RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14193
(239 letters)
>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 = 106 bits (266), Expect = 7e-28
Identities = 23/180 (12%), Positives = 49/180 (27%), Gaps = 58/180 (32%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRK 157
A+V N E E A+ + + E + V + + N+P +++ +
Sbjct: 60 AFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----PTDALLCVANLPPSLTQQQFEE 114
Query: 158 AFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE------------------------- 192
G ++ L+ + T KG+G+ + ++
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDA 174
Query: 193 --------------------------ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
L +A + +L Q KGF + +
Sbjct: 175 GQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEY 233
Score = 84.3 bits (209), Expect = 1e-19
Identities = 24/155 (15%), Positives = 51/155 (32%), Gaps = 31/155 (20%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
+ +P+G +E V+ +RT + + + +S +A
Sbjct: 114 ELVRPFGSLERCFL--------------------VYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 113 LE-MNGHVIDEHTIRVDKA----LTTTKSNSHSIFIGNIPFEA-EEEELRKAFESCGEID 166
+ G + T+ V LT +S + + +P + + L +A +
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213
Query: 167 NVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESC 201
+L Q KGF + + E +A +
Sbjct: 214 FCQLACGQ-DGQLKGFAVLEY-ETAEMAEEAQQQA 246
Score = 81.2 bits (201), Expect = 2e-18
Identities = 20/152 (13%), Positives = 40/152 (26%), Gaps = 49/152 (32%)
Query: 118 HVIDEHTIRVDKALT-TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHT 176
H++D IR T N I I +P + +E+ + + +
Sbjct: 1 HMLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY--- 56
Query: 177 NIGKGFGYVNFKAEE-----------------------------------------EELR 195
KG +V E ++
Sbjct: 57 ---KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFE 113
Query: 196 KAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ G ++ L+ + T KG+G+ +
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 145
Score = 34.6 bits (80), Expect = 0.017
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKALTTTKSNSH 139
A + ++ E E+A + +G + +RV S
Sbjct: 229 AVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSM 270
>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 = 100 bits (251), Expect = 1e-26
Identities = 20/150 (13%), Positives = 60/150 (40%), Gaps = 16/150 (10%)
Query: 53 SVTSMFKPYGEVETVRF-RSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
++ F + + PV + + + A++ F++++ +
Sbjct: 20 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF-------------AFLEFRSVDETTQ 66
Query: 112 ALEMNGHVIDEHTIRVDKAL-TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL 170
A+ +G + ++++ + +H +FIG +P ++++++ S G + L
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 126
Query: 171 IRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
++D T + KG+ + + + +A
Sbjct: 127 VKDSATGLSKGYAFCEY-VDINVTDQAIAG 155
Score = 77.7 bits (192), Expect = 4e-18
Identities = 19/142 (13%), Positives = 46/142 (32%), Gaps = 51/142 (35%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL-----IRDQHTNIGKGFGYVNFKAE 190
++ +++GNIPF EE + F + + + + N K F ++ F++
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 191 E----------------------------------------------EELRKAFESCGEI 204
+ +++++ S G +
Sbjct: 62 DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL 121
Query: 205 DNVRLIRDQHTNIGKGFGYVNF 226
L++D T + KG+ + +
Sbjct: 122 KAFNLVKDSATGLSKGYAFCEY 143
Score = 35.7 bits (83), Expect = 0.005
Identities = 6/33 (18%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+ + ++ ++A+ +NG + + + V +A
Sbjct: 139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 100 bits (252), Expect = 2e-26
Identities = 25/115 (21%), Positives = 55/115 (47%), Gaps = 14/115 (12%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA------------LTTTKSNSHSIFIGN 145
A+V ++ E+ + ALE MN ++ I+V + L + I++ +
Sbjct: 73 AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVAS 132
Query: 146 IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+ + +++++ FE+ G+I + L RD T KG+G++ + + + + A S
Sbjct: 133 VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY-EKAQSSQDAVSS 186
Score = 67.3 bits (165), Expect = 7e-14
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 123 HTIRVDKAL--TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK 180
+ A + +++G+I +E E+ +R+AF G I ++ + D T K
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
Query: 181 GFGYVNFKAEEE 192
GF +V ++ E
Sbjct: 71 GFAFVEYEVPEA 82
Score = 49.2 bits (118), Expect = 2e-07
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E+ +R+AF G I ++ + D T KGF +V ++
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78
Score = 36.9 bits (86), Expect = 0.003
Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
++ ++ +S + A+ MN + +RV KA
Sbjct: 170 GFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 99.7 bits (249), Expect = 3e-26
Identities = 18/123 (14%), Positives = 52/123 (42%), Gaps = 22/123 (17%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA---------------------LTTTKSN 137
A++ F++++ +A+ +G + ++++ + T +
Sbjct: 54 AFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS 113
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+H +FIG +P ++++++ S G + L++D T + KG+ + + + +A
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY-VDINVTDQA 172
Query: 198 FES 200
Sbjct: 173 IAG 175
Score = 58.9 bits (143), Expect = 5e-11
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL-----IRDQHTNIGKGFGYVNFKAEEE 192
+ +++GNIPF EE + F + + + + N K F ++ F++ +E
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Score = 36.9 bits (86), Expect = 0.002
Identities = 6/33 (18%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+ + ++ ++A+ +NG + + + V +A
Sbjct: 159 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>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 = 98.1 bits (245), Expect = 9e-26
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 9/105 (8%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA---LTTTKSNSHSIFIGNIPFEAEEEEL 155
YV F++ E +EKALE+ G + + I+++K + + ++ N+ F E+EL
Sbjct: 57 GYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDEL 116
Query: 156 RKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
++ FE EI KG Y+ FK E + K E
Sbjct: 117 KEVFEDALEI-----RLVSQDGKSKGIAYIEFK-SEADAEKNLEE 155
Score = 65.3 bits (160), Expect = 2e-13
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+ ++FIGN+ EL+ A +++ ++ + T + FGYV+F E+L
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDF-ESAEDL 67
Query: 195 RKAFESCGEIDNVRLIR 211
KA E G I+
Sbjct: 68 EKALELTGLKVFGNEIK 84
Score = 40.7 bits (96), Expect = 1e-04
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
AY+ FK+ EK LE G ID ++ +
Sbjct: 139 AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
>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 = 95.7 bits (239), Expect = 7e-25
Identities = 31/164 (18%), Positives = 73/164 (44%), Gaps = 30/164 (18%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
F+ G + ++ + + N N A+V + A
Sbjct: 19 QYFQVGGPIANIK----------IMID-----------KNNKNVNYAFVEYHQSHDANIA 57
Query: 113 LE-MNGHVIDEHTIRVDKAL---TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNV 168
L+ +NG I+ + ++++ A ++ ++ ++F+G++ ++E LR AF+ +
Sbjct: 58 LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117
Query: 169 RLIRDQHTNIGKGFGYVNFKAEEEELRKAFESC-GEIDNVRLIR 211
++ D T +G+G+V+F +++ + A +S G+ N R +R
Sbjct: 118 HVMWDMQTGSSRGYGFVSF-TSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 72.2 bits (178), Expect = 4e-16
Identities = 22/136 (16%), Positives = 46/136 (33%), Gaps = 50/136 (36%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE-------- 191
+++GN+ E+ L++ F+ G I N++++ D+ N + +V +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 192 -----------------------------------------EELRKAFESCGEIDNVRLI 210
E LR AF+ + ++
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120
Query: 211 RDQHTNIGKGFGYVNF 226
D T +G+G+V+F
Sbjct: 121 WDMQTGSSRGYGFVSF 136
Score = 34.0 bits (79), Expect = 0.019
Identities = 7/33 (21%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V F + + + A++ M G ++ +R++ A
Sbjct: 132 GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 95.8 bits (239), Expect = 1e-24
Identities = 30/150 (20%), Positives = 59/150 (39%), Gaps = 30/150 (20%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
S+ S F+ +G + + + T + +V + +E V
Sbjct: 29 SLRSHFEQWGTLTDCV----------------VMRDPN----TKRSRGFGFVTYATVEEV 68
Query: 110 EKALEMNGHVIDEHTIRVDKALTTTKSNSHS-------IFIGNIPFEAEEEELRKAFESC 162
+ A+ H +D + +A++ S IF+G I + EE LR FE
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 163 GEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
G+I+ + ++ D+ + +GF +V F +
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Score = 74.6 bits (184), Expect = 1e-16
Identities = 31/139 (22%), Positives = 53/139 (38%), Gaps = 52/139 (37%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE-------- 192
+FIG + FE +E LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 193 ---------ELRKA-----------------------------------FESCGEIDNVR 208
E ++A FE G+I+ +
Sbjct: 76 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 135
Query: 209 LIRDQHTNIGKGFGYVNFK 227
++ D+ + +GF +V F
Sbjct: 136 IMTDRGSGKKRGFAFVTFD 154
Score = 42.7 bits (101), Expect = 3e-05
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 23/77 (29%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKALE 114
F+ YG++E I + ++ + A+V F + +SV+K +
Sbjct: 125 FEQYGKIE----------VIEIMT----------DRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 115 MNGHVIDEHTIRVDKAL 131
H ++ H V KAL
Sbjct: 165 QKYHTVNGHNCEVRKAL 181
>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 = 93.7 bits (234), Expect = 3e-24
Identities = 28/162 (17%), Positives = 68/162 (41%), Gaps = 27/162 (16%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
++ F YG V ++ I + T + ++ F+ SV
Sbjct: 19 NLREYFGKYGTVTDLK----------------IMKDPA----TGRSRGFGFLSFEKPSSV 58
Query: 110 EKALEMNGHVIDEHTIRVDKALTTTKSN-SHSIFIGNIPFEAEEEELRKAFESCGEIDNV 168
++ ++ H++D I +A+ + + + IF+G I + +E + F G I +
Sbjct: 59 DEVVK-TQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117
Query: 169 RLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG-EIDNVRL 209
+L+ D+ T +GFG+V + + + + ++ + + ++
Sbjct: 118 QLMLDKDTGQSRGFGFVTYD-SADAVDRVCQNKFIDFKDRKI 158
Score = 81.0 bits (201), Expect = 2e-19
Identities = 25/132 (18%), Positives = 51/132 (38%), Gaps = 45/132 (34%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE-------- 192
+FIG + ++ E+ LR+ F G + ++++++D T +GFG+++F+
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 193 -------------------------------------ELRKAFESCGEIDNVRLIRDQHT 215
E + F G I + +L+ D+ T
Sbjct: 66 HILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT 125
Query: 216 NIGKGFGYVNFK 227
+GFG+V +
Sbjct: 126 GQSRGFGFVTYD 137
Score = 42.9 bits (102), Expect = 1e-05
Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 23/77 (29%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKALE 114
F +G + D L +K T + +V + + ++V++ +
Sbjct: 108 FSQWGTII----------DAQLML----------DKDTGQSRGFGFVTYDSADAVDRVCQ 147
Query: 115 MNGHVIDEHTIRVDKAL 131
+ I + +A
Sbjct: 148 NKFIDFKDRKIEIKRAE 164
>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 = 92.3 bits (230), Expect = 1e-23
Identities = 27/142 (19%), Positives = 59/142 (41%), Gaps = 25/142 (17%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
++F+ G + T R + R + +T + A+V F + ++A
Sbjct: 22 ALFRAIGPINTCR----------IMR----------DYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 113 LE-MNGHVIDEHTIRVDKA-LTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL 170
++ +NG + ++V A ++++ N+P +++L F G I +
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 171 IRDQHTNIGKGFGYVNFKAEEE 192
+RD+ T +G +V + EE
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREE 143
Score = 89.6 bits (223), Expect = 1e-22
Identities = 23/138 (16%), Positives = 48/138 (34%), Gaps = 47/138 (34%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE---- 191
+++ ++ + +P + + EL F + G I+ R++RD T G+ +V+F +E
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 192 -------------------------------------------EELRKAFESCGEIDNVR 208
++L F G I
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 209 LIRDQHTNIGKGFGYVNF 226
++RD+ T +G +V +
Sbjct: 121 ILRDKLTGRPRGVAFVRY 138
Score = 30.2 bits (69), Expect = 0.31
Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 20/77 (25%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F YG + + +T + A+VR+ E ++A+ +
Sbjct: 109 IFGKYGSIVQKN---ILRDKLTGRPRGV--------------AFVRYNKREEAQEAISAL 151
Query: 116 NGHVIDEHT--IRVDKA 130
N + + + + V A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
>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 = 88.4 bits (220), Expect = 3e-22
Identities = 33/142 (23%), Positives = 63/142 (44%), Gaps = 25/142 (17%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
S+F GE+E+ + L R +K T + +V + + + EKA
Sbjct: 21 SLFGSIGEIESCK----------LVR----------DKITGQSLGYGFVNYIDPKDAEKA 60
Query: 113 LE-MNGHVIDEHTIRVDKAL-TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL 170
+ +NG + TI+V A ++ ++++ +P ++EL + F G I R+
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 171 IRDQHTNIGKGFGYVNFKAEEE 192
+ DQ T + +G G++ F E
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIE 142
Score = 85.7 bits (213), Expect = 4e-21
Identities = 31/137 (22%), Positives = 54/137 (39%), Gaps = 47/137 (34%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK----AE-- 190
+ ++ + +P +EE R F S GEI++ +L+RD+ T G+G+VN+ AE
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 191 -----------------------------------------EEELRKAFESCGEIDNVRL 209
++EL + F G I R+
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 210 IRDQHTNIGKGFGYVNF 226
+ DQ T + +G G++ F
Sbjct: 121 LVDQVTGVSRGVGFIRF 137
Score = 56.0 bits (136), Expect = 4e-10
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
Y+ +EE R F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 8 NYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYI 52
Score = 29.5 bits (67), Expect = 0.67
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHT--IRVDKA 130
++RF E+A++ +NG T I V A
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 89.6 bits (223), Expect = 3e-22
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 40/172 (23%)
Query: 39 MNPSLTKSKNHAL------SSVT-----SMFKPYGEVETVRFRSVPVADITLPRKACIKM 87
MNPS +L VT F P G + ++R + R
Sbjct: 6 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR----------VCR------ 49
Query: 88 NKVHEKRTNMN---AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKAL---TTTKSNSHS 140
+ T + AYV F+ E+AL+ MN VI +R+ + + KS +
Sbjct: 50 ----DMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IFI N+ + + L F + G I + +++ D N KG+G+V+F+ +E
