ L+DS+ + L F G + K
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNK 46
>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 = 75.8 bits (187), Expect = 1e-17
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+YI N + L+++F + +V G+ FV Y +A +A++
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV----LLKSGYAFVDYPDQNWAIRAIETL 64
Query: 264 NGK-EVDGKILYVGRAQKKAERT 285
+GK E+ GKI+ V + K R+
Sbjct: 65 SGKVELHGKIMEVDYSVSKKLRS 87
Score = 64.2 bits (157), Expect = 2e-13
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG+ ++I NL ++ + F L+ +V GY FV + + A ++
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRA 60
Query: 168 IEKVNGML-LNSKIVFVGKFIPRKERE 193
IE ++G + L+ KI+ V + +K R
Sbjct: 61 IETLSGKVELHGKIMEVDYSVSKKLRS 87
Score = 34.5 bits (80), Expect = 0.006
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LY+ NL ++ + LR+ F + +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQ 39
Score = 27.2 bits (61), Expect = 2.4
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 76 DTERALDTMNFDA-LKGRPIRIMWSQRDPSLRKSG 109
RA++T++ L G+ + + +S LR SG
Sbjct: 56 WAIRAIETLSGKVELHGKIMEVDYS-VSKKLRSSG 89
>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 = 75.7 bits (187), Expect = 1e-17
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
+ + + L+E+F YG I ++ + +SRGF FV +E+ + A++A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 261 QAWNGKEVDGKILYVGRAQ 279
+ NG E+DG+ + V
Sbjct: 75 ERANGMELDGRRIRVSGPS 93
Score = 64.1 bits (157), Expect = 2e-13
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+ + L + + + FS +G I + D + S+G+ FV+FE + A ++ E+
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 171 VNGMLLNSKIVFV 183
NGM L+ + + V
Sbjct: 77 ANGMELDGRRIRV 89
Score = 37.6 bits (88), Expect = 7e-04
Identities = 10/38 (26%), Positives = 14/38 (36%)
Query: 299 RLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
R N L V L + LR+ F+ +G I
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS 46
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 75.8 bits (187), Expect = 1e-17
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 4/78 (5%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T YI N + L +F+ +G I ++ +G F+ Y++ E A + A
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY----PEKGCCFIKYDTHEQAAVCIVAL 83
Query: 264 NGKEVDGKILYVGRAQKK 281
G+ L G +++
Sbjct: 84 ANFPFQGRNLRTGWGKER 101
Score = 66.9 bits (164), Expect = 2e-14
Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 7/98 (7%)
Query: 89 LKGRPIRIMWSQRDPSLRKSGVGN--VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE 146
G P ++ D +R + +I N+ + F FG IL K +
Sbjct: 4 TIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE- 62
Query: 147 QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
KG F+ ++T E A I + + + G
Sbjct: 63 ----KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96
Score = 40.4 bits (95), Expect = 7e-05
Identities = 8/30 (26%), Positives = 11/30 (36%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
Y+ N+ + L F FG I K
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFK 58
Score = 29.6 bits (67), Expect = 0.48
Identities = 4/23 (17%), Positives = 8/23 (34%)
Query: 76 DTERALDTMNFDALKGRPIRIMW 98
+ + +GR +R W
Sbjct: 75 QAAVCIVALANFPFQGRNLRTGW 97
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 75.4 bits (186), Expect = 2e-17
Identities = 17/81 (20%), Positives = 36/81 (44%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ N D + + ++F G S +++ + + FV + A A+ A
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 264 NGKEVDGKILYVGRAQKKAER 284
NG+++ GK + V A + +
Sbjct: 76 NGRKILGKEVKVNWATTPSSQ 96
Score = 66.5 bits (163), Expect = 4e-14
Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 1/83 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+++ NL + + + FS G SCK+ + N Y FV F A ++ +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75
Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
NG + K V V ++
Sbjct: 76 NGRKILGKEVKVNWATTPSSQKS 98
Score = 54.2 bits (131), Expect = 1e-09
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
D AL MN + G+ +++ W+ PS +KSG +
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWA-TTPSSQKSGPSS 102
Score = 41.9 bits (99), Expect = 2e-05
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ Q LYV NL + + + + F+ G S K
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK 46
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 75.4 bits (186), Expect = 2e-17
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
+++ E+ +E + + F YG I + + N D G +G+ V YE+ + A+ A+
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHL-NLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 261 QAWNGKEVDGKILYVGRAQKKA 282
+ NG+++ G+ + V +
Sbjct: 83 EGLNGQDLMGQPISVDWCFVRG 104
Score = 63.4 bits (155), Expect = 6e-13
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+F+ + + + ++D F+ +G I + + D G KGY V +ET + A ++E
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 171 VNGMLLNSKIVFVGKFIPRK 190
+NG L + + V R
Sbjct: 85 LNGQDLMGQPISVDWCFVRG 104
Score = 33.4 bits (77), Expect = 0.022
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+G L+V + + +E + +F +G I +
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIH 54
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 75.0 bits (185), Expect = 4e-17
Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ + E+ +++++E F YG I + + N D G S+G+ V YE+ + A A +A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHL-NLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
NG E+ G+ + V K +
Sbjct: 88 LNGAEIMGQTIQVDWCFVKGPK 109
Score = 62.3 bits (152), Expect = 2e-12
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+F+ ++ + + + F +G I + + D G SKGY V +ET + A + E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 172 NGMLLNSKIVFVGKFIPRKER 192
NG + + + V + +
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPK 109
Score = 30.7 bits (70), Expect = 0.19
Identities = 6/33 (18%), Positives = 19/33 (57%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+G L+V ++ + ++ ++++F +G I +
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 57
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 75.1 bits (185), Expect = 5e-17
Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
++++ GE+ E + + F+ G I + + GK +G V+++ P
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
A+ A+ ++GKE G + V A ++A+ +
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100
Score = 58.2 bits (141), Expect = 6e-11
Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 9/98 (9%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNSKGYGFVHFETEE 162
+F++ L +++ +++ D F G I + + D E G KG V F+
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA 200
+A +I+ +G + + V R + + G
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGR 106
Score = 33.1 bits (76), Expect = 0.033
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V+ L +++ E + F G I + K
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNK 38
>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 = 74.2 bits (183), Expect = 5e-17
Identities = 16/81 (19%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
++I N + +++++ +FE YG + ++ + +GFV E AE A++
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNL 62
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+ ++ G + V ++ K++
Sbjct: 63 HHYKLHGVNINVEASKNKSKA 83
Score = 60.7 bits (148), Expect = 3e-12
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 104 SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEA 163
S SG+ +FI NL + + + F +G +L C + K YGFVH E + A
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTA 54
Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
A +I ++ L+ + V + +
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKNKSKASS 85
Score = 36.4 bits (85), Expect = 0.001
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
V L++ NL ++ +R F +G +
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECD 39
>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 = 74.2 bits (183), Expect = 6e-17
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
VY+ E ++ L E+F G + + + D G+ +G+GFV + S E A+ A++
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK-DRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
+ ++ GK + V +A +
Sbjct: 77 MDMIKLYGKPIRVNKASAHNKN 98
Score = 70.4 bits (173), Expect = 2e-15
Identities = 22/93 (23%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETE 161
P ++ V++ LD+ + +++ F G +++ + +D G +GYGFV F +E
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
E A+ +I+ ++ + L K + V K +
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100
Score = 47.3 bits (113), Expect = 2e-07
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 76 DTERALDTMNFDALKGRPIRIMW-SQRDPSLRKSGVG 111
D + A+ M+ L G+PIR+ S + +L G
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105
Score = 39.6 bits (93), Expect = 1e-04
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
R Q +YV LD+ + + L + F G + +
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTH 46
>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 = 74.7 bits (184), Expect = 7e-17
Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 4/84 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
+++ E+ +E + + F YG I + + N D G +G+ V YE+ + A+ A+
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHL-NLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
+ NG+++ G+ + V +
Sbjct: 82 EGLNGQDLMGQPISVDWCFVRGPP 105
Score = 64.3 bits (157), Expect = 5e-13
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+F+ + + + ++D F+ +G I + + D G KGY V +ET + A ++E
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKE 195
+NG L + + V R + +
Sbjct: 84 LNGQDLMGQPISVDWCFVRGPPKGK 108
Score = 33.1 bits (76), Expect = 0.036
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
G L+V + + +E + +F +G I +
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIH 53
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 73.8 bits (182), Expect = 8e-17
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T +++ N +++L+ FE YG + ++ + + FV E E A +A++
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV------KDYAFVHMERAEDAVEAIRGL 64
Query: 264 NGKEVDGKILYVGRAQKKAERT 285
+ E GK ++V + +
Sbjct: 65 DNTEFQGKRMHVQLSTSRLRTA 86
Score = 58.0 bits (141), Expect = 4e-11
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 7/83 (8%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+ + N+ + N+ + F +G ++ C + K Y FVH E E A ++I +
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGL 64
Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
+ K + V R
Sbjct: 65 DNTEFQGKRMHVQLSTSRLRTAS 87
Score = 36.8 bits (86), Expect = 0.001
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+V N+ + ++ LR +F +G +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECD 41
>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 = 73.4 bits (181), Expect = 8e-17
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 4/84 (4%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
+YI N DE L E G I + N +G+S+GF V S ++K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
+E+ G+ V + K
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHH 86
Score = 62.2 bits (152), Expect = 9e-13
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
++I NL ++ + + + G IL K ++ G SKG+ V +E ++ K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 169 EKVNGMLLNSKIVFVGKFIPRKER 192
+ + L+ + V +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHH 86
Score = 31.8 bits (73), Expect = 0.061
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGT--ITSAK 336
+ LY+ NL DE L + G I K
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK 34
>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 = 73.8 bits (182), Expect = 8e-17
Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 5/85 (5%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