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEA 155
Score = 77.7 bits (192), Expect = 9e-18
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 51/141 (36%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK----AE 190
S+++G++ + E L + F G I ++R+ RD T G+ YVNF+ AE
Sbjct: 12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 191 ---------------------------------------------EEELRKAFESCGEID 205
+ L F + G I
Sbjct: 72 RALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNIL 131
Query: 206 NVRLIRDQHTNIGKGFGYVNF 226
+ +++ D N KG+G+V+F
Sbjct: 132 SCKVVCD--ENGSKGYGFVHF 150
Score = 34.6 bits (80), Expect = 0.016
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V F+ E+ E+A+E MNG ++++ + V +
Sbjct: 146 GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
>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 = 88.9 bits (221), Expect = 3e-21
Identities = 19/185 (10%), Positives = 48/185 (25%), Gaps = 62/185 (33%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKA 158
A + F + A+ V+ ++ I V T +++ N P + +R
Sbjct: 84 ARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECT------LWMTNFPPSYTQRNIRDL 137
Query: 159 FESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE--------------------ELRKAF 198
+ + + N + F Y++ ++E+ ++
Sbjct: 138 LQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL 197
Query: 199 E-----------------------------------SCGEIDNVRLIRDQH-TNIGKGFG 222
E G I+ + + Q +
Sbjct: 198 EKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257
Query: 223 YVNFK 227
++ F+
Sbjct: 258 FMVFE 262
Score = 85.4 bits (212), Expect = 5e-20
Identities = 18/164 (10%), Positives = 41/164 (25%), Gaps = 41/164 (25%)
Query: 103 FKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESC 162
++ L+ T + T ++ + N+P + ++ K F+ C
Sbjct: 6 HHARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHC 65
Query: 163 GEIDNVRLIRDQHTNIGKGFGYVNFKAEE------------------------------- 191
G I +V + N F + F +
Sbjct: 66 GPIIHVDVADSLKKN--FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMT 123
Query: 192 --------EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+R + + + N + F Y++
Sbjct: 124 NFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVT 167
Score = 85.4 bits (212), Expect = 6e-20
Identities = 28/157 (17%), Positives = 54/157 (34%), Gaps = 35/157 (22%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKAL 113
+ + V I LP R N + AY+ + E +
Sbjct: 137 LLQDINVV---------ALSIRLPSL-----------RFNTSRRFAYIDVTSKEDARYCV 176
Query: 114 E-MNGHVIDEHTIRVDKA--------LTTTKSNSHSIFIGNIPFEA-EEEELRKAFESCG 163
E +NG I+ +T+ + + I I N+ E +E LR++FE G
Sbjct: 177 EKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFG 236
Query: 164 EIDNVRLIRDQH-TNIGKGFGYVNFKAEEEELRKAFE 199
I+ + + Q + ++ F ++ +A +
Sbjct: 237 SIEKINIPAGQKEHSFNNCCAFMVF-ENKDSAERALQ 272
Score = 45.4 bits (108), Expect = 6e-06
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 16/74 (21%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMN 116
F+ +G +E + I + N A++ F+N +S E+AL+MN
Sbjct: 231 SFEGFGSIEKIN----------------IPAGQKEHSFNNCCAFMVFENKDSAERALQMN 274
Query: 117 GHVIDEHTIRVDKA 130
++ I V A
Sbjct: 275 RSLLGNREISVSLA 288
>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 = 82.6 bits (205), Expect = 8e-21
Identities = 20/64 (31%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+++ SI++GN+ + A EEL F CG ++ V ++ D+ + KGF Y+ F +++E +R
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVR 62
Query: 196 KAFE 199
+
Sbjct: 63 TSLA 66
Score = 62.1 bits (152), Expect = 4e-13
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G V++ A EEL F CG ++ V ++ D+ + KGF Y+ F
Sbjct: 12 GNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 56
Score = 44.0 bits (105), Expect = 2e-06
Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 23/81 (28%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ + F G V V + +K + AY+ F + ESV
Sbjct: 22 ELEAHFHGCGSVNRVTI--------------------LCDKFSGHPKGFAYIEFSDKESV 61
Query: 110 EKALEMNGHVIDEHTIRVDKA 130
+L ++ + I+V
Sbjct: 62 RTSLALDESLFRGRQIKVIPK 82
>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 = 86.7 bits (215), Expect = 1e-20
Identities = 30/148 (20%), Positives = 57/148 (38%), Gaps = 31/148 (20%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F+ YGE V + R ++R ++ E A +
Sbjct: 42 LFERYGEPSEVF----------INRDRG-------------FGFIRLESRTLAEIAKAEL 78
Query: 116 NGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQH 175
+G ++ +R+ A ++ ++ + N+ E L +AF G ++ ++ D
Sbjct: 79 DGTILKSRPLRIRFA-----THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD- 132
Query: 176 TNIGKGFGYVNFKAEEEELRKAFESCGE 203
G G+V F A + RKA E CG+
Sbjct: 133 RGRATGKGFVEF-AAKPPARKALERCGD 159
Score = 77.0 bits (190), Expect = 5e-17
Identities = 30/148 (20%), Positives = 51/148 (34%), Gaps = 51/148 (34%)
Query: 123 HTIRVDKALT---TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG 179
TI + L T + +F+GN+P + EE+ ++ FE GE V + RD
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------ 57
Query: 180 KGFGYVNFKAEE-----------------------------------------EELRKAF 198
+GFG++ ++ E L +AF
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAF 117
Query: 199 ESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ ++ D G G+V F
Sbjct: 118 SQFGPVEKAVVVVDD-RGRATGKGFVEF 144
Score = 47.0 bits (112), Expect = 1e-06
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + EE+ ++ FE GE V + RD +GFG++ +
Sbjct: 28 GNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLE 66
>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 = 81.2 bits (201), Expect = 5e-20
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 129 KALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
L+ + ++ ++F + +L F + G++ +VR+I D+++ KG YV F
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF- 74
Query: 189 AEEEELRKA 197
E + + A
Sbjct: 75 CEIQSVPLA 83
Score = 63.1 bits (154), Expect = 3e-13
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + +L F + G++ +VR+I D+++ KG YV F
Sbjct: 31 MQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Score = 45.8 bits (109), Expect = 7e-07
Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 23/76 (30%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKALE 114
F G+V VR + ++ + + AYV F ++SV A+
Sbjct: 46 FSAVGKVRDVRI--------------------ISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 115 MNGHVIDEHTIRVDKA 130
+ G + I V +
Sbjct: 86 LTGQRLLGVPIIVQAS 101
>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 = 80.1 bits (198), Expect = 2e-19
Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ S+++GN+ + + ++L F SCG I+ + ++ D+ + KG+ Y+ F AE +
Sbjct: 34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF-AERNSVD 92
Query: 196 KAFE 199
A
Sbjct: 93 AAVA 96
Score = 60.1 bits (146), Expect = 6e-12
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G V++ + ++L F SCG I+ + ++ D+ + KG+ Y+ F
Sbjct: 42 GNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA 86
Score = 40.5 bits (95), Expect = 7e-05
Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 23/81 (28%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ + F G + + + +K + AY+ F SV
Sbjct: 52 DLEAHFSSCGSINRITI--------------------LCDKFSGHPKGYAYIEFAERNSV 91
Query: 110 EKALEMNGHVIDEHTIRVDKA 130
+ A+ M+ V TI+V
Sbjct: 92 DAAVAMDETVFRGRTIKVLPK 112
>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 = 78.8 bits (195), Expect = 2e-19
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ S S +F+ N+ + + EE+L K F + G + + D T KGF +V F E
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 193 ELRKAFESC-GEIDNVRLIR 211
KA+ G++ R++
Sbjct: 63 A-VKAYAEVDGQVFQGRMLH 81
Score = 54.5 bits (132), Expect = 3e-10
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ + EE+L K F + G + + D T KGF +V F
Sbjct: 17 SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Score = 34.5 bits (80), Expect = 0.006
Identities = 14/82 (17%), Positives = 25/82 (30%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ +F YG + + P+ + T A+V F E
Sbjct: 24 DLEKLFSAYGPLSELH---YPI-----------------DSLTKKPKGFAFVTFMFPEHA 63
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
KA ++G V + V +
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPS 85
>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 = 81.1 bits (201), Expect = 2e-19
Identities = 27/144 (18%), Positives = 51/144 (35%), Gaps = 54/144 (37%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEEE- 192
S++ +F+G +P E++LR+ FE G + + ++RD+ N KG +V F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 193 --------------------------------------------------ELRKAFESCG 202
++R F S G
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 203 EIDNVRLIRDQHTNIGKGFGYVNF 226
+I+ R++R + +G +V F
Sbjct: 121 QIEECRILRGP-DGLSRGCAFVTF 143
Score = 80.3 bits (199), Expect = 5e-19
Identities = 25/148 (16%), Positives = 50/148 (33%), Gaps = 32/148 (21%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN-----AYVRFKNLESVE 110
+F+ YG V +I + R ++ N +V F ++
Sbjct: 22 ELFEQYGAVY----------EINVLR----------DRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 111 KALE-MNGHVIDEHTIRVDKALTTT-----KSNSHSIFIGNIPFEAEEEELRKAFESCGE 164
+A ++ + + +FIG I + E ++R F S G+
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 165 IDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
I+ R++R + +G +V F
Sbjct: 122 IEECRILRGP-DGLSRGCAFVTFTTRAM 148
Score = 53.4 bits (129), Expect = 4e-09
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFK 227
G V E++LR+ FE G + + ++RD+ N KG +V F
Sbjct: 9 GQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFY 55
Score = 26.4 bits (59), Expect = 6.4
Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 19/70 (27%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ MF +G++E R + + C A+V F + A+
Sbjct: 112 IRVMFSSFGQIEECRI----LRGPDGLSRGC--------------AFVTFTTRAMAQTAI 153
Query: 114 -EMNGHVIDE 122
M+ E
Sbjct: 154 KAMHQAQTME 163
>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 = 76.9 bits (190), Expect = 2e-18
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 125 IRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGY 184
+ D + + ++FIGN+ EL+ A +++ + D T + FGY
Sbjct: 4 MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGY 62
Query: 185 VNFKAEEEELRKAFE 199
V+F E+L KA E
Sbjct: 63 VDF-ESAEDLEKALE 76
Score = 49.2 bits (118), Expect = 3e-08
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
N EL+ A +++ + D T + FGYV+F
Sbjct: 26 NPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDF 65
Score = 49.2 bits (118), Expect = 3e-08
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 24/81 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ + V + RT N YV F++ E +
Sbjct: 33 ELKVAISELFAKNDLA---------------------VVDVRTGTNRKFGYVDFESAEDL 71
Query: 110 EKALEMNGHVIDEHTIRVDKA 130
EKALE+ G + + I+++K
Sbjct: 72 EKALELTGLKVFGNEIKLEKP 92
>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 = 2e-18
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ ++FI N+ F++EEE L + + G++ VR++ T KG + F +E +
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF-MTQEAAQ 71
Query: 196 KAFES 200
K +
Sbjct: 72 KCLAA 76
Score = 54.3 bits (131), Expect = 6e-10
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
F +EEE L + + G++ VR++ T KG + F
Sbjct: 25 FDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFM 65
Score = 31.2 bits (71), Expect = 0.099
Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 30/90 (33%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNM---NAYVRFKNLESV 109
++ + + +G+++ VR V T A+ +F E+
Sbjct: 31 ALGEVLQQFGDLKYVRV--------------------VLHPDTEHSKGCAFAQFMTQEAA 70
Query: 110 EKALE-------MNGHVIDEHTIRVDKALT 132
+K L G +D ++VD A+T
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 76.1 bits (188), Expect = 3e-18
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+F+ + EA EE++ F GEI N+ L D+ T KG+ V ++ +E + A
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA-QAA 81
Query: 198 FE 199
E
Sbjct: 82 ME 83
Score = 53.8 bits (130), Expect = 7e-10
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V+ +A EE++ F GEI N+ L D+ T KG+ V +
Sbjct: 29 TGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Score = 38.4 bits (90), Expect = 3e-04
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ F YGE++ + L ++RT V ++ +
Sbjct: 39 DIHDKFAEYGEIKNIH----------LNL----------DRRTGYLKGYTLVEYETYKEA 78
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
+ A+E +NG + I VD
Sbjct: 79 QAAMEGLNGQDLMGQPISVDWC 100
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 75.7 bits (187), Expect = 4e-18
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
++ +I + N+ + E +L++ F G I + L +D+ T KGF +++F E+
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA-A 71
Query: 196 KAFESC--GEIDNVRLIR 211
+A D+ ++
Sbjct: 72 RAIAGVSGFGYDH-LILN 88
Score = 58.4 bits (142), Expect = 1e-11
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 172 RDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
D + I ++ E +L++ F G I + L +D+ T KGF +++F
Sbjct: 12 ADDNATIR--VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Score = 40.3 bits (95), Expect = 4e-05
Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 24/79 (30%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
+F+P+G + + L + +K T + A++ F E +A
Sbjct: 34 ELFRPFGSISRIY----------LAK----------DKTTGQSKGFAFISFHRREDAARA 73
Query: 113 LE-MNGHVIDEHTIRVDKA 130
+ ++G D + V+ A
Sbjct: 74 IAGVSGFGYDHLILNVEWA 92
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 75.3 bits (186), Expect = 5e-18
Identities = 24/64 (37%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S S +++G++ F E+ LR FE G+IDN+ L++D T KG+G++ F ++ E R
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITF-SDSECAR 61
Query: 196 KAFE 199
+A E
Sbjct: 62 RALE 65
Score = 52.9 bits (128), Expect = 1e-09
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV +F E+ LR FE G+IDN+ L++D T KG+G++ F
Sbjct: 9 YVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITF 54
Score = 34.1 bits (79), Expect = 0.007
Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ +F+P+G+++ + + + T + ++ F + E
Sbjct: 21 MLRGIFEPFGKIDNIVL--------------------MKDSDTGRSKGYGFITFSDSECA 60
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
+ALE +NG + +RV
Sbjct: 61 RRALEQLNGFELAGRPMRVGHV 82
>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 = 75.8 bits (187), Expect = 5e-18
Identities = 24/68 (35%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQH-TNIGKGFGYVNFKAEEE 192
K + I + NIPF+A + E+R+ F + GE+ VRL + T +GFG+V+F +++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 193 ELRKAFES 200
+KAF +
Sbjct: 71 A-KKAFNA 77
Score = 53.8 bits (130), Expect = 8e-10
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQH-TNIGKGFGYVNFK 227
+ F+A + E+R+ F + GE+ VRL + T +GFG+V+F
Sbjct: 21 RNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Score = 36.1 bits (84), Expect = 0.002
Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 24/91 (26%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ +F +GE++TVR LP+K T + +V F +
Sbjct: 31 EIRELFSTFGELKTVR----------LPKK---------MTGTGAHRGFGFVDFITKQDA 71
Query: 110 EKALE--MNGHVIDEHTIRVDKALTTTKSNS 138
+KA + + + ++ A + S
Sbjct: 72 KKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 75.4 bits (186), Expect = 6e-18
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
++ ++GN+PF + ++ F+ I +VRL+RD+ T+ KGF YV F E + L++A
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEA 72
Query: 198 FESCGEIDNVRLIR 211
G + R +R
Sbjct: 73 LTYDGALLGDRSLR 86
Score = 41.1 bits (97), Expect = 2e-05
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
YV F ++S+++AL +G ++ + ++RVD A
Sbjct: 59 CYVEFDEVDSLKEALTYDGALLGDRSLRVDIA 90
>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 = 76.0 bits (187), Expect = 1e-17
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S ++++GN+ F EE++ + F G+I + + D+ GF +V + + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA-E 95
Query: 196 KAFESCG--EIDNVRLIR 211
A +D+ R+IR
Sbjct: 96 NAMRYINGTRLDD-RIIR 112
Score = 54.4 bits (131), Expect = 1e-09
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F EE++ + F G+I + + D+ GF +V +
Sbjct: 45 GNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Score = 39.8 bits (93), Expect = 2e-04
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V + + E A+ +NG +D+ IR D
Sbjct: 84 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 116
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 74.6 bits (184), Expect = 1e-17
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+F+ +I EA+E+E+++ F GEI N+ L D+ T KG+ V ++ ++ A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA-LAA 84
Query: 198 FE 199
E
Sbjct: 85 KE 86
Score = 52.7 bits (127), Expect = 2e-09
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ +A+E+E+++ F GEI N+ L D+ T KG+ V +
Sbjct: 32 TSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Score = 37.7 bits (88), Expect = 5e-04
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ F YGE++ + L ++RT + A V ++ +
Sbjct: 42 EIQEKFCDYGEIKNIH----------LNL----------DRRTGFSKGYALVEYETHKQA 81
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
A E +NG I TI+VD
Sbjct: 82 LAAKEALNGAEIMGQTIQVDWC 103
>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 = 75.1 bits (185), Expect = 1e-17
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+F+ + EA EE++ F GEI N+ L D+ T KG+ V ++ +E + A
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA-QAA 80
Query: 198 FE 199
E
Sbjct: 81 ME 82
Score = 54.3 bits (131), Expect = 7e-10
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V+ +A EE++ F GEI N+ L D+ T KG+ V +
Sbjct: 28 TGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Score = 40.4 bits (95), Expect = 8e-05
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ F YGE++ + L ++RT V ++ +
Sbjct: 38 DIHDKFAEYGEIKNIH----------LNL----------DRRTGYLKGYTLVEYETYKEA 77
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
+ A+E +NG + I VD
Sbjct: 78 QAAMEGLNGQDLMGQPISVDWC 99
>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 = 75.1 bits (185), Expect = 2e-17
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+ + + + E +LR+ F G I +V ++ DQ + +GF +V F ++ ++A
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF-ENVDDAKEA 104
Query: 198 FESC--GEIDNVRLIR 211
E E+D R IR
Sbjct: 105 KERANGMELDG-RRIR 119
Score = 54.0 bits (130), Expect = 1e-09
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 55 SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Score = 41.3 bits (97), Expect = 4e-05
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 24/84 (28%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ +F YG + V V+++++ + A+V F+N++
Sbjct: 62 DLREVFSKYGPIADVSI--------------------VYDQQSRRSRGFAFVYFENVDDA 101
Query: 110 EKALE-MNGHVIDEHTIRVDKALT 132
++A E NG +D IRVD ++T
Sbjct: 102 KEAKERANGMELDGRRIRVDFSIT 125
>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 = 73.4 bits (181), Expect = 2e-17
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ +F+G++ E + AF G I + R+++D T KG+G+V+F + +
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF-FNKWDAE 62
Query: 196 KAFESCG--EIDNVRLIR 211
A + G + R IR
Sbjct: 63 NAIQQMGGQWLGG-RQIR 79
Score = 51.4 bits (124), Expect = 4e-09
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ AF G I + R+++D T KG+G+V+F
Sbjct: 20 TAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF 55
Score = 37.9 bits (89), Expect = 3e-04
Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 24/77 (31%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKAL- 113
F P+G + R V + T + +V F N E A+
Sbjct: 27 FAPFGRISDARV--------------------VKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 114 EMNGHVIDEHTIRVDKA 130
+M G + IR + A
Sbjct: 67 QMGGQWLGGRQIRTNWA 83
>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 = 74.3 bits (183), Expect = 2e-17
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
SN +F+G++ E E+++ AF G I + R+++D T KG+G+V+F + +
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF-FNKWDAE 71
Query: 196 KAFESCG--EIDNVRLIR 211
A + G + R IR
Sbjct: 72 NAIQQMGGQWLGG-RQIR 88
Score = 53.1 bits (128), Expect = 2e-09
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + E+++ AF G I + R+++D T KG+G+V+F
Sbjct: 21 GDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Score = 38.1 bits (89), Expect = 4e-04
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 24/79 (30%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
+ F P+G + R V + T + +V F N E A
Sbjct: 34 AAFAPFGRISDARV--------------------VKDMATGKSKGYGFVSFFNKWDAENA 73
Query: 113 L-EMNGHVIDEHTIRVDKA 130
+ +M G + IR + A
Sbjct: 74 IQQMGGQWLGGRQIRTNWA 92
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 75.6 bits (186), Expect = 2e-17
Identities = 21/98 (21%), Positives = 41/98 (41%), Gaps = 1/98 (1%)
Query: 102 RFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFES 161
R +S + + + + +F+ +I EA+E+E+++ F
Sbjct: 36 RGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCD 95
Query: 162 CGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
GEI N+ L D+ T KG+ V ++ ++ A E
Sbjct: 96 YGEIKNIHLNLDRRTGFSKGYALVEYETHKQA-LAAKE 132
Score = 54.1 bits (130), Expect = 2e-09
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ +A+E+E+++ F GEI N+ L D+ T KG+ V +
Sbjct: 78 TSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
Score = 38.7 bits (90), Expect = 4e-04
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 24/81 (29%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVE 110
+ F YGE++ + L ++RT + A V ++ +
Sbjct: 89 IQEKFCDYGEIKNIH----------LNL----------DRRTGFSKGYALVEYETHKQAL 128
Query: 111 KALE-MNGHVIDEHTIRVDKA 130
A E +NG I TI+VD
Sbjct: 129 AAKEALNGAEIMGQTIQVDWC 149
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 74.8 bits (184), Expect = 2e-17
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+ + N+ + + LR+ FE G + +V + RD++T +GF +V F ++ +
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF-HDKRDAE 103
Query: 196 KAFESCG--EIDNVRLIR 211
A ++ +D R +R
Sbjct: 104 DAMDAMDGAVLDG-RELR 120
Score = 54.4 bits (131), Expect = 8e-10
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V ++ + LR+ FE G + +V + RD++T +GF +V F
Sbjct: 51 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96
Score = 37.4 bits (87), Expect = 0.001
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 24/91 (26%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
++ +F+ YG V V +PR ++ T + A+VRF +
Sbjct: 63 TLRRVFEKYGRVGDVY----------IPR----------DRYTKESRGFAFVRFHDKRDA 102
Query: 110 EKALE-MNGHVIDEHTIRVDKALTTTKSNSH 139
E A++ M+G V+D +RV A +SH
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133
>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 = 73.4 bits (181), Expect = 3e-17
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
++ + N+ + + LR+ FE G + +V + R+ HT +GF +V F + + +
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF-HDRRDAQ 69
Query: 196 KAFES 200
A +
Sbjct: 70 DAEAA 74
Score = 53.0 bits (128), Expect = 1e-09
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V ++ + LR+ FE G + +V + R+ HT +GF +V F
Sbjct: 17 KVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Score = 37.6 bits (88), Expect = 5e-04
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS 138
A+VRF + + A M+G +D +RV A + S
Sbjct: 58 AFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLS 98
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 73.4 bits (181), Expect = 3e-17
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ + + + E +LR+ F G I +V ++ DQ + +GF +V F ++ +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF-ENVDDAK 71
Query: 196 KAFESC--GEIDNVRLIR 211
+A E E+D R IR
Sbjct: 72 EAKERANGMELDG-RRIR 88
Score = 52.6 bits (127), Expect = 2e-09
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V + E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 19 GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Score = 38.0 bits (89), Expect = 3e-04
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+V F+N++ ++A E NG +D IRV
Sbjct: 60 AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92
>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 = 73.5 bits (181), Expect = 4e-17
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNFKAEEEELRK 196
++ F+GN+P++ EE +++ F I VRL R+ + KGFGY F + + L
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF-EDLDSLLS 72
Query: 197 AFESCGEIDNVRLIR 211
A E + IR
Sbjct: 73 ALSLNEESLGNKRIR 87
Score = 43.8 bits (104), Expect = 3e-06
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
Y F++L+S+ AL +N + IRVD A
Sbjct: 60 GYAEFEDLDSLLSALSLNEESLGNKRIRVDVA 91
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 73.0 bits (180), Expect = 4e-17
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S +++G+IP++ EE++ + G + N++++ D T KG+ ++ F + E A
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF-RDLESSASA 60
Query: 198 FES 200
+
Sbjct: 61 VRN 63
Score = 52.2 bits (126), Expect = 3e-09
Identities = 10/45 (22%), Positives = 24/45 (53%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + EE++ + G + N++++ D T KG+ ++ F+
Sbjct: 8 GSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFR 52
Score = 33.7 bits (78), Expect = 0.008
Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ + G V ++ + + +T + A++ F++LES
Sbjct: 18 QILDLCSNVGPVINLKM--------------------MFDPQTGRSKGYAFIEFRDLESS 57
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
A+ +NG+ + ++ +
Sbjct: 58 ASAVRNLNGYQLGSRFLKCGYS 79
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 72.7 bits (179), Expect = 5e-17
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG-KGFGYVNFKAEEEELRK 196
++ F+GN+P++ EE +++ F I VRL R+ KGFGY F + + L
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF-EDLDSLLS 76
Query: 197 AFESCGEIDNVRLIR 211
A E R IR
Sbjct: 77 ALSLNEESLGNRRIR 91
Score = 43.4 bits (103), Expect = 3e-06
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 14/66 (21%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMN----AYVRFKNLESVEKALEMNGHVIDEHT 124
FR + ++ + LPR E Y F++L+S+ AL +N +
Sbjct: 40 FRGLNISAVRLPR----------EPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRR 89
Query: 125 IRVDKA 130
IRVD A
Sbjct: 90 IRVDVA 95
>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 = 73.0 bits (180), Expect = 5e-17
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ +++G + E +++ L AF G+I ++++ D T +GF +V F E+
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF-ELAEDAA 68
Query: 196 KAFE 199
A +
Sbjct: 69 AAID 72
Score = 51.8 bits (125), Expect = 3e-09
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV + +++ L AF G+I ++++ D T +GF +V F
Sbjct: 16 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Score = 32.6 bits (75), Expect = 0.026
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 24/82 (29%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ + F P+G++ ++ +P+ + T + A+V F+ E
Sbjct: 28 VLHAAFIPFGDITDIQ---IPL-----------------DYETEKHRGFAFVEFELAEDA 67
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
A++ MN + TIRV+ A
Sbjct: 68 AAAIDNMNESELFGRTIRVNLA 89
>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 = 72.7 bits (179), Expect = 6e-17
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+ S+F+GNIP+EA EE+L+ F G + + RL+ D+ T KG+G+ ++ +E
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 194 LRKAFES 200
A +
Sbjct: 64 -LSAMRN 69
Score = 51.1 bits (123), Expect = 7e-09
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + ++A EE+L+ F G + + RL+ D+ T KG+G+ +
Sbjct: 14 GNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY 57
Score = 32.6 bits (75), Expect = 0.023
Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 24/83 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ +F G V + R V+++ T + +++ E+
Sbjct: 23 EQLKDIFSEVGPVVSFRL--------------------VYDRETGKPKGYGFCEYQDQET 62
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
A+ +NG +RVD A
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNA 85
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 73.7 bits (181), Expect = 7e-17
Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ +++G + E +++ L AF G+I ++++ D T +GF +V F+ E+
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA-A 119
Query: 196 KAFES 200
A ++
Sbjct: 120 AAIDN 124
Score = 53.2 bits (128), Expect = 3e-09
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
YV + +++ L AF G+I ++++ D T +GF +V F+
Sbjct: 67 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113
Score = 35.9 bits (83), Expect = 0.003
Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 24/83 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ + F P+G++ ++ +P + T + A+V F+ E
Sbjct: 78 KVLHAAFIPFGDITDIQ----------IPL----------DYETEKHRGFAFVEFELAED 117
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
A++ MN + TIRV+ A
Sbjct: 118 AAAAIDNMNESELFGRTIRVNLA 140
>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 = 72.0 bits (177), Expect = 1e-16
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ +++G++ F E+ LR FE G I++++L+ D T KG+G++ F E +
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA-K 82
Query: 196 KAFES 200
KA E
Sbjct: 83 KALEQ 87
Score = 50.8 bits (122), Expect = 8e-09
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
YV +F E+ LR FE G I++++L+ D T KG+G++ F
Sbjct: 30 YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Score = 32.3 bits (74), Expect = 0.032
Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 24/83 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ +F+P+G +E+++ + + T + ++ F + E
Sbjct: 41 DMLRGIFEPFGRIESIQL--------------------MMDSETGRSKGYGFITFSDSEC 80
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
+KALE +NG + ++V
Sbjct: 81 AKKALEQLNGFELAGRPMKVGHV 103