+++K ED +E LKE F+ R++ + G S+GFGFV + S E A+ A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 261 QAWNGKEVDGKILYVGRAQKKAERT 285
+A E+DG + + A+ K E
Sbjct: 72 EAMEDGEIDGNKVTLDWAKPKGEGG 96
Score = 63.0 bits (154), Expect = 6e-13
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 4/95 (4%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
P+ R +F+K L + + + + +F + ++ D E G+SKG+GFV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVD 60
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
F +EE A + E + ++ V + P+ E
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95
Score = 29.5 bits (67), Expect = 0.48
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+VK L + +E L++ F A+
Sbjct: 17 TLFVKGLSEDTTEETLKES---FDGSVRAR 43
>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 = 74.2 bits (183), Expect = 9e-17
Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 7/100 (7%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRG 244
+P + +++E + KLF I + +E L+ +E +G +T VM +SRG
Sbjct: 15 VPLERKKREKEQFRKLF----IGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
FGFV + S + A+ A +DG+++ RA + E
Sbjct: 71 FGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES 109
Score = 51.9 bits (125), Expect = 9e-09
Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 7/95 (7%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
+ RK +FI L +++ + + +G + C V +D S+G+GFV
Sbjct: 21 KREKEQFRK-----LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
F + + ++ ++ ++V + + R+E
Sbjct: 76 FSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 109
Score = 27.6 bits (62), Expect = 2.3
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L++ L +E LR + +G +T
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCV 58
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 75.0 bits (184), Expect = 1e-16
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 4/92 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNND--GKSRGFGFVAYESPEFAEKA 259
VY+ +F D++L ++ G + + N G+S+G+ V S K
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
++ GK ++G+ + V A ++ E + R
Sbjct: 116 LELLPGKVLNGEKVDVRPATRQNLSQFEAQAR 147
Score = 64.9 bits (158), Expect = 5e-13
Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 3/93 (3%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGS--ILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
V++ + ++ + + G ++ K A++ G SKGY V +E + +K +
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
E + G +LN + V V + + E + +
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149
Score = 34.9 bits (80), Expect = 0.014
Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 7/80 (8%)
Query: 264 NGKEVDGKILYVGRAQKKAERTQEL-----KRRFEMLKIERLNRYQGVNLYVKNLDDSID 318
+G ++ + LY + QE + +L R + +YV +
Sbjct: 9 SGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTT 68
Query: 319 DERLRKEFTPFGT--ITSAK 336
D++L + G + K
Sbjct: 69 DQQLIQVIRSIGVYDVVELK 88
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 73.0 bits (180), Expect = 1e-16
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
N+Y+ N E++KE+F +G + + +++ K +GFGFV + +A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
+ + G+ + V A K
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSL 83
Score = 60.6 bits (148), Expect = 3e-12
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+++ NL S ++ + + FS FG + + K+ D E KG+GFV + E +++I K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKE 195
++ + + V + P+K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLEHH 86
Score = 35.6 bits (83), Expect = 0.003
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
N+YV NL S E++++ F+ FG + + K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVK 32
>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 = 74.8 bits (184), Expect = 2e-16
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 6/100 (6%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFG 246
+E+EK L + L Y+ N +E++ E+F G I + + + GF
Sbjct: 29 NEEQEKLLKKSCTL----YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
FV Y S AE A++ NG +D +I+ E Q
Sbjct: 85 FVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124
Score = 64.1 bits (156), Expect = 1e-12
Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 1/97 (1%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
+ +++ NL + +Y+ FS G I + D + + G+ FV
Sbjct: 28 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
+ + A ++ +NG L+ +I+ KE +
Sbjct: 88 YYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124
Score = 42.9 bits (101), Expect = 3e-05
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
D E A+ +N L R IR W R+ G G
Sbjct: 93 DAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGR 129
Score = 37.9 bits (88), Expect = 0.001
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 270 GKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ-GVNLYVKNLDDSIDDERLRKEFTP 328
G +L R+ E +Q + F E+ + LYV NL +E++ + F+
Sbjct: 3 GGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK 62
Query: 329 FGTITSAK 336
G I
Sbjct: 63 SGDIKKII 70
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 72.6 bits (179), Expect = 2e-16
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+++ N ++L+ +FE G + V+ + + FV E A+ A+
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KDYAFVHMEKEADAKAAIAQL 63
Query: 264 NGKEVDGKILYVGRAQKKAERT 285
NGKEV GK + V + K +++
Sbjct: 64 NGKEVKGKRINVELSTKGQKKS 85
Score = 58.0 bits (141), Expect = 3e-11
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ N+ + ++ + F G ++ C V K Y FVH E E A +I ++N
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLN 64
Query: 173 GMLLNSKIVFVGKFIPRKER 192
G + K + V +++
Sbjct: 65 GKEVKGKRINVELSTKGQKK 84
Score = 35.6 bits (83), Expect = 0.003
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V N+ + + LR F G +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECD 40
>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 = 71.8 bits (177), Expect = 4e-16
Identities = 18/81 (22%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
+++ + + +L+E F+ +G +T ++ + RGFGF+ +E + ++AV
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM- 71
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+ ++ GK + V RA+ + +
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
Score = 58.0 bits (141), Expect = 4e-11
Identities = 17/86 (19%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
+F+ + + + + F FG + + D E+ +G+GF+ FE E++ ++++
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREK 194
+ + K V V + PR +
Sbjct: 70 NM-HFHDIMGKKVEVKRAEPRDSKSS 94
Score = 30.2 bits (69), Expect = 0.21
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V + + + LR+ F FG +T
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVV 41
>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 = 72.0 bits (177), Expect = 5e-16
Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 5/93 (5%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPE 254
G K ++I + +++ LK +FE +G I V+ G +G F+ Y E
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66
Query: 255 FAEKAVQAWNGKEV---DGKILYVGRAQKKAER 284
A KA A + ++ + + V A ++
Sbjct: 67 SALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99
Score = 65.0 bits (159), Expect = 2e-13
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 98 WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFV 156
+D K +FI + +++D K + F FG I V +D G KG F+
Sbjct: 6 SGMKDHDAIK-----LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 157 HFETEEAANKSIEKVNGM 174
+ E+A K+ ++
Sbjct: 61 TYCERESALKAQSALHEQ 78
Score = 34.6 bits (80), Expect = 0.008
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ L++ + ++D++ L+ F FG I
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELT 44
>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 = 71.8 bits (176), Expect = 7e-16
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 4/87 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T + KN +++E F +G++ + + V + P A KA +
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL----PEGGITAIVEFLEPLEARKAFRHL 66
Query: 264 NGKEVDGKILYVGRAQKKAERTQELKR 290
+ LY+ A K+
Sbjct: 67 AYSKFHHVPLYLEWAPIGVFGAAPQKK 93
Score = 50.2 bits (120), Expect = 3e-08
Identities = 16/94 (17%), Positives = 31/94 (32%), Gaps = 10/94 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ KNL + +TFS FGS+ + V F A K+ +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67
Query: 173 GMLLNSKIVFV-----GKFIPRKEREKELGEKAK 201
+ +++ G F +++ E+
Sbjct: 68 YSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101
Score = 37.1 bits (86), Expect = 0.001
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITS 334
+ KNL +++ F+ FG++
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGR 39
Score = 26.7 bits (59), Expect = 4.8
Identities = 5/37 (13%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 66 LVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRD 102
+V+ +P + +A + + P+ + W+
Sbjct: 50 IVEFLEPL--EARKAFRHLAYSKFHHVPLYLEWAPIG 84
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 72.2 bits (177), Expect = 8e-16
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 5/88 (5%)
Query: 204 TNVYIKNFGEDFNDEKLKE----MFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA 259
V I N + EKL+ + G I V + + G ++ + + E A+
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS-DDNSGKAYIVFATQESAQAF 88
Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQE 287
V+A+ G G L + ++ + E
Sbjct: 89 VEAFQGYPFQGNPLVITFSETPQSQVAE 116
Score = 60.3 bits (146), Expect = 1e-11
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 112 NVFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
V I N++ + +Y S+ G IL V ++ G ++ F T+E+A
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAF 88
Query: 168 IEKVNGMLLNSKIVFV 183
+E G + +
Sbjct: 89 VEAFQGYPFQGNPLVI 104
Score = 36.8 bits (85), Expect = 0.002
Identities = 7/63 (11%), Positives = 19/63 (30%), Gaps = 4/63 (6%)
Query: 278 AQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKE----FTPFGTIT 333
+ A + + L + + + N++ + E+L+ + G I
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61
Query: 334 SAK 336
Sbjct: 62 DIV 64
Score = 27.6 bits (61), Expect = 2.9
Identities = 4/27 (14%), Positives = 11/27 (40%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRD 102
+ ++ +G P+ I +S+
Sbjct: 84 SAQAFVEAFQGYPFQGNPLVITFSETP 110
>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 = 71.2 bits (175), Expect = 9e-16
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ N D + ++++F YG I + N F FV +E P AE AV
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+G + DG L V +
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGT 102
Score = 54.2 bits (131), Expect = 1e-09
Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 3/93 (3%)
Query: 91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
G + +++ NL I K + D F +G+I +
Sbjct: 4 GSSGMSGGGVIRGPAGNND-CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGG 60
Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ FV FE A ++ +G + + V
Sbjct: 61 PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93
Score = 31.5 bits (72), Expect = 0.10
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+YV NL I + + F +G I
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDID 53
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 70.8 bits (174), Expect = 1e-15
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
VY+ N G +L+ F YG + + + N GF FV +E P AE AV+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 265 GKEVDGKILYVGRAQKKAER 284
GK + G + V + R
Sbjct: 59 GKVICGSRVRVELSTGMPRR 78
Score = 52.7 bits (127), Expect = 4e-09
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
V++ NL + FS +G + + +A++ G+ FV FE A ++ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 172 NG 173
+G
Sbjct: 58 DG 59
Score = 34.2 bits (79), Expect = 0.009