>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 = 71.5 bits (176), Expect = 1e-16
Identities = 12/64 (18%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRK 196
+ ++++ N+PF +L + F G++ V +++D+ T KG ++ F +++ +
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF-LDKDSAQN 73
Query: 197 AFES 200
+
Sbjct: 74 CTRA 77
Score = 51.5 bits (124), Expect = 4e-09
Identities = 10/45 (22%), Positives = 21/45 (46%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ F +L + F G++ V +++D+ T KG ++ F
Sbjct: 22 SNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFL 66
Score = 35.3 bits (82), Expect = 0.003
Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 24/84 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ + +F YG+V V + +K T + A++ F + +S
Sbjct: 31 NDLYRIFSKYGKVVKVTI--------------------MKDKDTRKSKGVAFILFLDKDS 70
Query: 109 VEKALE-MNGHVIDEHTIRVDKAL 131
+ +N + I+ A+
Sbjct: 71 AQNCTRAINNKQLFGRVIKASIAI 94
>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 = 71.9 bits (177), Expect = 1e-16
Identities = 14/61 (22%), Positives = 32/61 (52%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
++ ++++G + + E L + F G + N + +D+ T +G+G+V F +EE+
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 195 R 195
Sbjct: 72 Y 72
Score = 51.9 bits (125), Expect = 4e-09
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
YV + K E L + F G + N + +D+ T +G+G+V F
Sbjct: 19 YVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 65
Score = 36.9 bits (86), Expect = 8e-04
Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 24/83 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ +F G V +P+ ++ T + +V F + E
Sbjct: 30 PLLWELFLQAGPVVNTH----------MPK----------DRVTGQHQGYGFVEFLSEED 69
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
+ A++ M+ + IRV+KA
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 70.6 bits (174), Expect = 2e-16
Identities = 14/58 (24%), Positives = 31/58 (53%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+ +++G + E +++ L AF G+I ++++ D T +GF +V F+ E+
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Score = 50.6 bits (122), Expect = 6e-09
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV + +++ L AF G+I ++++ D T +GF +V F
Sbjct: 11 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
Score = 31.3 bits (72), Expect = 0.044
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 24/83 (28%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ + F P+G++ ++ + T + A+V F+ E
Sbjct: 22 KVLHAAFIPFGDITDIQI--------------------PLDYETEKHRGFAFVEFELAED 61
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
A++ MN + TIRV+ A
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84
>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 = 70.6 bits (174), Expect = 2e-16
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S S ++I + +++L K + G+I + + I D+ TN KG+G+V+F +
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF-DSPSAAQ 61
Query: 196 KAFES 200
KA +
Sbjct: 62 KAVTA 66
Score = 52.9 bits (128), Expect = 9e-10
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ +++L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 11 RGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 71.2 bits (175), Expect = 2e-16
Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 3/75 (4%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCG--EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+I + NI + + A ++N+RLI+D+ T +GF +V + +
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL-SSAMDAS 67
Query: 196 KAFESCGEIDNVRLI 210
+ + + I
Sbjct: 68 QLLQILQSLHPPLKI 82
Score = 39.6 bits (93), Expect = 8e-05
Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 26/86 (30%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
S+ + PY S+ V +I L + +K+T N A+V+ +
Sbjct: 25 SIMTALSPYA--------SLAVNNIRLIK----------DKQTQQNRGFAFVQLSSAMDA 66
Query: 110 EKALE-MNG----HVIDEHTIRVDKA 130
+ L+ + ID TI VD A
Sbjct: 67 SQLLQILQSLHPPLKIDGKTIGVDFA 92
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 70.8 bits (174), Expect = 3e-16
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+T H +FI +PF +EEL + ++ G + ++RL+ + KG YV + E
Sbjct: 11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEY-ENE 68
Query: 192 EELRKAFES 200
+ +A
Sbjct: 69 SQASQAVMK 77
Score = 48.4 bits (116), Expect = 6e-08
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ F +EEL + ++ G + ++RL+ + KG YV +
Sbjct: 23 SGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEY 65
Score = 37.3 bits (87), Expect = 6e-04
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 19/79 (24%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA 112
+ + K +G V+ +R V + K AYV ++N +A
Sbjct: 33 ELEEICKAHGTVKDLRL----VTNRAGKPKGL--------------AYVEYENESQASQA 74
Query: 113 LE-MNGHVIDEHTIRVDKA 130
+ M+G I E+ I+V +
Sbjct: 75 VMKMDGMTIKENIIKVAIS 93
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 70.7 bits (174), Expect = 3e-16
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+ +F+G + F+ E+ L + F G+I V +++D+ T +GFG+V F ++ +
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF-ENIDDAK 68
Query: 196 KAFESC--GEIDNVRLIR 211
A + +D R IR
Sbjct: 69 DAMMAMNGKSVDG-RQIR 85
Score = 51.1 bits (123), Expect = 7e-09
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V +F E+ L + F G+I V +++D+ T +GFG+V F
Sbjct: 16 FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V F+N++ + A+ MNG +D IRVD+A
Sbjct: 57 GFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>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 = 72.2 bits (177), Expect = 3e-16
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+ + N+ + + LR+ FE G + +V + RD++T +GF +V F ++ +
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF-HDKRDAE 126
Query: 196 KAFES 200
A ++
Sbjct: 127 DAMDA 131
Score = 52.9 bits (127), Expect = 5e-09
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V ++ + LR+ FE G + +V + RD++T +GF +V F
Sbjct: 74 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 119
Score = 35.6 bits (82), Expect = 0.005
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+VRF + E A++ M+G V+D +RV A
Sbjct: 115 AFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>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 = 69.8 bits (172), Expect = 5e-16
Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+ ++F+G++ ++E LR AF+ + ++ D T +G+G+V+F +++ + A
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF-TSQDDAQNA 59
Query: 198 FES 200
+S
Sbjct: 60 MDS 62
Score = 49.8 bits (120), Expect = 1e-08
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
N ++E LR AF+ + ++ D T +G+G+V+F
Sbjct: 10 NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 50
Score = 33.6 bits (78), Expect = 0.008
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 100 YVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
+V F + + + A+ M G ++ +R++ A
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>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 = 70.0 bits (172), Expect = 7e-16
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG IP +E++L+ FE G+I + +++D+ T + KG ++ + E
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Score = 53.5 bits (129), Expect = 9e-10
Identities = 11/44 (25%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + +E++L+ FE G+I + +++D+ T + KG ++ +
Sbjct: 19 GQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Score = 31.9 bits (73), Expect = 0.047
Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 27/85 (31%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
+ +F+ +G++ ++T+ + ++ T M+ A++ + ES
Sbjct: 29 DLKPLFEEFGKIY----------ELTVLK----------DRFTGMHKGCAFLTYCERESA 68
Query: 110 EKALE-MNGHVIDE---HTIRVDKA 130
KA ++ I+V A
Sbjct: 69 LKAQSALHEQKTLPGMNRPIQVKPA 93
>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 = 70.2 bits (172), Expect = 1e-15
Identities = 16/53 (30%), Positives = 33/53 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++ + IP +E +LR+ FE G I++V+++ D+ T +G+G+V F++
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96
Score = 55.5 bits (134), Expect = 4e-10
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ +E +LR+ FE G I++V+++ D+ T +G+G+V F
Sbjct: 48 NYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91
Score = 35.1 bits (81), Expect = 0.006
Identities = 17/98 (17%), Positives = 41/98 (41%), Gaps = 24/98 (24%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ +F+ YG +E+V+ V ++ T + +V+F++ S
Sbjct: 57 VQLRQLFERYGPIESVKI--------------------VCDRETRQSRGYGFVKFQSGSS 96
Query: 109 VEKALE-MNGHVIDEHTIRVDKALTTTKSNSHSIFIGN 145
++A+ +NG I ++V A + + + +G+
Sbjct: 97 AQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGD 134
>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 = 68.7 bits (169), Expect = 1e-15
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNFKAEEEELRK 196
+ IG + ++ + + F + G+I + + + H ++ KG+ YV F+ +E K
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA-EK 62
Query: 197 AFESC--GEIDNVRLIR 211
A + G+ID + I
Sbjct: 63 ALKHMDGGQIDG-QEIT 78
Score = 50.6 bits (122), Expect = 8e-09
Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNF 226
++ ++ + + F + G+I + + + H ++ KG+ YV F
Sbjct: 8 HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF 54
Score = 39.1 bits (92), Expect = 1e-04
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 17/81 (20%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
+ +F YG+++ + + + ++H + AYV F+N + EK
Sbjct: 19 DHIMEIFSTYGKIKMID----------------MPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 112 ALE-MNGHVIDEHTIRVDKAL 131
AL+ M+G ID I L
Sbjct: 63 ALKHMDGGQIDGQEITATAVL 83
>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 = 69.2 bits (170), Expect = 1e-15
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
K +++F+G I +E E+R F G + V++I D T + KG+G+V+F + ++
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF-YNDVDV 63
Query: 195 RKAFESCGEID 205
+K ES
Sbjct: 64 QKIVESQINFH 74
Score = 46.8 bits (112), Expect = 2e-07
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + +E E+R F G + V++I D T + KG+G+V+F
Sbjct: 15 GGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
Score = 31.8 bits (73), Expect = 0.053
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL 131
+V F N V+K +E + +++ A+
Sbjct: 53 GFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAI 84
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 69.3 bits (170), Expect = 2e-15
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FI ++P E + +L F G + + ++ D+ T++ K FG+V+F +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Score = 53.9 bits (130), Expect = 8e-10
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 154 ELRKAFESCGEIDNVRLIRDQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRD 212
L A + ++ + N+ F ++ + + +L F G + + ++ D
Sbjct: 22 ALSAAAAA---AAGKQIEGPEGCNL---FIYHLPQEFTDTDLASTFLPFGNVISAKVFID 75
Query: 213 QHTNIGKGFGYVNF 226
+ T++ K FG+V+F
Sbjct: 76 KQTSLSKCFGFVSF 89
Score = 31.6 bits (72), Expect = 0.064
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 24/79 (30%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
S F P+G V + + +K+T+++ +V F N +S + A
Sbjct: 59 STFLPFGNVISAKV--------------------FIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 113 L-EMNGHVIDEHTIRVDKA 130
+ MNG + ++V
Sbjct: 99 IKAMNGFQVGTKRLKVQLK 117
>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 = 68.4 bits (168), Expect = 2e-15
Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+I++GN+ + A E++++ F G++ NV+LI D+ T KGFG+V + E
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS 56
Score = 47.9 bits (115), Expect = 6e-08
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV + A E++++ F G++ NV+LI D+ T KGFG+V
Sbjct: 5 YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM 50
Score = 26.0 bits (58), Expect = 4.7
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 25/83 (30%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
V +F +G+V V+ ++++ T +V + ES
Sbjct: 16 EQVKELFSQFGKVFNVKL--------------------IYDRETKKPKGFGFVEMQE-ES 54
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
V +A+ ++ TIRV +A
Sbjct: 55 VSEAIAKLDNTDFMGRTIRVTEA 77
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 68.0 bits (167), Expect = 3e-15
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ ++F+GN+ EE L + F G + V + +D K FG+V FK E
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPES 69
Score = 50.7 bits (122), Expect = 8e-09
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 172 RDQHTNIGKGFGYV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + +V + EE L + F G + V + +D K FG+V FK
Sbjct: 13 EEADRTV-----FVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFK 65
Score = 34.5 bits (80), Expect = 0.004
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V FK+ ESV A+ +NG + I V
Sbjct: 60 GFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92
>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 = 67.7 bits (166), Expect = 5e-15
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG---KGFGYVNFKAEEE 192
S S +FI N+ F EE L+ F G I + + + ++ GFG+V +K E+
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Score = 50.3 bits (121), Expect = 1e-08
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIG---KGFGYVNFK 227
++ NF EE L+ F G I + + + ++ GFG+V +K
Sbjct: 9 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYK 58
Score = 37.2 bits (87), Expect = 5e-04
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 27/85 (31%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN------AYVRFKNL 106
++ +F G +++ I +K +V +K
Sbjct: 21 TLKGVFSKVGAIKSCT----------------ISK----KKNKAGVLLSMGFGFVEYKKP 60
Query: 107 ESVEKAL-EMNGHVIDEHTIRVDKA 130
E +KAL ++ GH +D H + V +
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRIS 85
>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 = 68.1 bits (167), Expect = 5e-15
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FI ++P E +++L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79
Score = 51.9 bits (125), Expect = 5e-09
Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 172 RDQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ N+ F ++ + +++L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 22 GPEGANL---FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Score = 29.2 bits (66), Expect = 0.47
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 24/79 (30%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKA 112
MF P+G V + + +K+TN++ +V + N S + A
Sbjct: 44 QMFMPFGNVVSAKV--------------------FIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 113 L-EMNGHVIDEHTIRVDKA 130
+ MNG I ++V
Sbjct: 84 IQSMNGFQIGMKRLKVQLK 102
>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 = 67.3 bits (165), Expect = 6e-15
Identities = 8/61 (13%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
++++GN+ + E + + F G + ++I + + + +V F +
Sbjct: 12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAA 69
Query: 195 R 195
Sbjct: 70 A 70
Score = 51.5 bits (124), Expect = 5e-09
Identities = 9/58 (15%), Positives = 20/58 (34%), Gaps = 10/58 (17%)
Query: 172 RDQHTNIGKGFGYV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Q + YV + E + + F G + ++I + + + +V F
Sbjct: 12 DGQPRTL-----YVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEF 62
Score = 38.8 bits (91), Expect = 2e-04
Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 22/76 (28%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN-AYVRFKNLESVEKALE- 114
+F G ++ + + E +N +V F AL
Sbjct: 35 LFSQIGPCKSCK----------MIT----------EHTSNDPYCFVEFYEHRDAAAALAA 74
Query: 115 MNGHVIDEHTIRVDKA 130
MNG I ++V+ A
Sbjct: 75 MNGRKILGKEVKVNWA 90
>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 = 67.3 bits (165), Expect = 7e-15
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
T + +F+GN+P + EEE+RK FE G+ V + +D KGFG++ +
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTL 63
Score = 46.1 bits (110), Expect = 4e-07
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V EEE+RK FE G+ V + +D KGFG++
Sbjct: 19 FVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRL 58
Score = 37.6 bits (88), Expect = 4e-04
Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 26/77 (33%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPR-KACIKMNKVHEKRTNMNAYVRFKNLESVEKAL- 113
+F+ YG+ V + + K ++R + E A
Sbjct: 34 KLFEKYGKAGEVF----------IHKDKGF--------------GFIRLETRTLAEIAKV 69
Query: 114 EMNGHVIDEHTIRVDKA 130
E++ + +RV A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 67.3 bits (165), Expect = 7e-15
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+ +KS + + NIPF + +LR+ F G+I +V +I ++ KGFG+V F
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF-ENS 65
Query: 192 EELRKAFES 200
+ +A E
Sbjct: 66 ADADRAREK 74
Score = 46.5 bits (111), Expect = 3e-07
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V F+ + +LR+ F G+I +V +I ++ KGFG+V F
Sbjct: 19 HVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62
Score = 32.6 bits (75), Expect = 0.029
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V F+N ++A E ++G V++ I V+ A
Sbjct: 58 GFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 67.0 bits (164), Expect = 1e-14
Identities = 9/53 (16%), Positives = 17/53 (32%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + E L+ GE++ V ++ T G V F +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60
Score = 54.3 bits (131), Expect = 5e-10
Identities = 11/46 (23%), Positives = 17/46 (36%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
F +N E L+ GE++ V ++ T G V F
Sbjct: 11 FARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFT 56
Score = 37.8 bits (88), Expect = 4e-04
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 24/76 (31%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKAL 113
M + YGEVE V + RT + A V F + ++ +
Sbjct: 26 MCRKYGEVEEVEI--------------------LLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 114 E-MNGHVIDEHTIRVD 128
+ ++ + + I
Sbjct: 66 KNLHLTSVMGNIIHAQ 81
>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 = 67.0 bits (164), Expect = 1e-14
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+ +FIG + E E+ L+ F G I V LI+D+ T+ +GF ++ F +
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITF-ENPADA 61
Query: 195 RKAFE 199
+ A +
Sbjct: 62 KNAAK 66
Score = 51.6 bits (124), Expect = 7e-09
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 173 DQHTNIGKGFGYV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
D + ++ N + E+ L+ F G I V LI+D+ T+ +GF ++ F
Sbjct: 5 DHPGKL-----FIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITF 55
Score = 37.3 bits (87), Expect = 8e-04
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A++ F+N + A + MNG + I+V++A
Sbjct: 51 AFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 66.2 bits (162), Expect = 2e-14
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 126 RVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 185
R T KS + + NIPF + +LR+ F G+I +V +I ++ KGFG+V
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFV 74
Query: 186 NFKAEEEELRKAFE 199
F + +A E
Sbjct: 75 TF-ENSADADRARE 87
Score = 45.0 bits (107), Expect = 1e-06
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V F+ + +LR+ F G+I +V +I ++ KGFG+V F
Sbjct: 33 HVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 76
Score = 32.3 bits (74), Expect = 0.038
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+V F+N ++A E ++G V++ I V+ A
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>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 = 65.8 bits (161), Expect = 2e-14
Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGE-IDNVRLIRDQHTNIGKGFGYVNFKAE 190
+ + + S+++G++ +E + +AF + GE + +V++IR++ T I G+ +V F A+
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF-AD 61
Query: 191 EEELRKAFES 200
K
Sbjct: 62 LATAEKCLHK 71
Score = 50.4 bits (121), Expect = 1e-08
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGE-IDNVRLIRDQHTNIGKGFGYVNF 226
G + +E + +AF + GE + +V++IR++ T I G+ +V F
Sbjct: 15 GDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF 59
Score = 30.0 bits (68), Expect = 0.19
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 99 AYVRFKNLESVEKALE-MNGHVID----EHTIRVDKA 130
+V F +L + EK L +NG + +++ A
Sbjct: 55 CFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYA 91
>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 = 68.6 bits (167), Expect = 3e-14
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEID--NVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+++IGN+ + +E+L +A S G D ++ ++ KGF V E
Sbjct: 66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGV-GSEAS 124
Query: 194 LRKAFES 200
+K +
Sbjct: 125 SKKLMDL 131
Score = 38.5 bits (89), Expect = 0.001
Identities = 12/83 (14%), Positives = 22/83 (26%), Gaps = 24/83 (28%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN----AYVRFKNLES 108
+T G + + +I K E R N A V + S
Sbjct: 84 DLTEAVHSLGVND--------ILEI-----------KFFENRANGQSKGFALVGVGSEAS 124
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
+K ++ + + V
Sbjct: 125 SKKLMDLLPKRELHGQNPVVTPV 147
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 65.0 bits (159), Expect = 5e-14
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 127 VDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 186
VD + + + +IGNIP A E +L F++ G I + + + KG ++
Sbjct: 16 VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIK 69
Query: 187 FKAEEE 192
+ E+
Sbjct: 70 YDTHEQ 75
Score = 47.7 bits (114), Expect = 1e-07
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + A E +L F++ G I + + + KG ++ +
Sbjct: 33 GNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKY 70
Score = 40.0 bits (94), Expect = 7e-05
Identities = 7/73 (9%), Positives = 19/73 (26%), Gaps = 24/73 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F+ +G + + P K C ++++ E + +
Sbjct: 47 LFQNFGFILDFKH---------YPEKGC--------------CFIKYDTHEQAAVCIVAL 83
Query: 116 NGHVIDEHTIRVD 128
+R
Sbjct: 84 ANFPFQGRNLRTG 96
>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 = 64.2 bits (157), Expect = 9e-14
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+ + +P++ E++L++ F + GE+ V++ +D T KGFG+V F E E K
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF-TEYETQVKVMSQ 76
Query: 201 CGEIDN 206
ID
Sbjct: 77 RHMIDG 82
Score = 48.0 bits (115), Expect = 1e-07
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 172 RDQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + +K E++L++ F + GE+ V++ +D T KGFG+V F
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
Score = 35.7 bits (83), Expect = 0.002
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL 131
+VRF E+ K + H+ID
Sbjct: 60 GFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN 91
>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 = 64.1 bits (157), Expect = 9e-14
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+G IP E ELR+ F+ G + V +I D +GFG++ F+ E+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64
Score = 46.8 bits (112), Expect = 3e-07
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + E ELR+ F+ G + V +I D +GFG++ F+
Sbjct: 16 GGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
Score = 41.4 bits (98), Expect = 2e-05
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL 131
++ F++ +SV++A+ M+ H I + V +A
Sbjct: 55 GFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAE 87
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 64.3 bits (157), Expect = 1e-13
Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 121 DEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK 180
+ +R + + + + +++ G I ++ +R+ F G+I +R+ + K
Sbjct: 8 NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------K 61
Query: 181 GFGYVNFKAEEE 192
G+ +V F E
Sbjct: 62 GYSFVRFSTHES 73
Score = 46.6 bits (111), Expect = 3e-07
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y ++ +R+ F G+I +R+ + KG+ +V F
Sbjct: 29 YCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRF 68
Score = 38.9 bits (91), Expect = 2e-04
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 24/72 (33%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
F P+G++ +R P K ++VRF ES A+ +
Sbjct: 45 TFSPFGQIMEIRV---------FPEKGY--------------SFVRFSTHESAAHAIVSV 81
Query: 116 NGHVIDEHTIRV 127
NG I+ H ++
Sbjct: 82 NGTTIEGHVVKC 93
>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 = 64.2 bits (157), Expect = 1e-13
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S ++F+ + + EE L+++F R++ D+ T KGFG+V+F EE+ + A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDF-NSEEDAKAA 70
Query: 198 FESC--GEIDNVRLIR 211
E+ GEID +
Sbjct: 71 KEAMEDGEIDG-NKVT 85
Score = 42.2 bits (100), Expect = 9e-06
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V + EE L+++F R++ D+ T KGFG+V+F
Sbjct: 19 FVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDF 61
Score = 36.5 bits (85), Expect = 0.001
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS 138
+V F + E + A E M ID + + +D A + S
Sbjct: 57 GFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGS 97
>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 = 63.8 bits (156), Expect = 1e-13
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S ++ + N+ + A EE L++ FE I + KG+ ++ F A E+ ++A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF-ASFEDAKEA 69
Query: 198 FESC--GEIDNVRLIR 211
SC EI+ R IR
Sbjct: 70 LNSCNKREIEG-RAIR 84
Score = 37.3 bits (87), Expect = 6e-04
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS 138
A++ F + E ++AL N I+ IR++ NS
Sbjct: 56 AFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNS 96
>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 = 63.8 bits (156), Expect = 2e-13
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
T+ ++++ N+ ++E LRKAF G I + +++ + KGFG+V F + EE
Sbjct: 11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEE 67
Score = 49.5 bits (119), Expect = 3e-08
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 169 RLIRDQHTNIGKGFGYV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 225
R+ R Q N+ YV + ++E LRKAF G I + +++ + KGFG+V
Sbjct: 9 RITRYQVVNL-----YVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVC 61
Query: 226 F 226
F
Sbjct: 62 F 62
Score = 29.1 bits (66), Expect = 0.37
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 100 YVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
+V F + E KA+ EMNG ++ + V A
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90
>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 = 63.5 bits (155), Expect = 2e-13
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ +F+G + + EE++ + F+ G ID ++R KG +V F + E
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTE 68
Score = 45.7 bits (109), Expect = 6e-07
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +N + EE++ + F+ G ID ++R KG +V F
Sbjct: 21 GMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKF 63
>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 = 63.1 bits (154), Expect = 2e-13
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 9/76 (11%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+ ++ N+ F E+EL++ FE EI KG Y+ FK+E + K
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADA-EKN 69
Query: 198 FES--CGEIDNVRLIR 211
E EID R +
Sbjct: 70 LEEKQGAEIDG-RSVS 84
Score = 38.0 bits (89), Expect = 3e-04
Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 29/83 (34%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
+ +F+ E+ V + + AY+ FK+
Sbjct: 31 DELKEVFEDALEIRLVS-------------------------QDGKSKGIAYIEFKSEAD 65
Query: 109 VEKALE-MNGHVIDEHTIRVDKA 130
EK LE G ID ++ +
Sbjct: 66 AEKNLEEKQGAEIDGRSVSLYYT 88
>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 = 62.6 bits (153), Expect = 3e-13
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S S IFIGN+ E +E+ L F + G I +++RD T KG+ ++NF + +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Score = 32.9 bits (76), Expect = 0.017
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A++ F + ++ + A+E MNG + I V A
Sbjct: 51 AFINFASFDASDAAIEAMNGQYLCNRPITVSYA 83
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 64.6 bits (157), Expect = 3e-13
Identities = 15/119 (12%), Positives = 45/119 (37%), Gaps = 6/119 (5%)
Query: 87 MNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTI---RVDKALTTTKSNSHSIFI 143
M+ H + ++ +S+E + + + + ++ ++++
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYV 60
Query: 144 GNIPFEAEEEELRKAFESCG--EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
G+ + +++L + S G ++ ++ ++ KG+ V A E + K E
Sbjct: 61 GSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVV-ASENSVHKLLEL 118
Score = 34.5 bits (79), Expect = 0.011
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A V + SV K LE + G V++ + V A
Sbjct: 102 AEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134
>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 = 61.7 bits (151), Expect = 3e-13
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
IF+G + + EE++R+ F GE++++ L D TN +GF ++ F EEE ++K E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF-KEEEPVKKIME 59
Score = 47.1 bits (113), Expect = 1e-07
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++ EE++R+ F GE++++ L D TN +GF ++ FK
Sbjct: 5 GGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK 49
Score = 39.8 bits (94), Expect = 4e-05
Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 23/76 (30%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKALE 114
F +GEVE I LP + +TN ++ FK E V+K +E
Sbjct: 20 FGGFGEVE----------SIELPM----------DNKTNKRRGFCFITFKEEEPVKKIME 59
Query: 115 MNGHVIDEHTIRVDKA 130
H + + A
Sbjct: 60 KKYHNVGLSKCEIKVA 75
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 63.2 bits (154), Expect = 4e-13
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 8/67 (11%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDN--------VRLIRDQHTNIGKGFGYVN 186