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ +YV NL L + F+ +G + +
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVW 31
>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 = 71.2 bits (175), Expect = 1e-15
Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 216 NDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
D L++ FE +G I V+ GKSRG+GFV AE+A + N +DG+
Sbjct: 30 TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKA 88
Query: 274 YVGRAQKKAERTQELKRR 291
V A A+
Sbjct: 89 NVNLAYLGAKPRSLQTGF 106
Score = 61.2 bits (149), Expect = 4e-12
Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 7/103 (6%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
SQ+D + K +F+ L + ++ F FG I V D Q G S+GYGFV
Sbjct: 11 SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA 200
AA ++ + N + ++ + V + A
Sbjct: 66 MADRAAAERACKDPNPI-IDGRKANVNLAYLGAKPRSLQTGFA 107
Score = 31.9 bits (73), Expect = 0.086
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V L D LRK F FG I A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAV 48
>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 = 70.0 bits (172), Expect = 1e-15
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T +Y+ G+ + L+ F +G I + V+ + + F+ + + + AE A +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVV----QRQQCAFIQFATRQAAEVAAEKS 68
Query: 264 -NGKEVDGKILYVG 276
N V+G+ L V
Sbjct: 69 FNKLIVNGRRLNVK 82
Score = 58.8 bits (143), Expect = 1e-11
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
S D ++ +++ L +I + + F FG I + V Q + F+ F
Sbjct: 6 SGEDKTIT-----TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQF 55
Query: 159 ETEEAANKSIEKV-NGMLLNSKIVFVG 184
T +AA + EK N +++N + + V
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNGRRLNVK 82
Score = 39.9 bits (94), Expect = 7e-05
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
LYV L D+I + LR F FG I +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTIT 43
>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 = 70.3 bits (173), Expect = 2e-15
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
E L+ F YG + +M +SRGFGFV ++ P + + +DG+ +
Sbjct: 29 TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI 87
Query: 274 YVGRAQKKAER 284
+ +
Sbjct: 88 DPKPCTPRGMQ 98
Score = 51.5 bits (124), Expect = 9e-09
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 7/95 (7%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
+ + K +F+ LD S + + FS +G ++ C + +D+ S+G+GFV
Sbjct: 10 NSGADEIGK-----LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
F+ + L+ + + PR +
Sbjct: 65 FKDPNCVGTVLA-SRPHTLDGRNIDPKPCTPRGMQ 98
Score = 27.2 bits (61), Expect = 3.0
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
L+V LD S E LR F+ +G +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDC 46
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 9/103 (8%)
Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGK 241
+PR K+F I E L+E F +G + VM +
Sbjct: 12 SGLVPRGSHMGS--SGCKMF----IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR 65
Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
SRGFGFV + +K + + E+D K + A + +
Sbjct: 66 SRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRAQ 107
Score = 55.7 bits (135), Expect = 3e-10
Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 7/97 (7%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
S S K +FI L + + + F FG + C V +D S+G+GFV
Sbjct: 19 SHMGSSGCK-----MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
F + +K + + L+SK + PR+ + K
Sbjct: 74 FMDQAGVDKVLA-QSRHELDSKTIDPKVAFPRRAQPK 109
Score = 26.8 bits (60), Expect = 3.8
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
+++ L E LR+ F FG +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKEC 55
>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 = 69.3 bits (170), Expect = 3e-15
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
++++ +L+ +D + F+ G +++S K+ ++ G GY FV F A K +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 170 KVNGMLLN 177
K+NG L
Sbjct: 71 KINGKPLP 78
Score = 60.0 bits (146), Expect = 7e-12
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
++++ + ++ + F G T+ S +++ N G G+ FV + AEK +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 261 QAWNGKEVDGKILYV 275
NGK + G
Sbjct: 70 HKINGKPLPGATPAK 84
Score = 33.8 bits (78), Expect = 0.015
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 5/34 (14%)
Query: 76 DTERALDTMNFDALKG----RPIRIMW-SQRDPS 104
E+ L +N L G + ++ + + PS
Sbjct: 64 TAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97
Score = 33.4 bits (77), Expect = 0.021
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFG-TITSAK 336
+ +L++ +L+ +D+ + + F G T+ S K
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVK 41
>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 = 18/101 (17%), Positives = 38/101 (37%), Gaps = 3/101 (2%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGF 245
P +E L + + V+ L++ F G + R++ N +S+G
Sbjct: 10 PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
+V + + A+ G+ + G + V +Q + R
Sbjct: 70 AYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLS 109
Score = 63.5 bits (155), Expect = 6e-13
Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
VF L I + + D FSA G + ++ D SKG +V F ++ +I
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL- 86
Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
G L + V K R
Sbjct: 87 TGQRLLGVPIIVQASQAEKNRL 108
Score = 31.9 bits (73), Expect = 0.074
Identities = 8/59 (13%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 278 AQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ + ++ + + ER R ++ L I L F+ G + +
Sbjct: 2 SSGSSGKSPVREPVDNLSPEERDAR----TVFCMQLAARIRPRDLEDFFSAVGKVRDVR 56
>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 = 70.3 bits (172), Expect = 5e-15
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
VY+ N G + N +L+ F YG + S V N GF FV +E P A AV+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVREL 130
Query: 264 NGKEVDGKILYVGRAQKK 281
+G+ + G + V + +
Sbjct: 131 DGRTLCGCRVRVELSNGE 148
Score = 52.2 bits (125), Expect = 1e-08
Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 6/97 (6%)
Query: 83 TMNFDALKGRPIRIMWSQRDPSLRKSGVGN--VFIKNLDKSIDNKAMYDTFSAFGSILSC 140
T + R S + V++ NL + + + F +G + S
Sbjct: 44 TYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV 103
Query: 141 KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
VA++ G+ FV FE A ++ +++G L
Sbjct: 104 WVARN----PPGFAFVEFEDPRDAADAVRELDGRTLC 136
Score = 48.0 bits (114), Expect = 5e-07
Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 4/105 (3%)
Query: 233 YRVMNNDGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVGRAQKKAERTQELKRR 291
Y+++ N +G AEK + + N VDG+ Y +
Sbjct: 3 YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHH 62
Query: 292 FEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
M R + +YV NL ++ + L + F +G + S
Sbjct: 63 HHM---HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW 104
>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 = 68.5 bits (168), Expect = 7e-15
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
++++ GE+ E + + F+ G I + + GK +G V+++ P
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 254 EFAEKAVQAWNGKEVDGKILYVGRA 278
A+ A+ ++GKE G + V A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 55.4 bits (134), Expect = 3e-10
Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 9/93 (9%)
Query: 100 QRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNS 150
S +F++ L +++ +++ D F G I + + D E G
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
KG V F+ +A +I+ +G + + V
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95
Score = 30.7 bits (70), Expect = 0.15
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V+ L +++ E + F G I + K
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNK 44
>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 = 67.7 bits (166), Expect = 1e-14
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 2/81 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSY--RVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
T + ++N + +++ + F Y I N G G VA+ES + A AV
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 262 AWNGKEVDGKILYVGRAQKKA 282
N + + + + + +
Sbjct: 76 DLNDRPIGSRKVKLVLGSGPS 96
Score = 56.5 bits (137), Expect = 1e-10
Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI-LSCKVAQDEQGNSKGYGFVHFETE 161
S K G + ++N+ ++ + D F + I S + +E+G G V FE+
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 162 EAANKSIEKVNGMLLNSKIVFV 183
+ A ++ +N + S+ V +
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKL 89
Score = 26.9 bits (60), Expect = 4.1
Identities = 4/29 (13%), Positives = 12/29 (41%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPS 104
+ A+ +N + R ++++ S
Sbjct: 69 EATAAVIDLNDRPIGSRKVKLVLGSGPSS 97
Score = 25.7 bits (57), Expect = 9.5
Identities = 4/28 (14%), Positives = 13/28 (46%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
+ V+N+ ++ + + F + I +
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGS 45
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 8/93 (8%)
Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYE 251
+ + + + L + ++ LKE F +G + +V G S+GFGFV +
Sbjct: 10 RAVQKTSDLI----VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
Query: 252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
E K + + +DG+ K +
Sbjct: 66 EYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 96
Score = 56.9 bits (138), Expect = 1e-10
Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI 168
++ + L + + + FS FG +L +V +D + G+SKG+GFV F E K +
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Query: 169 EKVNGMLLNSKIVFVGKFIPRKERE 193
+ + +++ + ++ ++
Sbjct: 75 SQRH--MIDGRWCDCKLPNSKQSQD 97
Score = 29.1 bits (66), Expect = 0.66
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L V L ++ L++ F+ FG + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQ 46
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 66.7 bits (164), Expect = 2e-14
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
E L+E F +G + VM +SRGFGFV + +K + + E+D K +
Sbjct: 13 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTI 71
Query: 274 YVGRA 278
A
Sbjct: 72 DPKVA 76
Score = 49.0 bits (118), Expect = 3e-08
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
+FI L + + + F FG + C V +D S+G+GFV F + +K +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Score = 27.1 bits (61), Expect = 1.8
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
+++ L E LR+ F FG +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKEC 30
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 67.0 bits (164), Expect = 2e-14
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKA 259
+ ++N + + PY + + + R++ + ++RGF FV S A +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 260 VQAWNGKE----VDGKILYVGRAQK 280
+Q +DGK + V A+
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 58.9 bits (143), Expect = 2e-11
Identities = 10/72 (13%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI 168
+ ++N+ ++ S + ++ + ++ +D+Q ++G+ FV + A++ +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 169 EKVNGMLLNSKI 180
+ + + KI
Sbjct: 71 QILQSLHPPLKI 82
Score = 33.1 bits (76), Expect = 0.026
Identities = 2/30 (6%), Positives = 12/30 (40%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ ++N+ + + +P+ ++
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNN 40
>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 = 66.6 bits (163), Expect = 3e-14
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 2/79 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
T + ++N + +++ + F Y I + N G G VA+ES + A AV
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 262 AWNGKEVDGKILYVGRAQK 280
N + + + + +
Sbjct: 76 DLNDRPIGSRKVKLSGPSS 94
Score = 54.6 bits (132), Expect = 6e-10
Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAAN 165
K G + ++N+ ++ + D F + I + +E+G G V FE+ + A
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 166 KSIEKVNGMLLNSKIVFV 183
++ +N + S+ V +
Sbjct: 72 AAVIDLNDRPIGSRKVKL 89
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 66.0 bits (162), Expect = 3e-14
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 213 EDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+ E +K FE +G + +M + RGFGFV +ES + EK + + E++
Sbjct: 9 VNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINN 67
Query: 271 KILYVGRA 278
K++ +A
Sbjct: 68 KMVECKKA 75
Score = 51.3 bits (124), Expect = 5e-09
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ L + + + F FG + + D+ +G+GFV FE+E+ K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60
Query: 172 NGMLLNSKIV 181
+ +N+K+V
Sbjct: 61 HFHEINNKMV 70
Score = 25.9 bits (58), Expect = 5.0
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V L + E ++ F FG + A
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAM 30
>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 = 67.2 bits (164), Expect = 4e-14
Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 11/108 (10%)
Query: 186 FIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGF 245
+PR + ++I+ D + ++ + P+G +T+ ++ K +
Sbjct: 14 LVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQ 69
Query: 246 GFVAYESPEFAEKAVQ--AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
F+ + E A V + G+ +Y+ + K ELK
Sbjct: 70 AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK-----ELKTD 112
Score = 44.5 bits (105), Expect = 3e-06
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 7/73 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
+ I+ L + + FG + + + + K F+ TEEAAN +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88
Query: 171 VNGMLLNSKIVFV 183
+L + +++
Sbjct: 89 SVTPVLRGQPIYI 101
Score = 36.0 bits (83), Expect = 0.003
Identities = 5/29 (17%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++++ L + + + PFG +T+
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLL 62
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 65.9 bits (161), Expect = 4e-14
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
+ ++F +G IT+ DGK++G+ F+ Y SP A AV+ +G ++D +
Sbjct: 22 NVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75
Score = 49.3 bits (118), Expect = 3e-08
Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 113 VFIKNL------DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
+ + N+ ++ FS FG I + +++ G +KGY F+ + + A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 62
Query: 167 SIEKVNGMLLNSKIVF 182
+++ +G L+ + F
Sbjct: 63 AVKNADGYKLDKQHTF 78
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 66.4 bits (162), Expect = 5e-14
Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 6/84 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA--W 263
++I+ D + ++ + P+G +T+ ++ K + F+ + E A V
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQAFIEMNTEEAANTMVNYYTS 74
Query: 264 NGKEVDGKILYVGRAQKKAERTQE 287
+ G+ +Y+ + K +T
Sbjct: 75 VTPVLRGQPIYIQFSNHKELKTDS 98
Score = 44.8 bits (106), Expect = 2e-06
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
+ I+ L + + FG + + + + K F+ TEEAAN +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73
Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
+L + +++ +F KE
Sbjct: 74 SVTPVLRGQPIYI-QFSNHKE 93
Score = 37.1 bits (86), Expect = 0.001
Identities = 5/29 (17%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++++ L + + + PFG +T+
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLL 47
>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 = 66.7 bits (163), Expect = 7e-14
Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 7/105 (6%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
P EK+ +K +VY+ N + L+ F G+I ++ + G +G+
Sbjct: 25 PLSAEEKKEIDK----RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGY 80
Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
++ + + AV A + G+ + V + R
Sbjct: 81 AYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPGISSTDR 124
Score = 55.1 bits (133), Expect = 9e-10
Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 2/85 (2%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
+V++ N+D + + FS+ GSI + D G+ KGY ++ F + + ++
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 170 KVNGMLLNSKIVFVGKFIPRKEREK 194
++ + + + V
Sbjct: 97 -MDETVFRGRTIKVLPKRTNMPGIS 120
Score = 32.8 bits (75), Expect = 0.053
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++YV N+D + L F+ G+I
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67
>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 = 64.8 bits (159), Expect = 1e-13
Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
++Y+ N E+L+ F G++ ++ + G +GF ++ + E ++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65
Query: 262 AWNGKEVDGKILYVGRAQKK 281
A + G+ + V +
Sbjct: 66 ALDESLFRGRQIKVIPKRTN 85
Score = 57.1 bits (139), Expect = 6e-11
Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
++++ N+D + + F GS+ + D G+ KG+ ++ F +E+ S+
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 171 VNGMLLNSKIVFVGKFIPRK 190
+ L + + V +
Sbjct: 68 -DESLFRGRQIKVIPKRTNR 86
Score = 33.6 bits (78), Expect = 0.012
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++YV N+D E L F G++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVT 37
>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 = 64.9 bits (159), Expect = 1e-13
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
+ + LK+ F +G + + N G+SRGFGF+ ++ EK + +DG+++
Sbjct: 24 SKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVI 82
Query: 274 YVGRA 278
+A
Sbjct: 83 DPKKA 87
Score = 49.9 bits (120), Expect = 2e-08
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
S+ + K +F+ L K + D F+ FG ++ C + D G S+G+GF+
Sbjct: 5 SKNEEDAGK-----MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFIL 59
Query: 158 FETEEAANKSIEKVNGMLLNSKI 180
F+ + K +++ L I
Sbjct: 60 FKDAASVEKVLDQKEHRLDGRVI 82
Score = 28.3 bits (64), Expect = 0.93
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
++V L + L+ FT FG +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDC 41
>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 = 64.7 bits (158), Expect = 1e-13
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+ + +KN +D N +++ ++ + Y Y +++ FV + E A+ A+Q +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 264 NGKEVDGKILYVGRAQKKA 282
+ GK L V A
Sbjct: 61 HQYSFRGKDLIVQLQPTDA 79
Score = 54.0 bits (130), Expect = 7e-10
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG + +KNL + + + ++D + + C V +K FV E A +
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNA 56
Query: 168 IEKVNGMLLNSKIVFV 183
I+ + K + V
Sbjct: 57 IQMFHQYSFRGKDLIV 72
Score = 29.7 bits (67), Expect = 0.31
Identities = 4/23 (17%), Positives = 9/23 (39%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFG 330
+ VKNL + + + +
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD 30
>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 = 64.5 bits (158), Expect = 2e-13
Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 5/81 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V++ D +++L+E F YG + + R F FV + + A+
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCG--ED 62
Query: 266 KEVDGKILYVGRAQKKAERTQ 286
+ G +++ A+ K
Sbjct: 63 LIIKGISVHISNAEPKHNSNS 83
Score = 49.9 bits (120), Expect = 2e-08
Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 6/82 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
VF+ + + + FS +G ++ + + + + FV F ++ A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--E 61
Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
+++ V + P+
Sbjct: 62 DLIIKGISVHISNAEPKHNSNS 83
Score = 28.0 bits (63), Expect = 1.2
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
++V + ++ LR+ F+ +G +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDV 35
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 64.8 bits (158), Expect = 2e-13
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
+ ++F +G IT+ DGK++G+ F+ Y SP A AV+ +G ++D +
Sbjct: 36 NVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89
Score = 49.0 bits (117), Expect = 7e-08
Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 113 VFIKNL------DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
+ + N+ ++ FS FG I + +++ G +KGY F+ + + A
Sbjct: 18 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 76
Query: 167 SIEKVNGMLLNSKIVF 182
+++ +G L+ + F
Sbjct: 77 AVKNADGYKLDKQHTF 92
>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 = 64.2 bits (157), Expect = 2e-13
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 5/79 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V++ ED E+L++ F YG + + R F FV + + A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK---PFRAFAFVTFADDKVAQSLCG--ED 68
Query: 266 KEVDGKILYVGRAQKKAER 284
+ G +++ A+ K +
Sbjct: 69 LIIKGISVHISNAEPKHNK 87
Score = 48.4 bits (116), Expect = 9e-08
Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
VF+ + + + + F +G ++ + + + + FV F ++ A +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69
Query: 173 GMLLNSKIVFVGKFIPRKER 192
++ V + P+ +
Sbjct: 70 --IIKGISVHISNAEPKHNK 87
Score = 27.6 bits (62), Expect = 1.9
Identities = 6/41 (14%), Positives = 18/41 (43%)
Query: 295 LKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
++ + + G ++V + + E L++ F +G +
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDV 41
>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 = 64.1 bits (156), Expect = 3e-13
Identities = 11/78 (14%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--AW 263
++I+ + + ++ + P+G +T+ ++ K + F+ + E A V +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML----KGKNQAFLELATEEAAITMVNYYSA 73
Query: 264 NGKEVDGKILYVGRAQKK 281
+ + +Y+ + K
Sbjct: 74 VTPHLRNQPIYIQYSNHK 91
Score = 42.5 bits (100), Expect = 1e-05
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 8/81 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
+ I+ L + + FG + + + K F+ TEEAA +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72
Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
L ++ +++ ++ KE
Sbjct: 73 AVTPHLRNQPIYI-QYSNHKE 92
Score = 37.1 bits (86), Expect = 0.001
Identities = 6/39 (15%), Positives = 18/39 (46%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++++ L+++ L + + + PFG +T+
Sbjct: 8 DKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNIL 46
>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 = 63.4 bits (155), Expect = 4e-13
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
KA T +++ G + + L F+ +G+I + + K F ++ YES + A+
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV----KGDSFAYIQYESLDAAQA 68
Query: 259 AVQAWNGKEVDGK 271
A G + G
Sbjct: 69 ACAKMRGFPLGGP 81
Score = 58.8 bits (143), Expect = 2e-11
Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 11/87 (12%)
Query: 91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
G +I + + +P+ R +++ L + A+ F FGSI + +
Sbjct: 4 GSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----- 52
Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLN 177
+ ++ +E+ +AA + K+ G L
Sbjct: 53 DSFAYIQYESLDAAQAACAKMRGFPLG 79
Score = 37.2 bits (87), Expect = 7e-04
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
L+V L + L +EF FG+I +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTID 48
>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 = 62.5 bits (153), Expect = 5e-13
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 213 EDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
D +EK++E F +G + S + N K RGF F+ ++ E +K ++ V
Sbjct: 9 PDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL 67
Query: 271 KILYVGRA 278
+ A
Sbjct: 68 SKCEIKVA 75
Score = 48.7 bits (117), Expect = 4e-08
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