S++++IF+ + E + F+ G I + L D+ T KG V+
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 187 FKAEEEE 193
F
Sbjct: 64 FDDPPSA 70
Score = 36.2 bits (84), Expect = 0.002
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
SV FK G ++T + P I L ++ T A V F + S
Sbjct: 23 SVADYFKQIGIIKTNKKTGQP--MINLYT----------DRETGKLKGEATVSFDDPPSA 70
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
+ A++ +G + I+V A
Sbjct: 71 KAAIDWFDGKEFSGNPIKVSFA 92
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 62.2 bits (152), Expect = 5e-13
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++ S + IF+ N+PF+ + L+ F CG + + + KG G V F++ E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59
Query: 192 E 192
Sbjct: 60 V 60
Score = 40.6 bits (96), Expect = 3e-05
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
F + L+ F CG + + + KG G V F
Sbjct: 18 FDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKF 55
Score = 29.8 bits (68), Expect = 0.20
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
V+F++ E E+A MNG + I V
Sbjct: 51 GVVKFESPEVAERACRMMNGMKLSGREIDVRID 83
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 61.3 bits (150), Expect = 6e-13
Identities = 18/52 (34%), Positives = 33/52 (63%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+G + E+++ FE G++D+ L+ D+ TN +GFG+V F++E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI 53
Score = 45.5 bits (109), Expect = 3e-07
Identities = 14/42 (33%), Positives = 26/42 (61%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ E+++ FE G++D+ L+ D+ TN +GFG+V F+
Sbjct: 8 SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE 49
Score = 41.7 bits (99), Expect = 9e-06
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+V F++ + VEK E++ H I+ + KA
Sbjct: 44 GFVTFESEDIVEKVCEIHFHEINNKMVECKKA 75
>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 = 62.3 bits (152), Expect = 6e-13
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
IF+G +P+ + LRK FE G+I+ +I D+ T +G+G+V A+ +A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM-ADRAAAERACKD 78
Query: 201 CG-EIDNVRLIR 211
ID R
Sbjct: 79 PNPIIDG-RKAN 89
Score = 46.1 bits (110), Expect = 5e-07
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 173 DQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ T K F G + + + LRK FE G+I+ +I D+ T +G+G+V
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67
Score = 37.3 bits (87), Expect = 7e-04
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 4/52 (7%)
Query: 100 YVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHS----IFIGNIP 147
+V + + E+A + +ID V+ A K S I +
Sbjct: 63 FVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPS 114
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 62.1 bits (151), Expect = 8e-13
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 3/78 (3%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+ + + +PF A E ++R F +D V L++D G G V F ++
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLVKF-LSPQD 68
Query: 194 LRKAFESCGEIDNVRLIR 211
+A + + R +
Sbjct: 69 TFEALKRNRMLMIQRYVE 86
Score = 49.4 bits (118), Expect = 3e-08
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
F + V + L + H R N N V+F + + +AL+ N ++ + + V
Sbjct: 37 FHGLRVDAVHLLKD--------HVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVS 88
Query: 129 KA 130
A
Sbjct: 89 PA 90
>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 = 60.8 bits (148), Expect = 2e-12
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 8/68 (11%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEID--------NVRLIRDQHTNIGKGFGYV 185
+ S++++IF+ + E + F+ G I + L D+ T KG V
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 186 NFKAEEEE 193
+F
Sbjct: 69 SFDDPPSA 76
Score = 34.2 bits (79), Expect = 0.006
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 16/82 (19%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESV 109
SV FK G ++T + P+ I + ++ T A V F + S
Sbjct: 29 SVADYFKQIGIIKTNKKTGQPM----------INL--YTDRETGKLKGEATVSFDDPPSA 76
Query: 110 EKALE-MNGHVIDEHTIRVDKA 130
+ A++ +G + I+V A
Sbjct: 77 KAAIDWFDGKEFSGNPIKVSFA 98
>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 = 60.7 bits (148), Expect = 2e-12
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+G + + +E LR F GE+ + +++D+ TN +GFG+V F + + S
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF-KDPNCVGTVLAS 77
Query: 201 CG-EIDN 206
+D
Sbjct: 78 RPHTLDG 84
Score = 46.8 bits (112), Expect = 2e-07
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 176 TNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
IGK F G +++ +E LR F GE+ + +++D+ TN +GFG+V FK
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Score = 40.7 bits (96), Expect = 4e-05
Identities = 8/32 (25%), Positives = 12/32 (37%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+V+FK+ V L H +D I
Sbjct: 61 GFVKFKDPNCVGTVLASRPHTLDGRNIDPKPC 92
>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 = 60.3 bits (147), Expect = 2e-12
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCG--EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRK 196
+++IGN+ + +E+L +A S G +I ++ ++ KGF V E +K
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGV-GSEASSKK 60
Query: 197 AFES 200
+
Sbjct: 61 LMDL 64
Score = 30.6 bits (70), Expect = 0.11
Identities = 5/33 (15%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A V + S +K ++ + + V +
Sbjct: 48 ALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS 80
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + FE EE LR +E G++ + ++RD + +GFG+V F + E
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Score = 46.1 bits (110), Expect = 5e-07
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 172 RDQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + K F G ++F+ EE LR +E G++ + ++RD + +GFG+V F
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Score = 41.5 bits (98), Expect = 3e-05
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL 131
+V F ++ V+ A+ H ID + +A+
Sbjct: 72 GFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV 104
>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 = 59.9 bits (146), Expect = 3e-12
Identities = 13/52 (25%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+F+G + ++ +++L+ F GE+ + + D +T +GFG++ FK
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS 65
Score = 46.4 bits (111), Expect = 2e-07
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 176 TNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ GK F G +++ +++L+ F GE+ + + D +T +GFG++ FK
Sbjct: 9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Score = 38.7 bits (91), Expect = 2e-04
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
++ FK+ SVEK L+ H +D I KA
Sbjct: 56 GFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 59.4 bits (145), Expect = 3e-12
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + ++ +E LR+ F GE+ ++RD T +GFG+V F +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 54
Score = 44.8 bits (107), Expect = 7e-07
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 9 SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50
Score = 42.1 bits (100), Expect = 7e-06
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL 131
+V F + V+K L + H +D TI A
Sbjct: 45 GFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF 77
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 9/55 (16%), Positives = 20/55 (36%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ +++ N+ E +L F E + T +G ++ F +E
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79
Score = 47.7 bits (114), Expect = 1e-07
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 3/47 (6%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
Y+ + + E +L F E + T +G ++ F
Sbjct: 29 YLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP 75
Score = 34.2 bits (79), Expect = 0.008
Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 18/76 (23%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE- 114
S+F + E + + +T + A++ F N E +AL
Sbjct: 44 SLFARFQEKKGPP---IQFRMMTGRMRGQ--------------AFITFPNKEIAWQALHL 86
Query: 115 MNGHVIDEHTIRVDKA 130
+NG+ + + ++
Sbjct: 87 VNGYKLYGKILVIEFG 102
>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 = 60.3 bits (147), Expect = 3e-12
Identities = 13/59 (22%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + +++I N+P +E+EL + G++ + R++RD + +G G+ ++ E+
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 78
Score = 49.6 bits (119), Expect = 3e-08
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV---NFKAEEEELRKAFESCGEIDNVR 208
L+ + + + TN+ Y+ +E+EL + G++ + R
Sbjct: 5 SSGLKASGV---QAQMAKQQEQDPTNL-----YISNLPLSMDEQELENMLKPFGQVISTR 56
Query: 209 LIRDQHTNIGKGFGYVNF 226
++RD + +G G+
Sbjct: 57 ILRDS-SGTSRGVGFARM 73
>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 = 60.0 bits (146), Expect = 5e-12
Identities = 8/58 (13%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + N+ F + ++++ F G + + D+ + G V+F+ + +
Sbjct: 26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKAD 82
Score = 42.7 bits (101), Expect = 9e-06
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V +F + ++++ F G + + D+ + G V+F
Sbjct: 33 LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHF 77
Score = 29.2 bits (66), Expect = 0.48
Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 25/78 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKAL 113
+F +G ++ VH R+ + A V F+ KA+
Sbjct: 49 LFAEFGTLKKA---------------------AVHYDRSGRSLGTADVHFERKADALKAM 87
Query: 114 -EMNGHVIDEHTIRVDKA 130
+ NG +D + +
Sbjct: 88 KQYNGVPLDGRPMNIQLV 105
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 60.1 bits (146), Expect = 5e-12
Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEI--------DNVRLIRDQHTNIGKGFGYVN 186
S++ +I++ + ++L F+ CG + + + D+ T KG V+
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71
Query: 187 FKAEEEE 193
++
Sbjct: 72 YEDPPTA 78
Score = 33.1 bits (76), Expect = 0.021
Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 16/89 (17%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVE 110
+ FK G V+ + P+ I +K T A V +++ + +
Sbjct: 32 LADFFKQCGVVKMNKRTGQPMIHI------------YLDKETGKPKGDATVSYEDPPTAK 79
Query: 111 KALE-MNGHVIDEHTIRVDKALTTTKSNS 138
A+E +G ++V A NS
Sbjct: 80 AAVEWFDGKDFQGSKLKVSLARKKPPMNS 108
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 59.8 bits (145), Expect = 5e-12
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 3/79 (3%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S I NIPF + ++ + E + V ++ D + G G V FK E+
Sbjct: 11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-GLGQALVQFK-NED 68
Query: 193 ELRKAFESCGEIDNVRLIR 211
+ RK+ + N R
Sbjct: 69 DARKSERLHRKKLNGREAF 87
Score = 40.5 bits (95), Expect = 6e-05
Identities = 8/73 (10%), Positives = 20/73 (27%), Gaps = 17/73 (23%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNG 117
+ E + + + + A V+FKN + K+ ++
Sbjct: 36 LEGIPVDEN---------AVHVLVD--------NNGQGLGQALVQFKNEDDARKSERLHR 78
Query: 118 HVIDEHTIRVDKA 130
++ V
Sbjct: 79 KKLNGREAFVHVV 91
>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 = 59.6 bits (145), Expect = 6e-12
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + ++ +E LR+ F GE+ ++RD T +GFG+V F +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Score = 45.3 bits (108), Expect = 9e-07
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 176 TNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++ K F G ++++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Score = 39.9 bits (94), Expect = 7e-05
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+V F + V+K L + H +D TI A
Sbjct: 70 GFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 101
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 58.9 bits (143), Expect = 1e-11
Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+ ++I N+P++ EE+ F G I +R+ T +G YV ++ + + + A
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYE-DIFDAKNA 63
Query: 198 FESCGEID-NVRLIRDQHTNIGKGF 221
+ + + R + + N + F
Sbjct: 64 VDHLSGFNVSNRYLVVLYYNANRAF 88
Score = 42.0 bits (99), Expect = 1e-05
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
Y+ +K EE+ F G I +R+ T +G YV ++
Sbjct: 12 YIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYE 55
Score = 31.2 bits (71), Expect = 0.084
Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 21/78 (26%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ +F YG + +R + T AYV ++++ + A+
Sbjct: 25 MYDIFGKYGPIRQIR--------------------VGNTPETRGTAYVVYEDIFDAKNAV 64
Query: 114 E-MNGHVIDEHTIRVDKA 130
+ ++G + + V
Sbjct: 65 DHLSGFNVSNRYLVVLYY 82
>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 = 58.8 bits (143), Expect = 1e-11
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IFI N+ + + L F + G I + +++ D++ + KG+G+V+F+ +E
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEA 57
Score = 41.5 bits (98), Expect = 3e-05
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ L F + G I + +++ D++ + KG+G+V+F+
Sbjct: 19 NKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFE 53
Score = 40.3 bits (95), Expect = 7e-05
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA---------LTTTKSNSHSIFIGNIPF 148
+V F+ E+ E+A+E MNG ++++ + V + L +++I N
Sbjct: 48 GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGP 107
Query: 149 EAEEEE 154
+
Sbjct: 108 GSTRAA 113
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 58.1 bits (141), Expect = 2e-11
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+ ++ +F+ P + +E EL + F G + V+++ GF +V F E E
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEF-EEAES 77
Query: 194 LRKAFE 199
KA E
Sbjct: 78 AAKAIE 83
Score = 40.7 bits (96), Expect = 4e-05
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 8/44 (18%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E EL + F G + V+++ GF +V F
Sbjct: 37 RPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEF 72
Score = 28.8 bits (65), Expect = 0.57
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
A+V F+ ES KA+ E++G + V +
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>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 = 57.3 bits (139), Expect = 3e-11
Identities = 13/67 (19%), Positives = 21/67 (31%), Gaps = 1/67 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
K I + N+PF +E+ F I ++ + G V F +E
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF-ESRDEA 70
Query: 195 RKAFESC 201
A
Sbjct: 71 TAAVIDL 77
Score = 38.8 bits (91), Expect = 1e-04
Identities = 7/40 (17%), Positives = 12/40 (30%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
F +E+ F I ++ + G V F
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64
Score = 34.2 bits (79), Expect = 0.007
Identities = 6/52 (11%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 80 PRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
+ + + A V F++ + A+ ++N I +++
Sbjct: 41 VIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 57.3 bits (139), Expect = 3e-11
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ H++ + PF E+ + + +R++R+ H N G+ +V+F + EEE++
Sbjct: 8 TTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGN-KTGYIFVDF-SNEEEVK 64
Query: 196 KAFESCGEIDNVRLIR 211
+A + E R I
Sbjct: 65 QALKCNREYMGGRYIE 80
Score = 41.1 bits (97), Expect = 2e-05
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
+ I + R +V F N E V++AL+ N + I V
Sbjct: 31 LAPLKPVAIRIVRN--------AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVF 82
Query: 129 KA 130
+
Sbjct: 83 RE 84
Score = 37.7 bits (88), Expect = 4e-04
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
F E+ + + +R++R+ H N G+ +V+F
Sbjct: 20 FNVTEKNVMEFLAPLK-PVAIRIVRNAHGN-KTGYIFVDFS 58
>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 = 57.7 bits (140), Expect = 3e-11
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++ + +F+ N+ EE L KAF G+++ V+ ++D + +++F E
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF-DER 55
Query: 192 EELRKAFE 199
+ KA E
Sbjct: 56 DGAVKAME 63
Score = 38.4 bits (90), Expect = 2e-04
Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 8/36 (22%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE L KAF G+++ V+ ++D + +++F
Sbjct: 25 EEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Score = 33.4 bits (77), Expect = 0.012
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A++ F + KA+E MNG ++ I + A
Sbjct: 48 AFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
>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 = 57.8 bits (140), Expect = 3e-11
Identities = 8/58 (13%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + N+ F + ++++ F G + + D+ + G V+F+ +
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 88
Score = 40.8 bits (96), Expect = 5e-05
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V +F + ++++ F G + + D+ + G V+F+
Sbjct: 39 LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE 84
Score = 30.0 bits (68), Expect = 0.24
Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 25/78 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKAL 113
+F +G ++ V R+ + A V F+ KA+
Sbjct: 55 LFAEFGTLKKA---------------------AVDYDRSGRSLGTADVHFERRADALKAM 93
Query: 114 -EMNGHVIDEHTIRVDKA 130
+ G +D + +
Sbjct: 94 KQYKGVPLDGRPMDIQLV 111
>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 = 57.4 bits (139), Expect = 3e-11
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 1/77 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+N + + +PF +EE+ + F + N + G +V F A +E
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF-ASQEIA 70
Query: 195 RKAFESCGEIDNVRLIR 211
KA + E R I
Sbjct: 71 EKALKKHKERIGHRYIE 87
Score = 43.2 bits (102), Expect = 5e-06
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+ + + R+ A+V+F + E EKAL+ + I I + K+
Sbjct: 45 GMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 91
Score = 38.2 bits (89), Expect = 3e-04
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
F +EE+ + F + N + G +V F
Sbjct: 25 FGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 57.3 bits (139), Expect = 4e-11
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+N I++GN+P + +++ F G I ++ L G F +V F+ +
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRD 73
Score = 40.0 bits (94), Expect = 7e-05
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
YV +++ F G I ++ L G F +V F+
Sbjct: 26 YVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFE 69
Score = 29.6 bits (67), Expect = 0.31
Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 21/78 (26%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ +F YG + + +K + A+V F++ E A+
Sbjct: 39 IEDVFYKYGAIRDID----------------LKNRR----GGPPFAFVEFEDPRDAEDAV 78
Query: 114 -EMNGHVIDEHTIRVDKA 130
+G+ D + +RV+
Sbjct: 79 YGRDGYDYDGYRLRVEFP 96
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 57.3 bits (139), Expect = 4e-11
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESC-GEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
+ + +S+F+G++ + ++ L + F +++ DQ T + KG+G+V F E
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDE 61
Query: 191 EEELR 195
E+ R
Sbjct: 62 LEQKR 66
>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 = 57.3 bits (139), Expect = 4e-11
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++F+ N+ ++ ++L++ F G + ++ D +G G V F+ E
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIE 68
Score = 40.0 bits (94), Expect = 8e-05
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+K ++L++ F G + ++ D +G G V F
Sbjct: 25 YKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTF 63
>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 = 56.9 bits (138), Expect = 5e-11
Identities = 13/67 (19%), Positives = 21/67 (31%), Gaps = 1/67 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
K I + N+PF +E+ F I ++ + G V F +E
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF-ESRDEA 70
Query: 195 RKAFESC 201
A
Sbjct: 71 TAAVIDL 77
Score = 37.7 bits (88), Expect = 4e-04
Identities = 7/40 (17%), Positives = 12/40 (30%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
F +E+ F I ++ + G V F
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64
Score = 36.9 bits (86), Expect = 8e-04
Identities = 8/78 (10%), Positives = 22/78 (28%), Gaps = 18/78 (23%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ F Y + + + + A V F++ + A+
Sbjct: 32 ILDFFYGYQVIP-----------------GSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 114 -EMNGHVIDEHTIRVDKA 130
++N I +++
Sbjct: 75 IDLNDRPIGSRKVKLVLG 92
>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 = 55.9 bits (135), Expect = 1e-10
Identities = 12/72 (16%), Positives = 23/72 (31%), Gaps = 3/72 (4%)
Query: 128 DKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + H + + +P+ A E ++ F V + + G V F
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRV-TGEADVEF 62
Query: 188 KAEEEELRKAFE 199
A E+ A
Sbjct: 63 -ATHEDAVAAMA 73
Score = 39.7 bits (93), Expect = 7e-05
Identities = 10/70 (14%), Positives = 19/70 (27%), Gaps = 8/70 (11%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
F + + + + R A V F E A+ + + + +
Sbjct: 36 FSPLNPMRVHIEIG--------PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF 87
Query: 129 KALTTTKSNS 138
T S S
Sbjct: 88 LNSTAGTSGS 97
Score = 35.8 bits (83), Expect = 0.002
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++A E ++ F V + + G V F
Sbjct: 25 YRATENDIYNFFSPLN-PMRVHIEIGPDGRV-TGEADVEFA 63
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 55.8 bits (135), Expect = 1e-10
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++GN+ A + EL +AF G + V + R+ GF +V F+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRD 49
Score = 40.4 bits (95), Expect = 4e-05
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV A + EL +AF G + V + R+ GF +V F
Sbjct: 4 YVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEF 44
Score = 29.2 bits (66), Expect = 0.35
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
A+V F++ E A+ ++G VI +RV+ +
Sbjct: 40 AFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 55.3 bits (134), Expect = 1e-10
Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S + ++IGN+ ++LR+ F L + G+ +V++ +
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWA-I 58
Query: 196 KAFES 200
+A E+
Sbjct: 59 RAIET 63
Score = 35.3 bits (82), Expect = 0.002
Identities = 7/47 (14%), Positives = 17/47 (36%), Gaps = 9/47 (19%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
Y+ + ++LR+ F L + G+ +V++
Sbjct: 12 YIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYP 52
Score = 28.4 bits (64), Expect = 0.61
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 89 KVHEKRTNMN---AYVRFKNLESVEKALE-MNGHV-IDEHTIRVDKA 130
+ + A+V + + +A+E ++G V + + VD +
Sbjct: 34 LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS 80
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 59.1 bits (142), Expect = 2e-10
Identities = 15/75 (20%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+ + ++ E +LR+ FE G I + ++ + + +G+ ++ ++ E ++ A++
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE-HERDMHSAYK 162
Query: 200 SCG--EIDNVRLIRD 212
+ID R++ D
Sbjct: 163 HADGKKIDGRRVLVD 177
Score = 46.4 bits (109), Expect = 4e-06
Identities = 9/42 (21%), Positives = 23/42 (54%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
N+ E +LR+ FE G I + ++ + + +G+ ++ ++
Sbjct: 111 NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Score = 30.2 bits (67), Expect = 0.67
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 84 CIKMNKVHEKRTNMN---AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKALTTTKSN 137
+++ V+ KR+ A++ +++ + A +G ID + VD T
Sbjct: 129 IKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKG 186
>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 = 54.9 bits (133), Expect = 2e-10
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
N+ IF+GN+ +ELR FE G + ++ K + +V+ + E +
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEAD 55
Score = 36.8 bits (86), Expect = 6e-04
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 11/46 (23%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V + +ELR FE G + ++ K + +V+
Sbjct: 13 FVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHM 50
Score = 28.3 bits (64), Expect = 0.67
Identities = 7/33 (21%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
A+V + + A+ ++NG + I V+ +
Sbjct: 46 AFVHMEKEADAKAAIAQLNGKEVKGKRINVELS 78
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 55.0 bits (133), Expect = 2e-10
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S S+F+ P + +L + F + G + +V + +D+ F V +
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEM-GDVGARE 59
Query: 196 KAFE 199
Sbjct: 60 AVLS 63
Score = 40.0 bits (94), Expect = 6e-05
Identities = 14/73 (19%), Positives = 24/73 (32%), Gaps = 22/73 (30%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNG 117
F +G V +V V +K + A V ++ + E L +
Sbjct: 29 FLAFGPVASV----------------------VMDKDKGVFAIVEMGDVGAREAVLSQSQ 66
Query: 118 HVIDEHTIRVDKA 130
H + H +RV
Sbjct: 67 HSLGGHRLRVRPR 79
Score = 36.1 bits (84), Expect = 0.001
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ +L + F + G + +V + +D+ F V
Sbjct: 14 SGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMG 53
>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 = 56.0 bits (135), Expect = 2e-10
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 3/78 (3%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+++ +PFEAE + + F+ + D++ + + G G+V F E +
Sbjct: 22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGFVEF-RNEAD 79
Query: 194 LRKAFESCGEIDNVRLIR 211
+ A + R I+
Sbjct: 80 YKAALCRHKQYMGNRFIQ 97
Score = 44.1 bits (104), Expect = 3e-06
Identities = 13/77 (16%), Positives = 21/77 (27%), Gaps = 17/77 (22%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
V FK VE I + + +V F+N + AL
Sbjct: 42 VIDFFKKLDIVE---------DSIYIAYG--------PNGKATGEGFVEFRNEADYKAAL 84
Query: 114 EMNGHVIDEHTIRVDKA 130
+ + I+V
Sbjct: 85 CRHKQYMGNRFIQVHPI 101
Score = 37.1 bits (86), Expect = 9e-04
Identities = 9/42 (21%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 187 FKAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFK 227
F+AE + + F+ + D++ + + G G+V F+
Sbjct: 35 FEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGFVEFR 75
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGE-IDNVRLIRD-QHTNIGKGFGYVNFKAEEE 192
+ +FIG IP + EE+ + E + +V + +GF +V +++
Sbjct: 7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA 64
Score = 37.1 bits (86), Expect = 8e-04
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 183 GYVNFKAEEEELRKAFESCGE-IDNVRLIRD-QHTNIGKGFGYVNFK 227
G + + EE+ + E + +V + +GF +V ++
Sbjct: 14 GGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60
Score = 29.4 bits (66), Expect = 0.39
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 18/80 (22%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA- 112
+ E V D+ + + + + A+V +++ + A
Sbjct: 25 ILEEIAKVTEG---------VLDVIVYA------SAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 113 --LEMNGHVIDEHTIRVDKA 130
L + H I VD A
Sbjct: 70 RKLMPGRIQLWGHQIAVDWA 89
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 55.7 bits (134), Expect = 2e-10
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEI----DNVRLIRDQHTNIGKGFGYVNFK 188
+K N + + +PF A EE+ F I + + + G +V F
Sbjct: 18 LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAFVLF- 75
Query: 189 AEEEELRKAFESCGEIDNVRLIR 211
A EE + A ++ R I
Sbjct: 76 ACEEYAQNALRKHKDLLGKRYIE 98
Score = 39.1 bits (91), Expect = 2e-04
Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 14/77 (18%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
V + F + + I + R +A+V F E + AL
Sbjct: 40 VVAFFGQHCPIT------GGKEGILFVTY--------PDGRPTGDAFVLFACEEYAQNAL 85
Query: 114 EMNGHVIDEHTIRVDKA 130
+ ++ + I + ++
Sbjct: 86 RKHKDLLGKRYIELFRS 102
>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 = 57.7 bits (139), Expect = 2e-10
Identities = 27/173 (15%), Positives = 51/173 (29%), Gaps = 63/173 (36%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F YG+V+ V+ + K+ N A V+ + + A+ +
Sbjct: 55 LFGVYGDVQRVKI--------------------LFNKKEN--ALVQMADGNQAQLAMSHL 92
Query: 116 NGHVIDEHTIRVDKALTTTKSN------------------------------------SH 139
NGH + IR+ + S
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++ + NIP EE+L+ F S G + + + + + EE
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEE 201
>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 = 55.7 bits (134), Expect = 2e-10
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 3/80 (3%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFKAEE 191
+N + + +PF +EE+ + F + + + L D I G +V F A +
Sbjct: 37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKI-TGEAFVQF-ASQ 94
Query: 192 EELRKAFESCGEIDNVRLIR 211
E KA E R I
Sbjct: 95 ELAEKALGKHKERIGHRYIE 114
Score = 44.1 bits (104), Expect = 4e-06
Identities = 16/77 (20%), Positives = 24/77 (31%), Gaps = 17/77 (22%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ F V I + E + A+V+F + E EKAL
Sbjct: 59 IVQFFSGLEIVPN-----------------GITLPVDPEGKITGEAFVQFASQELAEKAL 101
Query: 114 EMNGHVIDEHTIRVDKA 130
+ I I V K+
Sbjct: 102 GKHKERIGHRYIEVFKS 118
Score = 36.0 bits (83), Expect = 0.003
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 187 FKAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFK 227
F +EE+ + F + + + L D I G +V F
Sbjct: 52 FGCTKEEIVQFFSGLEIVPNGITLPVDPEGKI-TGEAFVQFA 92
>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 = 54.5 bits (132), Expect = 3e-10
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S +FIGN+P EA E+E+R FE G++ +I K +G+V+ + +
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54
Score = 37.2 bits (87), Expect = 5e-04
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 11/46 (23%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ +A E+E+R FE G++ +I K +G+V+