+F+ L + + + F FG + S ++ D + +G+ F+ F+ EE K +EK
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 25.5 bits (57), Expect = 7.7
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
++V L +E++R+ F FG + S
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESI 29
>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 = 65.1 bits (158), Expect = 6e-13
Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 6/102 (5%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVF---IKNLDKSIDNKAMYDTFS 132
+ AL +N + + D + +G V ++NL + ++ FS
Sbjct: 9 SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFS 68
Query: 133 AFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM 174
FG++L N++ + + +A + ++G
Sbjct: 69 KFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQ 107
Score = 50.9 bits (121), Expect = 5e-08
Identities = 16/112 (14%), Positives = 40/112 (35%), Gaps = 5/112 (4%)
Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFN 216
H +A +++ VN + + + G+ L + ++N
Sbjct: 3 HHHHHGSAQAALQAVNSVQSGNLAL-AASAAAVDAGMAMAGQSPVLR--IIVENLFYPVT 59
Query: 217 DEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV 268
+ L ++F +GT+ ++ + Y P A+ A + +G+ +
Sbjct: 60 LDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNI 109
Score = 32.4 bits (73), Expect = 0.11
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 13/87 (14%)
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLY 309
+ A+ A+QA N + L A A + + +
Sbjct: 4 HHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPV-------------LRII 50
Query: 310 VKNLDDSIDDERLRKEFTPFGTITSAK 336
V+NL + + L + F+ FGT+
Sbjct: 51 VENLFYPVTLDVLHQIFSKFGTVLKII 77
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 62.5 bits (152), Expect = 1e-12
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 3/88 (3%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFA 256
GE A L +VY+ N D LK G++ R F+ Y A
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG---PRRRAFLHYPDSAAA 69
Query: 257 EKAVQAWNGKEVDGKILYVGRAQKKAER 284
++AV G + L V A+++ ++
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQQRDK 97
Score = 46.7 bits (111), Expect = 3e-07
Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+V++ NL + + GS+ Q + F+H+ AA +++ +
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCL 76
Query: 172 NGMLLN 177
G+ L
Sbjct: 77 QGLRLG 82
Score = 27.5 bits (61), Expect = 2.1
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTI 332
++YV NL L++ G++
Sbjct: 18 LAADVYVGNLPRDARVSDLKRALRELGSV 46
>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 = 64.1 bits (155), Expect = 2e-12
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 2/86 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
+VYIK F D + +KE E G + + ++ +G FV ++S E A+K V+
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQE 287
G++ L + + E
Sbjct: 169 T-PGQKYKETDLLILFKDDYFAKKNE 193
Score = 50.6 bits (120), Expect = 1e-07
Identities = 17/117 (14%), Positives = 41/117 (35%), Gaps = 7/117 (5%)
Query: 85 NFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQ 144
+ ++ P + + D +V+IK + + G +L+ ++ +
Sbjct: 84 DKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR 143
Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
KG FV F++ E+A K +E + + ++ +K +
Sbjct: 144 TLHKAFKGSIFVVFDSIESAKKFVETPG-------QKYKETDLLILFKDDYFAKKNE 193
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 204 TNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ V+I N + ++ +F YG + V +G+ FV Y + A AV
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH------KGYAFVQYSNERHARAAVLG 81
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
NG+ + G+ L + A +
Sbjct: 82 ENGRVLAGQTLDINMAGEPKPD 103
Score = 57.0 bits (138), Expect = 1e-10
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKA-MYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
++ DP S VFI NL+ ++ K+ + FS +G + C V KGY FV
Sbjct: 19 NKNDPKSINS---RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQ 68
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFV 183
+ E A ++ NG +L + + +
Sbjct: 69 YSNERHARAAVLGENGRVLAGQTLDI 94
Score = 27.7 bits (62), Expect = 2.2
Identities = 4/30 (13%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 308 LYVKNLD-DSIDDERLRKEFTPFGTITSAK 336
+++ NL+ + + F+ +G +
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCS 59
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 60.3 bits (147), Expect = 5e-12
Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 7/89 (7%)
Query: 204 TNVYIKNF-GEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ ++I N ++ + E L +F PYG I + FGF+ +++P+ A++
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEC 64
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRR 291
+ + GK L + + A +
Sbjct: 65 ESQEMNFGKKLILEVSSSNARPQFDHGDH 93
Score = 51.1 bits (123), Expect = 1e-08
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 113 VFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+FI NL K++ + ++ FS +G I+ + +GF+ F+ ++ +IE
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECE 65
Query: 172 NGMLLNSKIVFV 183
+ + K + +
Sbjct: 66 SQEMNFGKKLIL 77
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 61.0 bits (148), Expect = 5e-12
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+ +KN E + + LK++ T++ +N G G + + S E +A++ N
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-DFDGTGALEFPSEEILVEALERLNN 89
Query: 266 KEVDGKILYV 275
E G ++ V
Sbjct: 90 IEFRGSVITV 99
Score = 52.5 bits (126), Expect = 5e-09
Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ +KNL + + + D L + + G G + F +EE +++E++N
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENS--LETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88
Query: 173 GMLLNSKIVFV 183
+ ++ V
Sbjct: 89 NIEFRGSVITV 99
>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 = 60.6 bits (147), Expect = 7e-12
Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 5/79 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V + + + LK+ G + V G G V + E AV+ +
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVY-----RDGTGVVEFVRKEDMTYAVRKLDN 72
Query: 266 KEVDGKILYVGRAQKKAER 284
+ + K +
Sbjct: 73 TKFRSHEGETAYIRVKVDG 91
Score = 58.3 bits (141), Expect = 5e-11
Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 6/82 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V + L S + + D G + V G G V F +E ++ K++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 71
Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
S + + +
Sbjct: 72 NTKFRSHEGETAYIRVKVDGPR 93
Score = 27.8 bits (62), Expect = 1.7
Identities = 7/36 (19%), Positives = 12/36 (33%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+R + V L S + L+ G + A
Sbjct: 11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYAD 46
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.1 bits (146), Expect = 9e-12
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
I + + L +F G + + + GK++GF FV S A+K +++++
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 265 GKEVDGK 271
GK +D K
Sbjct: 76 GKRLDLK 82
Score = 52.8 bits (127), Expect = 3e-09
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 110 VGNV-FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKS 167
V I + + KA+ FS G +++ + DE G +KG+ FV + A K
Sbjct: 11 VNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKI 70
Query: 168 IEKVNGMLLNSKIVF-VGKF 186
I+ +G L+ K +
Sbjct: 71 IKSFHGKRLDLKHRLFLYTM 90
Score = 25.8 bits (57), Expect = 9.2
Identities = 3/28 (10%), Positives = 11/28 (39%)
Query: 309 YVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ + + + L F+ G + + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNME 43
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 60.3 bits (146), Expect = 9e-12
Identities = 20/84 (23%), Positives = 30/84 (35%), Gaps = 8/84 (9%)
Query: 206 VYIKNFGEDFNDE---KLKEMFEPYGTITSYRVMNNDG-----KSRGFGFVAYESPEFAE 257
V++ + D K E F +G I + N+ +V Y E A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 258 KAVQAWNGKEVDGKILYVGRAQKK 281
+A+Q N VDG+ L K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
Score = 49.9 bits (119), Expect = 4e-08
Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 113 VFIKNLDKSIDNKAM---YDTFSAFGSILSCKVAQD----EQGNSKGYGFVHFETEEAAN 165
VF+ L + + + + + F FG I + +V + E A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 166 KSIEKVNGMLLNSKIVFV 183
++I+ VN ++++ + +
Sbjct: 78 RAIQCVNNVVVDGRTLKA 95
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 59.0 bits (143), Expect = 2e-11
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--AW 263
V+I+ + + L E + +G I+ VM + V +E A AV A
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM----PKKRQALVEFEDVLGACNAVNYAAD 79
Query: 264 NGKEVDGKILYV 275
N + G +V
Sbjct: 80 NQIYIAGHPAFV 91
Score = 45.1 bits (107), Expect = 1e-06
Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 7/73 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
V I+ L + + + FG I V K V FE A ++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAA 78
Query: 171 VNGMLLNSKIVFV 183
N + + FV
Sbjct: 79 DNQIYIAGHPAFV 91
Score = 35.9 bits (83), Expect = 0.003
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++++ L D + + L + FG I+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVV 52
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA-- 262
V+++ E + L E E +GTI +M + V +E+ + A++ V
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMM----PFKRQALVEFENIDSAKECVTFAA 72
Query: 263 WNGKEVDGKILYVGRAQKK 281
+ G+ + + K
Sbjct: 73 DVPVYIAGQQAFFNYSTSK 91
Score = 46.7 bits (111), Expect = 4e-07
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 7/74 (9%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE-- 169
V ++ L +S+ + + FG+I + K V FE ++A + +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71
Query: 170 KVNGMLLNSKIVFV 183
+ + + F
Sbjct: 72 ADVPVYIAGQQAFF 85
Score = 36.3 bits (84), Expect = 0.002
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
++V+ L +S+ + L + FGTI
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVM 46
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 58.8 bits (143), Expect = 3e-11
Identities = 15/81 (18%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
Y+ N + + +F+ I S R++ + K +GF +V ++ + ++A+ +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+G + + L V A+ + +
Sbjct: 76 DGALLGDRSLRVDIAEGRKQD 96
Score = 52.7 bits (127), Expect = 3e-09
Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
++ NL + + F I S ++ +D + KG+ +V F+ ++ +++
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY- 75
Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
+G LL + + V RK+ +
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDK 97
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV---MNNDGKSRGFGFVAYESPEFAEKAVQA 262
++ N D +E +KE F I++ R+ +N + +GFG+ +E + A+
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76
Query: 263 WNGKEVDGKILYVGRAQKKAER 284
N + + K + V A + ++
Sbjct: 77 -NEESLGNKRIRVDVADQAQDK 97
Score = 50.7 bits (122), Expect = 2e-08
Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 4/84 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIEK 170
F+ NL + +++ + F I + ++ ++ KG+G+ FE ++ ++
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76
Query: 171 VNGMLLNSKIVFVGKFIPRKEREK 194
N L +K + V ++++
Sbjct: 77 -NEESLGNKRIRVDVADQAQDKDS 99
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.1 bits (141), Expect = 3e-11
Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
+V++ F + +L E F +G + S + + G F V E + +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV---FAIVEMGDVGAREAVLSQ-S 65
Query: 265 GKEVDGKILYVGRAQKKAERTQ 286
+ G L V ++K ++
Sbjct: 66 QHSLGGHRLRVRPREQKEFQSP 87
Score = 50.4 bits (121), Expect = 2e-08
Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG+ +VF+ + +D+ + + F AFG + S + +D + V A
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAV 61
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREK 194
+ + + L + V PR+++E
Sbjct: 62 LSQ-SQHSLGGHRLRVR---PREQKEF 84
Score = 30.8 bits (70), Expect = 0.15
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITS 334
+++V +D +L + F FG + S
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVAS 37
>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 = 58.1 bits (141), Expect = 4e-11
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 204 TNVYIKNF-GEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ ++I N ++ + E L +F PYG I + FGF+ +++P+ A++
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEX 76
Query: 263 WNGKEVDGKILYV 275
+ + GK L +
Sbjct: 77 ESQEMNFGKKLIL 89
Score = 50.4 bits (121), Expect = 2e-08
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 113 VFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
+FI NL K++ + ++ FS +G I+ + +GF+ F+ ++ +IE
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXE 77
Query: 172 NGMLLNSKIVFV 183
+ + K + +
Sbjct: 78 SQEMNFGKKLIL 89
>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 = 58.7 bits (142), Expect = 4e-11
Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 10/100 (10%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT----ITSYRVMNNDGKSRGFGFVAYESP 253
+LF I + E++ E + Y + K+RGF FV YES
Sbjct: 7 GNCRLF----IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 254 EFAEKAVQA--WNGKEVDGKILYVGRAQKKAERTQELKRR 291
A A + ++ G + V A+ + + +++
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102
Score = 52.5 bits (126), Expect = 4e-09
Identities = 16/94 (17%), Positives = 39/94 (41%), Gaps = 5/94 (5%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
+FI + K + + + + +L V ++ ++G+ FV +E+ AA +
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 170 KVN--GMLLNSKIVFVGKFIPRKEREKELGEKAK 201
K+ + L + V P + ++++ E
Sbjct: 71 KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVS 104
Score = 30.1 bits (68), Expect = 0.27
Identities = 3/25 (12%), Positives = 8/25 (32%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTI 332
L++ + E + +E
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEG 35
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 56.5 bits (137), Expect = 1e-10
Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPEFAEKAVQA 262
++ N D +E +KE F I++ R+ +N + +GFG+ +E + A+
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80
Query: 263 WNGKEVDGKILYVGRAQKKAE 283
N + + + + V A + +
Sbjct: 81 -NEESLGNRRIRVDVADQAQD 100
Score = 48.8 bits (117), Expect = 7e-08
Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 4/81 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIEK 170
F+ NL + +++ + F I + ++ ++ KG+G+ FE ++ ++
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80
Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
N L ++ + V ++
Sbjct: 81 -NEESLGNRRIRVDVADQAQD 100
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 56.8 bits (137), Expect = 2e-10
Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 5/79 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V + + + LK+ G + V G G V + E AV+ +
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVY-----RDGTGVVEFVRKEDMTYAVRKLDN 73
Query: 266 KEVDGKILYVGRAQKKAER 284
+ + K +
Sbjct: 74 TKFRSHEGETAYIRVKVDG 92
Score = 54.1 bits (130), Expect = 1e-09
Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 6/82 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V + L S + + D G + V G G V F +E ++ K++
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 72
Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
S + + +
Sbjct: 73 NTKFRSHEGETAYIRVKVDGPR 94
Score = 26.3 bits (58), Expect = 7.6
Identities = 7/36 (19%), Positives = 12/36 (33%)
Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+R + V L S + L+ G + A
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYAD 47
>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 = 55.1 bits (133), Expect = 5e-10
Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR--VMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+I N + + E + +++N+G+ G V +++ + A K+ +
Sbjct: 18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL- 76
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+ K+++G+ +V + R
Sbjct: 77 HRKKLNGREAFVHVVTLEDMR 97
Score = 52.8 bits (127), Expect = 4e-09
Identities = 22/94 (23%), Positives = 29/94 (30%), Gaps = 2/94 (2%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQDEQGNSKGYGFVHFETE 161
S I N+ SI + + V D G G V F+ E
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
+ A KS + LN + FV RE E
Sbjct: 68 DDARKSERL-HRKKLNGREAFVHVVTLEDMREIE 100
Score = 26.2 bits (58), Expect = 8.3
Identities = 4/28 (14%), Positives = 10/28 (35%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSA 335
++ N+ SI + + +A
Sbjct: 18 AHITNIPFSITKMDVLQFLEGIPVDENA 45
>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 = 54.5 bits (131), Expect = 1e-09
Identities = 15/96 (15%), Positives = 37/96 (38%), Gaps = 3/96 (3%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR--VMNNDGKSRGF 245
P ++ + VY+K + ++ + + F+ + +GK+ G
Sbjct: 10 PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 69
Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
GFV + + + A+ + + + + + V KK
Sbjct: 70 GFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKK 104
Score = 52.1 bits (125), Expect = 8e-09
Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 3/90 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
V++K L +NK + D F + +A G + G GFV F E ++ +
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR- 86
Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
+ + ++ + V I +K +++ K
Sbjct: 87 HKQYMGNRFIQV-HPITKKGMLEKIDMIRK 115
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 55.9 bits (134), Expect = 3e-09
Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
+ + K+ + +++ +F G I R + +S+ GFV ++ AE A +
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV----ESKNCGFVKFKYQANAEFAKE 197
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
A + + + +++
Sbjct: 198 AMSNQTLLLPSDKEWDDRREGTG 220
Score = 46.3 bits (109), Expect = 5e-06
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 112 NVFIKNLDKSIDNKA---------MYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEE 162
+++ +D ++++K + FS G I + + SK GFV F+ +
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQA 190
Query: 163 AANKSIEKVNGMLL 176
A + E ++ L
Sbjct: 191 NAEFAKEAMSNQTL 204
Score = 30.1 bits (67), Expect = 0.74
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 307 NLYVKNLDDSID---------DERLRKEFTPFGTITSAK 336
LYV +D +++ + R+R F+ G I +
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIR 174
>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 = 53.4 bits (128), Expect = 3e-09
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 11/83 (13%)
Query: 205 NVYIKNFG--EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
++ + N G + +L + E G + + + N + + F Y + E +++A
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVT 82
Query: 263 WNGKEVDGK-----ILYVGRAQK 280
NGKEV LY+ +K
Sbjct: 83 LNGKEVVDDLGQKITLYLNFVEK 105
Score = 47.2 bits (112), Expect = 4e-07
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 112 NVFIKN--LDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
++ + N L + + G + + + + K Y F + T E + ++
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81
Query: 170 KVNG 173
+NG
Sbjct: 82 TLNG 85
Score = 28.7 bits (64), Expect = 1.0
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 10/47 (21%)
Query: 298 ERLNRYQGV--------NLYVKN--LDDSIDDERLRKEFTPFGTITS 334
L R++G+ +L V N L + + +L G + +
Sbjct: 10 HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDA 56
>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 = 53.0 bits (127), Expect = 3e-09
Identities = 19/102 (18%), Positives = 43/102 (42%), Gaps = 7/102 (6%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFG 246
P + +++ +K +L +++ N + + ++ EPYG I +Y +M + +
Sbjct: 10 PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM----RMKSQA 65
Query: 247 FVAYESPEFAEKAVQ--AWNGKEVDGKILYVGRAQKKAERTQ 286
F+ E+ E A V G+ + V ++K +
Sbjct: 66 FIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVS 107
Score = 33.4 bits (76), Expect = 0.024
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 10/88 (11%)
Query: 99 SQRDPSLRKSGVGNVFIKNL-DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
+ D V + + NL + A+ +G I + + K F+
Sbjct: 16 QKFDQKQELGRV--IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-----MRMKSQAFIE 68
Query: 158 FETEEAANKSIE--KVNGMLLNSKIVFV 183
ET E A ++ + + V V
Sbjct: 69 METREDAMAMVDHCLKKALWFQGRCVKV 96
Score = 28.4 bits (63), Expect = 1.3
Identities = 7/27 (25%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 308 LYVKNL-DDSIDDERLRKEFTPFGTIT 333
+++ NL D + K P+G I
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIK 54
>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 = 51.8 bits (124), Expect = 8e-09
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
++V ++ ++F +E EM E YG + V N G +V + E AEKAV
Sbjct: 27 VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86
Query: 262 AWNGKEVDGKILYV 275
N + +G+ ++
Sbjct: 87 DLNNRWFNGQPIHA 100
Score = 37.9 bits (88), Expect = 6e-04
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
+G + V + + G +V F EE A K++ +N
Sbjct: 51 YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90
>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 = 51.1 bits (123), Expect = 1e-08
Identities = 13/71 (18%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V ++ ++ K + + + ++ ++ ++ GN GY FV F EE ++++ N
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-N 70
Query: 173 GMLLNSKIVFV 183
+ + + V
Sbjct: 71 REYMGGRYIEV 81
Score = 44.6 bits (106), Expect = 2e-06
Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V ++ + ++ + E P + V N G G+ FV + + E ++A++ N
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-NR 71
Query: 266 KEVDGKILYVGRAQKKAERT 285
+ + G+ + V R K +
Sbjct: 72 EYMGGRYIEVFRE-KSGPSS 90
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 50.1 bits (120), Expect = 2e-08
Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
+Y+ N +E + + F + + + + F F+ + S + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 259 AVQAWNGKEVDGKILYVGR 277
A+ ++G G+ L + R
Sbjct: 69 AMA-FDGIIFQGQSLKIRR 86
Score = 43.6 bits (103), Expect = 4e-06
Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCK------VAQDEQGNSKGYGFVHFETEEAANK 166
+++ N+ I +AM D F+A + V + K + F+ F + + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 167 SIEKVNGMLLN 177
++ +G++
Sbjct: 69 AMA-FDGIIFQ 78
Score = 25.5 bits (56), Expect = 10.0
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTI 332
LYV N+ I +E + F +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRL 33
>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 = 51.4 bits (123), Expect = 2e-08
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 1/87 (1%)
Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
G+ + R + E ++ V+++ + + F P + + + DG+
Sbjct: 27 GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVT 86
Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDG 270
G V + + E A A+ + +
Sbjct: 87 GEADVEFATHEEAVAAMSK-DRANMQH 112
Score = 50.6 bits (121), Expect = 4e-08
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V ++ L +Y+ FS + + G G V F T E A ++ K +
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-D 106
Query: 173 GMLLNSKIVFV 183
+ + + +
Sbjct: 107 RANMQHRYIEL 117
>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 = 50.1 bits (120), Expect = 4e-08
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V + + S + D F + + + +D G + G G V F + + +++++ N
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-N 76
Query: 173 GMLLNSKIVFV 183
ML+ + V V
Sbjct: 77 RMLMIQRYVEV 87
Score = 45.1 bits (107), Expect = 2e-06
Identities = 12/76 (15%), Positives = 33/76 (43%), Gaps = 1/76 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V + + +++ F + + ++ G++ G G V + SP+ +A++ N
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-NR 77
Query: 266 KEVDGKILYVGRAQKK 281
+ + + V A ++
Sbjct: 78 MLMIQRYVEVSPATER 93
>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 = 53.3 bits (127), Expect = 5e-08
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
F +++ D + KL+ FE YG I ++ + GK RG+ F+ YE A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 261 QAWNGKEVDGKILYVGRAQKKAERT 285
+ +GK++DG+ + V + + +
Sbjct: 162 KHADGKKIDGRRVLVDVERGRTVKG 186
Score = 47.2 bits (111), Expect = 4e-06
Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFET 160
DP+ + +F+ ++ + F +G I + G +GY F+ +E
Sbjct: 94 DPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153
Query: 161 EEAANKSIEKVNGMLLNSKIVFV 183
E + + + +G ++ + V V
Sbjct: 154 ERDMHSAYKHADGKKIDGRRVLV 176
Score = 32.5 bits (73), Expect = 0.18
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 277 RAQKKAERTQELKRRFEMLKIERLNRYQGV---NLYVKNLDDSIDDERLRKEFTPFGTIT 333
R +K R QE++ +M QG L+V ++ + +LR+EF +G I
Sbjct: 71 RREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIK 130
Query: 334 SAK 336
Sbjct: 131 RIH 133
>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 = 53.3 bits (127), Expect = 6e-08
Identities = 46/306 (15%), Positives = 90/306 (29%), Gaps = 80/306 (26%)
Query: 50 DWDSGYTCHQLGSGAILVQLGQPYM--LDTERALDTMNFDALKGRPIRIMWSQRDPSLRK 107
D+++G HQ IL ++ D + D L I + +D
Sbjct: 8 DFETGE--HQYQYKDILSVFEDAFVDNFDCKDVQDMPK-SILSKEEIDHIIMSKD---AV 61
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGF----VHFETEEA 163
SG +F L K + M F +L Y F + E +
Sbjct: 62 SGTLRLFWTLLSK---QEEMVQKF--VEEVLR-----------INYKFLMSPIKTEQRQP 105
Query: 164 ANKS---IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA-KLFTNVYI-----KNFG-- 212
+ + IE+ + L N VF + R + +L + +L + G
Sbjct: 106 SMMTRMYIEQRD-RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164
Query: 213 ----EDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
+ K++ + +++ +N SPE + +Q
Sbjct: 165 WVALDVCLSYKVQCKMD-------FKIFWLN-------LK--NCNSPETVLEMLQK---- 204
Query: 267 EVDGKILYV---GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNL---DDSIDDE 320
L +++ + +K R ++ L R Y L + + +
Sbjct: 205 ------LLYQIDPNWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYENCLLVLLN-VQNA 256
Query: 321 RLRKEF 326
+ F
Sbjct: 257 KAWNAF 262
Score = 49.5 bits (117), Expect = 1e-06
Identities = 58/402 (14%), Positives = 110/402 (27%), Gaps = 124/402 (30%)
Query: 1 MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCH-Q 59
MY Q +L + + K+NV +R + + ++L L V
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNV-SRL---QPYLKLRQALLELRPAKNV--------LIDGV 158
Query: 60 LGSG----AILVQLGQPYMLDTERALDTMNFD------ALKGRPIRIM------WSQRDP 103
LGSG A+ V + + M+F P ++ Q DP
Sbjct: 159 LGSGKTWVALDV-------CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 104 SL--RKSGVGNVF-----IKNLDKSIDNKAMY-------------DTFSAFGSILSCK-- 141
+ R N+ I+ + + Y ++AF LSCK
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN--LSCKIL 269
Query: 142 -------VAQDEQGNSKGY--------GFVHFETEE----AANKSIE-------KVNGML 175
V + + E + + + N
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 176 LNSKIV-FVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFE-----PYGT 229
L S I + + + K + T + I++ + ++MF+ P
Sbjct: 330 L-SIIAESIRDGLATWDNWKHVNCDK--LTTI-IESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 230 ITSYRVMN---NDGKSRGFGFVAYESPEFAEK-----AVQAWNGKEVDGKI--LYVGRAQ 279
+++ D + K V+ KE I +Y+ +
Sbjct: 386 HIPTILLSLIWFDVIK-------SDVMVVVNKLHKYSLVEKQP-KESTISIPSIYL-ELK 436
Query: 280 KKAERTQELKRRFEMLKIERLNRYQGVNLYVKN--LDDSIDD 319
K E L R ++ Y + + + +D
Sbjct: 437 VKLENEYALHRSI-------VDHYNIPKTFDSDDLIPPYLDQ 471
Score = 39.1 bits (90), Expect = 0.002
Identities = 34/252 (13%), Positives = 77/252 (30%), Gaps = 64/252 (25%)
Query: 21 VATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQ-LGQPYMLDTER 79
+ TR V+ LS+ + T + ++L++ L
Sbjct: 270 LTTRFKQ------VTDFLSAATTTHISLDHHSMTLTPDE--VKSLLLKYLDCRPQDLPRE 321
Query: 80 ALDTMNF------DALKGRPIRI-MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFS 132
L T ++++ W + + + + + L+ + + M+D S
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCD-KLTTIIESSLNVLE-PAEYRKMFDRLS 379
Query: 133 AFG----------SILSCKVAQDE--------------QGNSKGYGF----------VHF 158
F S++ V + + + K V
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439
Query: 159 ETEEAANKS-IEKVN--------GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIK 209
E E A ++S ++ N ++ + I + E E+ LF V++
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL- 498
Query: 210 NFGEDFNDEKLK 221
+F F ++K++
Sbjct: 499 DF--RFLEQKIR 508
>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 = 48.7 bits (116), Expect = 1e-07
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
V ++ L + + FS + + + D +G G FV F ++E A K++ K
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK- 103
Query: 172 NGMLLNSKIVFV 183
+ + + + V
Sbjct: 104 HKERIGHRYIEV 115
Score = 48.7 bits (116), Expect = 2e-07
Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
V ++ E++ + F + + + + +GK G FV + S E AEKA+
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK- 103
Query: 264 NGKEVDGKILYVGRAQKK 281
+ + + + + V ++ ++
Sbjct: 104 HKERIGHRYIEVFKSSQE 121
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V ++ L +Y+ FS + + G G V F T E A ++ K +
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-D 75
Query: 173 GMLLNSKIVFV 183
+ + V +
Sbjct: 76 KANMQHRYVEL 86
Score = 45.9 bits (109), Expect = 8e-07
Identities = 10/56 (17%), Positives = 22/56 (39%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
V+++ + + F P + + + DG+ G V + + E A A+
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73
>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 = 47.0 bits (112), Expect = 3e-07
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 4/86 (4%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVH 157
S P G V ++ L + + FS + + + D QG S G FV
Sbjct: 6 SGNSPDTANDGF--VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63
Query: 158 FETEEAANKSIEKVNGMLLNSKIVFV 183
F ++E A K+++K + + + + +
Sbjct: 64 FASQEIAEKALKK-HKERIGHRYIEI 88
Score = 45.1 bits (107), Expect = 2e-06
Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
V ++ + E++ + F + + + + G+S G FV + S E AEKA++
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK- 76
Query: 264 NGKEVDGKILYVGRAQKKAERT 285
+ + + + + + ++ + RT
Sbjct: 77 HKERIGHRYIEIFKSSRAEVRT 98
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 46.5 bits (110), Expect = 6e-07
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 1/87 (1%)
Query: 204 TNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
+ + +D F++ + + FE KS + + +P A A
Sbjct: 6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELK 289
+ E GK + + AQ + L
Sbjct: 66 LHKTEFLGKEMKLYFAQTLHIGSSHLA 92
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 46.2 bits (109), Expect = 1e-06
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 6/87 (6%)
Query: 91 GRPIRIMWSQRDPSLRKSGVGNV---FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ 147
+ + D + +G V ++NL + ++ FS FG++L
Sbjct: 6 NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-- 63
Query: 148 GNSKGYGFVHFETEEAANKSIEKVNGM 174
N++ + + +A + ++G
Sbjct: 64 -NNQFQALLQYADPVSAQHAKLSLDGQ 89
Score = 45.4 bits (107), Expect = 2e-06
Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+ ++N + L ++F +GT+ ++ + Y P A+ A + +G
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDG 88
Query: 266 KEV 268
+ +
Sbjct: 89 QNI 91
Score = 28.1 bits (62), Expect = 2.1
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+ V+NL + + L + F+ FGT+
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKII 59
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 45.2 bits (107), Expect = 1e-06
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 206 VYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
V+I +F N L ++ EP+G I+++ ++ F+ + E A+ AV +
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL----NKINEAFIEMATTEDAQAAVDYYT 73
Query: 265 GK--EVDGKILYVGRAQKKAE 283
V GK + V +QK
Sbjct: 74 TTPALVFGKPVRVHLSQKYKR 94
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 44.9 bits (106), Expect = 3e-06
Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 7/91 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR-----VMNNDGKSRGFGFVAYESPEFAEKAV 260
V ++ E++ F + IT + V DG+ G FV + E+A+ A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
+ + + + + + R+ AE Q L R
Sbjct: 86 RK-HKDLLGKRYIELFRS-TAAEVQQVLNRF 114
Score = 42.6 bits (100), Expect = 2e-05
Identities = 19/103 (18%), Positives = 32/103 (31%), Gaps = 10/103 (9%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL----SCKVAQDEQGNSKGYG 154
+ S + V ++ L + + + F I G G
Sbjct: 14 VAQFLSKENQVI--VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDA 71
Query: 155 FVHFETEEAANKSIEKVNGMLLNSKI-VFVGKFIPRKEREKEL 196
FV F EE A ++ K +L I +F E ++ L
Sbjct: 72 FVLFACEEYAQNALRKHKDLLGKRYIELFRST---AAEVQQVL 111
>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 = 43.0 bits (101), Expect = 1e-05
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
V ++ L S + + + S + +G G FV E+E+ +++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 170 KVNGMLLNSKI 180
K + + I
Sbjct: 80 KDRESMGHRYI 90
Score = 39.9 bits (93), Expect = 1e-04
Identities = 13/90 (14%), Positives = 33/90 (36%), Gaps = 6/90 (6%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSRGFGFVAYESPEFAEKAVQ 261
V ++ + E ++ + +G+ G FV ES + + A++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
+ + + + + V ++ + E LK
Sbjct: 80 -KDRESMGHRYIEVFKS-HRTEMDWVLKHS 107
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 42.7 bits (100), Expect = 2e-05
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+ I+N + L + P G + + ++ V +ES A+KA A NG
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK---RNGIQAMVEFESVLCAQKAKAALNG 84
Query: 266 KEVDGK 271
++
Sbjct: 85 ADIYAG 90
Score = 40.1 bits (93), Expect = 1e-04
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ I+N I +Y + G + + + + V FE+ A K+ +N
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK----RNGIQAMVEFESVLCAQKAKAALN 83
Query: 173 GMLLNSK 179
G + +
Sbjct: 84 GADIYAG 90
>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 = 42.1 bits (99), Expect = 2e-05
Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 6/88 (6%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGF 155
S+ + + + + + L S + + + FS + G +G
Sbjct: 2 SKLEEEVDDVFL--IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDAL 59
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ E+E+ K++EK + M + + V V
Sbjct: 60 IEMESEQDVQKALEK-HRMYMGQRYVEV 86
Score = 38.7 bits (90), Expect = 3e-04
Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 6/101 (5%)
Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSRGFGFVA 249
+L E+ + + E + F ++N DGK RG +
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
ES + +KA++ + + + + V + +K
Sbjct: 62 MESEQDVQKALE-KHRMYMGQRYVEVYEI-NNEDVDALMKS 100
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 41.9 bits (98), Expect = 2e-05
Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 6/76 (7%)
Query: 112 NVFIKNLDKSIDNKAM----YDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
+V + N+D + K + + F+ G + S +++ V E + A +
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGA 68
Query: 168 IEKVNGMLLNSKIVFV 183
+ ++ + SK + V
Sbjct: 69 VNSLHRYKIGSKKILV 84
Score = 28.8 bits (64), Expect = 0.76
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 305 GVNLYVKNLDDSIDDERLRKE----FTPFGTITSAK 336
G ++ V N+D + + L++ F G + S +
Sbjct: 9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVE 44
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 42.3 bits (99), Expect = 2e-05
Identities = 8/71 (11%), Positives = 26/71 (36%), Gaps = 5/71 (7%)
Query: 197 GEKAKLFTN-VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYE 251
G + V++ D +++++ F +G + + +G+ F+ ++
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 252 SPEFAEKAVQA 262
+ + A
Sbjct: 61 EESSVQALIDA 71
Score = 41.1 bits (96), Expect = 5e-05
Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 3/82 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ---GNSKGYGFVHFETEEAANKSIE 169
VF+ L ID + +F FG ++ + E KGY F+ F+ E + I+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 170 KVNGMLLNSKIVFVGKFIPRKE 191
+ I K
Sbjct: 71 ACLEEDGKLYLCVSSPTIKDKP 92
Score = 26.5 bits (58), Expect = 6.3
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
++V L ID++ + F FG +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLV 36
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
+ ++ L+ +G I + + G V++ PE A+ +Q +G+
Sbjct: 34 LVLNEIRED-LRVECSKFGQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFG 90
Query: 270 GKILYV 275
G+ +
Sbjct: 91 GRQITA 96
Score = 31.6 bits (72), Expect = 0.11
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
FG I + + G V F E A+ I+ ++G
Sbjct: 50 FGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDG 86
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 39.4 bits (92), Expect = 2e-04
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 213 EDFNDEKLKEMFEPYGTITS---YRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
++ + + KE E YG + + + F+ +E E A KAV NG+
Sbjct: 23 DEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG 82
Query: 270 GKILYV 275
G+++
Sbjct: 83 GRVVKA 88
Score = 34.4 bits (79), Expect = 0.009
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 132 SAFGSILSCKVAQDEQGNSKGYG--FVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
+G + C + + F+ FE E+A K++ +NG ++V +
Sbjct: 35 EKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLD 94
Query: 190 KEREKELGEK 199
K R +L E+
Sbjct: 95 KFRVLDLAEQ 104
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
E+ ++ +++ YG + S + + G FV + S +KA+Q G
Sbjct: 23 EEYEEIVED-VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
Query: 266 KEVDGKIL 273
++ +++
Sbjct: 82 RKFANRVV 89
Score = 35.2 bits (81), Expect = 0.005
Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 127 MYDTFSAFGSILSCKV---AQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV 181
+ D S +G + S ++ + G FV F + K+++ + G +++V
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 89
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 42.0 bits (98), Expect = 3e-04
Identities = 34/234 (14%), Positives = 63/234 (26%), Gaps = 71/234 (30%)
Query: 51 WDSG--YTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSL--R 106
W+ + G + + + P L T++F KG+ IR + ++
Sbjct: 1646 WNRADNHFKDTYGFSILDIVINNPVNL-------TIHFGGEKGKRIR----ENYSAMIFE 1694
Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFS--------------AFGSILSCKVAQ----DEQG 148
G + + + K I+ + TF A + + A +G
Sbjct: 1695 TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPA---LTLMEKAAFEDLKSKG 1751
Query: 149 NSKGYGFV--H--------------FETEEAANKSIEKVNGMLLNSKIVFV-GKFIPRKE 191
H E ++VF G +
Sbjct: 1752 LIPADATFAGHSLGEYAALASLADVMSIESLV--------------EVVFYRGMTMQVAV 1797
Query: 192 REKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV----MNNDGK 241
ELG + F+ E L+ + E G T + V N + +
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQ 1851
Score = 38.9 bits (90), Expect = 0.002
Identities = 33/207 (15%), Positives = 59/207 (28%), Gaps = 88/207 (42%)
Query: 87 DALKGRPIRI--------------MW---SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYD 129
DA RP+ + + SQ L++ F K L + + A D
Sbjct: 2 DAYSTRPLTLSHGSLEHVLLVPTASFFIASQ----LQEQ-----FNKILPEPTEGFAADD 52
Query: 130 TFSA----FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV---------NGMLL 176
+ G L G+V E + ++V N L
Sbjct: 53 EPTTPAELVGKFL---------------GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLE 97
Query: 177 NSKI-VFVGKFIPRKE---------------------REKELGEKAKLFTNVYIKN---- 210
+ I K + + R + + LF V N
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 211 --FG-----EDFNDEKLKEMFEPYGTI 230
FG +D+ +E L+++++ Y +
Sbjct: 158 AIFGGQGNTDDYFEE-LRDLYQTYHVL 183
Score = 30.4 bits (68), Expect = 1.1
Identities = 20/121 (16%), Positives = 34/121 (28%), Gaps = 49/121 (40%)
Query: 4 AQTVQLSEEGIIIPKHNVAT----RELSAKVVEGVSRSLSSLIDGNTVKY-DWDSGYTCH 58
V + + I IP ++ R LS + E ++D W++
Sbjct: 445 KNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISE-------RIVDCIIRLPVKWET----- 492
Query: 59 QLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNL 118
Q ++LD F P SG+G + +N
Sbjct: 493 -------TTQFKATHILD---------FG---------------PG-GASGLGVLTHRNK 520
Query: 119 D 119
D
Sbjct: 521 D 521
>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 = 39.2 bits (91), Expect = 4e-04
Identities = 11/71 (15%), Positives = 24/71 (33%), Gaps = 3/71 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
V ++ L S + + + S +G G FV +E+ +++
Sbjct: 47 VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106
Query: 170 KVNGMLLNSKI 180
K + + I
Sbjct: 107 KDRESMGHRYI 117
Score = 38.8 bits (90), Expect = 5e-04
Identities = 14/107 (13%), Positives = 35/107 (32%), Gaps = 6/107 (5%)
Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSR 243
LG + V ++ + E ++ + +G+
Sbjct: 29 QMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS 88
Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
G FV S + + A++ + + + + + V ++ + E LK
Sbjct: 89 GEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKS-HRTEMDWVLKH 133
>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 = 37.7 bits (88), Expect = 7e-04
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 3/66 (4%)
Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
+ + D+ + E +G + V N +G +V S A AV A +G+
Sbjct: 25 GWDTEIKDD-VIEECNKHGGVIHIYVDKNSA--QGNVYVKCPSIAAAIAAVNALHGRWFA 81
Query: 270 GKILYV 275
GK++
Sbjct: 82 GKMITA 87
Score = 29.6 bits (67), Expect = 0.55
Identities = 7/40 (17%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
G ++ V ++ G +V + AA ++ ++G
Sbjct: 41 HGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHG 77
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 36.6 bits (84), Expect = 0.001
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE 267
+KN + L+ + +G + S+ N G Y + E A KA A N
Sbjct: 12 LKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQG----IALCKYTTREEANKAQMALNNCV 67
Query: 268 VDG 270
+
Sbjct: 68 LAN 70
>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 = 36.3 bits (84), Expect = 0.002
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 9/72 (12%)
Query: 213 EDFNDEKLKEMFE---PYGTITSYRVMNN------DGKSRGFGFVAYESPEFAEKAVQAW 263
+D +D+ E+ E +G + + D + FV + KA+QA
Sbjct: 32 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 264 NGKEVDGKILYV 275
NG+ G+ +
Sbjct: 92 NGRWFAGRKVVA 103
Score = 31.3 bits (71), Expect = 0.16
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 5/53 (9%)
Query: 134 FGSILSCKV-----AQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV 181
FG++ + ++E FV F +K+I+ +NG + V
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKV 101
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 35.7 bits (82), Expect = 0.003
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 2/79 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
V ++ DE L FE V++ + G + + P AE+ V A
Sbjct: 11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-RLGCGGVLTFREPADAER-VLAQAD 68
Query: 266 KEVDGKILYVGRAQKKAER 284
E+ G L + A +A
Sbjct: 69 HELHGAQLSLRPAPPRAPA 87
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 37.1 bits (85), Expect = 0.006
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 205 NVYIKNFG--EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
++ + N G + +L + E G + ++ K F Y + E +++A
Sbjct: 20 SLVVANGGLGNGVSRNQLLPVLEKCGLV--DALLMPPNKPYSF--ARYRTTEESKRAYVT 75
Query: 263 WNGKE 267
NGKE
Sbjct: 76 LNGKE 80
Score = 33.2 bits (75), Expect = 0.10
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 112 NVFIKN--LDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
++ + N L + + G + + + +K Y F + T E + ++
Sbjct: 20 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-----PNKPYSFARYRTTEESKRAYV 74
Query: 170 KVNG 173
+NG
Sbjct: 75 TLNG 78
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 30.8 bits (69), Expect = 0.16
Identities = 14/84 (16%), Positives = 36/84 (42%), Gaps = 11/84 (13%)
Query: 204 TNVYIKNFGEDFNDE----KLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA 259
T +Y+ N + + + +L+ + + G +V++ + + + + + AE+A
Sbjct: 10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGG----KVLS---ITGCSAILRFINQDSAERA 62
Query: 260 VQAWNGKEVDGKILYVGRAQKKAE 283
+ ++V G + V K E
Sbjct: 63 QKRMENEDVFGNRIIVSFTPKNRE 86
Score = 26.2 bits (57), Expect = 6.0
Identities = 5/42 (11%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 150 SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE 191
+ + F +++A ++ +++ + + V F P+
Sbjct: 45 TGCSAILRFINQDSAERAQKRMENEDVFGNRIIV-SFTPKNR 85
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 28.6 bits (63), Expect = 1.1
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 131 FSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
+G +L+ ++ G V F T +AA +++ G++ N
Sbjct: 38 LQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVGLVDN 80
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 28.2 bits (62), Expect = 3.7
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 12/68 (17%)
Query: 224 FEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ-- 279
+EP+ I + + N + + K W+ K+ YV Q
Sbjct: 168 YEPFENI-AIELPPNEILFSENNDMDNNNDGVDELNKKCTFWD---AISKLYYV---QFF 220
Query: 280 -KKAERTQ 286
K+AE+ Q
Sbjct: 221 FKQAEQEQ 228
>3tvi_A Aspartokinase; structural genomics, ACT domains, regulatory
domains, kinase transferase, PSI-2, protein structure
initiative; HET: LYS; 3.00A {Clostridium acetobutylicum}
Length = 446
Score = 27.6 bits (62), Expect = 6.5
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCK----VAQDEQGNSKGYGFVHFETEEAANKSIE 169
+++ + K+I+N A D ++ G L+ E ++ F KS E
Sbjct: 95 YLEKVKKNIENGASSDYAASRGEYLNGVILAKYLNAEFIDAAEVIFFDKSGCFDEKKSYE 154
Query: 170 KVNGMLLNSKIVFVGKFI 187
K+ +L+ + F
Sbjct: 155 KIKEKVLSCNKAVIPGFY 172
>2d4y_A HAP1, flagellar HOOK-associated protein 1; multi-domain protein,
alpha-helical bundle, complex all- beta folds,
structural protein; 2.10A {Salmonella typhimurium}
Length = 463
Score = 27.6 bits (60), Expect = 6.8
Identities = 11/89 (12%), Positives = 23/89 (25%), Gaps = 2/89 (2%)
Query: 36 RSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR 95
L+ ++ D G + +G LVQ L + +
Sbjct: 143 SELNKIVGVEVSVQD--GGTYNLTMANGYTLVQGSTARQLAAVPSSADPTRTTVAYVDEA 200
Query: 96 IMWSQRDPSLRKSGVGNVFIKNLDKSIDN 124
+ L +G + + +D
Sbjct: 201 AGNIEIPEKLLNTGSLGGLLTFRSQDLDQ 229
>2ikb_A Hypothetical protein NMB1012; structural genomics, PSI-2, MCSG, PR
structure initiative; 1.70A {Neisseria meningitidis}
SCOP: d.2.1.9 PDB: 2is5_A*
Length = 167
Score = 26.6 bits (58), Expect = 8.6
Identities = 14/61 (22%), Positives = 17/61 (27%), Gaps = 3/61 (4%)
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
F A + +Q G DG I G KA + ERL Y
Sbjct: 82 FDACVNHGYGNAARMLQRAAGVPDDGVI---GAVSLKAINSLPENDLLLRFNAERLVFYT 138
Query: 305 G 305
Sbjct: 139 K 139
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.134 0.381
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: 5,182,258
Number of extensions: 318198
Number of successful extensions: 1761
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1293
Number of HSP's successfully gapped: 598
Length of query: 336
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 242
Effective length of database: 4,077,219
Effective search space: 986686998
Effective search space used: 986686998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.7 bits)