Sbjct: 12 FIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHI 49
Score = 27.9 bits (63), Expect = 1.0
Identities = 5/33 (15%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
+V ++ + E A+ ++ + + I V+ +
Sbjct: 45 GFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77
>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 = 54.2 bits (131), Expect = 3e-10
Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++G + E +LR F GEI + +++ + ++ F +
Sbjct: 11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQA 60
Score = 41.1 bits (97), Expect = 2e-05
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 6/45 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + E +LR F GEI + +++ + ++ F
Sbjct: 18 GGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA 56
Score = 38.4 bits (90), Expect = 2e-04
Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 25/74 (33%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE- 114
+ F +GE+ T+ + R+ C A+++F ++ E A E
Sbjct: 31 NHFYQFGEIRTITV---------VQRQQC--------------AFIQFATRQAAEVAAEK 67
Query: 115 -MNGHVIDEHTIRV 127
N +++ + V
Sbjct: 68 SFNKLIVNGRRLNV 81
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 54.0 bits (130), Expect = 5e-10
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ S++I P +A +++++ E G++ N+++ R H KG +V F + E
Sbjct: 8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIES 64
Score = 40.5 bits (95), Expect = 5e-05
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 180 KGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
KGF A +++++ E G++ N+++ R H KG +V F
Sbjct: 17 KGFPT---DATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFD 60
Score = 37.4 bits (87), Expect = 5e-04
Identities = 12/72 (16%), Positives = 25/72 (34%), Gaps = 18/72 (25%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEM 115
+ G+V ++ M + K + +V F ++ES +K +E
Sbjct: 30 EWLEDKGQVLNIQ------------------MRRTLHKAFKGSIFVVFDSIESAKKFVET 71
Query: 116 NGHVIDEHTIRV 127
G E + +
Sbjct: 72 PGQKYKETDLLI 83
>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 = 54.4 bits (131), Expect = 6e-10
Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 7/68 (10%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++ + I N+P E+++ F G + V L G V F E
Sbjct: 5 SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEF-LEPL 57
Query: 193 ELRKAFES 200
E RKAF
Sbjct: 58 EARKAFRH 65
Score = 34.8 bits (80), Expect = 0.005
Identities = 8/40 (20%), Positives = 12/40 (30%), Gaps = 6/40 (15%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+++ F G + V L G V F
Sbjct: 20 AGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEF 53
Score = 29.0 bits (65), Expect = 0.60
Identities = 9/75 (12%), Positives = 15/75 (20%), Gaps = 24/75 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
F +G + V A V F KA +
Sbjct: 30 TFSRFGSLGRVLLP---------EGGIT--------------AIVEFLEPLEARKAFRHL 66
Query: 116 NGHVIDEHTIRVDKA 130
+ ++ A
Sbjct: 67 AYSKFHHVPLYLEWA 81
>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 = 54.5 bits (131), Expect = 6e-10
Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 5/80 (6%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESC---GEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+ + + +P+ E+++ C + V I + G +V E
Sbjct: 14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVEL-ESE 71
Query: 192 EELRKAFESCGEIDNVRLIR 211
++++ A + E R I
Sbjct: 72 DDVKLALKKDRESMGHRYIE 91
Score = 37.6 bits (87), Expect = 6e-04
Identities = 10/46 (21%), Positives = 21/46 (45%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+ E R + A+V ++ + V+ AL+ + + I V K+
Sbjct: 50 VHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKS 95
Score = 36.4 bits (84), Expect = 0.002
Identities = 6/44 (13%), Positives = 14/44 (31%), Gaps = 4/44 (9%)
Query: 187 FKAEEEELRKAFESC---GEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ E+++ C + V I + G +V +
Sbjct: 27 WSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVELE 69
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 54.9 bits (132), Expect = 9e-10
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++GN+ + EL +AF G + +V + R+ GF +V F+ +
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRD 122
Score = 39.5 bits (92), Expect = 2e-04
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + EL +AF G + +V + R+ GF +V F+
Sbjct: 79 GNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFE 118
Score = 30.2 bits (68), Expect = 0.27
Identities = 8/33 (24%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
A+V F++ A+ E++G + +RV+ +
Sbjct: 113 AFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>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 = 53.4 bits (129), Expect = 9e-10
Identities = 8/56 (14%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ +++G + L + F+ G I + ++ G F Y+ +++ +
Sbjct: 16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK------GDSFAYIQYESLDA 65
Score = 39.5 bits (93), Expect = 7e-05
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 6/44 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + L + F+ G I + ++ G F Y+ +
Sbjct: 23 GGLGPNTSLAALAREFDRFGSIRTIDHVK------GDSFAYIQY 60
Score = 38.4 bits (90), Expect = 2e-04
Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 32/89 (35%)
Query: 51 LSSVTS------MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFK 104
L TS F +G + T+ + + AY++++
Sbjct: 25 LGPNTSLAALAREFDRFGSIRTIDH---------VKGDSF--------------AYIQYE 61
Query: 105 NLESVEKAL-EMNGHVID--EHTIRVDKA 130
+L++ + A +M G + + +RVD A
Sbjct: 62 SLDAAQAACAKMRGFPLGGPDRRLRVDFA 90
>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 = 55.1 bits (132), Expect = 1e-09
Identities = 25/173 (14%), Positives = 53/173 (30%), Gaps = 28/173 (16%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F YG VE V+F + K A V + +V++A+ +
Sbjct: 25 VFCLYGNVEKVKF--------------------MKSKPGA--AMVEMADGYAVDRAITHL 62
Query: 116 NGHVIDEHTIRVD--KALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRD 173
N + + + V K S+ + G+ ++ E F + + R+
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122
Query: 174 QHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ F + EE + + G + + G + +
Sbjct: 123 SNVLH---FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEW 172
Score = 31.2 bits (70), Expect = 0.17
Identities = 5/76 (6%), Positives = 18/76 (23%), Gaps = 18/76 (23%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ G +K+ +R++ + + + + L
Sbjct: 140 FFEICDELGVKRPTS----------------VKVFSGKSERSSS-GLLEWDSKSDALETL 182
Query: 114 -EMNGHVIDEHTIRVD 128
+N + +
Sbjct: 183 GFLNHYQMKNPNGPYP 198
>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 = 53.7 bits (129), Expect = 1e-09
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 3/72 (4%)
Query: 128 DKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
D T + H + + +P++A E ++ F V + + G V F
Sbjct: 36 DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRV-TGEADVEF 93
Query: 188 KAEEEELRKAFE 199
A EE A
Sbjct: 94 -ATHEEAVAAMS 104
Score = 40.2 bits (94), Expect = 1e-04
Identities = 12/70 (17%), Positives = 20/70 (28%), Gaps = 8/70 (11%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
F + + + + R A V F E A+ + + I +
Sbjct: 67 FSPLNPVRVHIEIG--------PDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELF 118
Query: 129 KALTTTKSNS 138
TT SN
Sbjct: 119 LNSTTGASNG 128
Score = 36.0 bits (83), Expect = 0.003
Identities = 8/41 (19%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+KA E ++ F V + + G V F
Sbjct: 56 YKATENDIYNFFSPLN-PVRVHIEIGPDGRV-TGEADVEFA 94
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 52.8 bits (127), Expect = 2e-09
Identities = 8/58 (13%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + I NIP + E L G +++ + V + ++++
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQ 66
Score = 40.5 bits (95), Expect = 4e-05
Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 21/84 (25%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ S+ YG VE+ +V+ V + + + +AL
Sbjct: 32 LDSLLVQYGVVESCE--------------------QVNTDSETAVVNVTYSSKDQARQAL 71
Query: 114 E-MNGHVIDEHTIRVDKALTTTKS 136
+ +NG ++ T++V +
Sbjct: 72 DKLNGFQLENFTLKVAYIPDEMAA 95
Score = 35.5 bits (82), Expect = 0.002
Identities = 4/44 (9%), Positives = 11/44 (25%), Gaps = 3/44 (6%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ + E L G +++ + V +
Sbjct: 21 RNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTY 61
>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 = 53.5 bits (128), Expect = 2e-09
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 3/88 (3%)
Query: 126 RVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFG 183
R L + + +P+ E+++ C D + +T G G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIR 211
+V E++++ A + E R I
Sbjct: 92 FVEL-GSEDDVKMALKKDRESMGHRYIE 118
Score = 37.7 bits (87), Expect = 8e-04
Identities = 10/46 (21%), Positives = 20/46 (43%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+ E R + A+V + + V+ AL+ + + I V K+
Sbjct: 77 VHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKS 122
Score = 36.9 bits (85), Expect = 0.001
Identities = 7/48 (14%), Positives = 15/48 (31%), Gaps = 2/48 (4%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFK 227
+ + E+++ C D + +T G G +V
Sbjct: 49 LRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELG 96
>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 = 54.1 bits (130), Expect = 3e-09
Identities = 31/195 (15%), Positives = 60/195 (30%), Gaps = 67/195 (34%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F YG+V+ V+ + K+ N A V+ + + A+ +
Sbjct: 24 LFGVYGDVQRVKI--------------------LFNKKEN--ALVQMADGNQAQLAMSHL 61
Query: 116 NGHVIDEHTIRVDKALTTTKSN------------------------------------SH 139
NGH + IR+ + S
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++ + NIP EE+L+ F S G + + + + + EE A +
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEE----AVQ 173
Query: 200 SCGEIDNVRLIRDQH 214
+ ++ N L + H
Sbjct: 174 ALIDLHNHDLGENHH 188
Score = 38.3 bits (89), Expect = 8e-04
Identities = 8/57 (14%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 137 NSHSIFIGNI-PFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + + N+ P + L F G++ V+++ ++ K V +
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQ 53
Score = 28.3 bits (63), Expect = 1.7
Identities = 6/37 (16%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ L F G++ V+++ ++ K V
Sbjct: 18 PQSLFILFGVYGDVQRVKILFNK-----KENALVQMA 49
>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 = 51.9 bits (125), Expect = 4e-09
Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
T S+ +++ N+ EE + K F + R+ + + + +V+F + E+
Sbjct: 11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHF-SNRED 63
Query: 194 LRKAFES 200
+A ++
Sbjct: 64 AVEAMKA 70
Score = 36.9 bits (86), Expect = 9e-04
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+V F N E +A++ +NG V+D I V A
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
Score = 34.9 bits (81), Expect = 0.003
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 9/46 (19%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV EE + K F + R+ + + + +V+F
Sbjct: 19 YVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHF 58
>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 = 51.5 bits (124), Expect = 4e-09
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+F+G + E+ELR+ F G++ +V + + + F +V F ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQ 53
Score = 35.7 bits (83), Expect = 0.001
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G E+ELR+ F G++ +V + + + F +V F
Sbjct: 11 GRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFA 50
Score = 32.2 bits (74), Expect = 0.030
Identities = 5/32 (15%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
A+V F + + + +I ++ + A
Sbjct: 45 AFVTFADDQIAQSLCG-EDLIIKGISVHISNA 75
>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 = 51.5 bits (124), Expect = 4e-09
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S + +GNI +ELR FE G + +++ + +V+ + E+
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAED 56
Score = 34.9 bits (81), Expect = 0.003
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 11/46 (23%)
Query: 184 YV---NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+V + +ELR FE G + +++ + +V+
Sbjct: 14 HVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHM 51
Score = 28.4 bits (64), Expect = 0.66
Identities = 5/33 (15%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A+V + E +A+ ++ + V +
Sbjct: 47 AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 51.9 bits (124), Expect = 4e-09
Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEEEE 193
S S +F+G +P + +E+E+ +F G + + + + KG+ ++ F+ EE
Sbjct: 6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ-EESS 64
Query: 194 LRKAFESCGEIDN 206
++ ++C E D
Sbjct: 65 VQALIDACLEEDG 77
Score = 33.4 bits (76), Expect = 0.018
Identities = 7/39 (17%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFK 227
E+E+ +F G + + + + KG+ ++ F+
Sbjct: 22 EDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 53.3 bits (128), Expect = 5e-09
Identities = 8/58 (13%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + N+ F + ++++ F G + + D+ + G V+F+ +
Sbjct: 85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRAD 141
Score = 37.1 bits (86), Expect = 0.002
Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
F + ++++ F G + + D+ + G V+F+
Sbjct: 98 FGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE 137
>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 = 50.7 bits (122), Expect = 7e-09
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+F+G + EEL++ F GE+ +V + + + F +V F ++
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDK 59
Score = 36.8 bits (86), Expect = 7e-04
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 173 DQHTNIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
H + K F G EEL++ F GE+ +V + + + F +V F
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFA 56
Score = 31.0 bits (71), Expect = 0.074
Identities = 5/32 (15%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
A+V F + + + +I ++ + A
Sbjct: 51 AFVTFADDKVAQSLCG-EDLIIKGISVHISNA 81
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 50.5 bits (121), Expect = 8e-09
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL-----IRDQHTNIGKGFGYVNFKAEE 191
++ +++GNIPF EE + F + + + + N K F ++ F++ +
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 192 E 192
E
Sbjct: 65 E 65
Score = 34.3 bits (79), Expect = 0.005
Identities = 6/51 (11%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 77 ITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
P + + +K A++ F++++ +A+ +G + ++++
Sbjct: 37 TQAPGNPVLAVQINQDKNF---AFLEFRSVDETTQAMAFDGIIFQGQSLKI 84
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 50.1 bits (120), Expect = 1e-08
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 141 IFIGNIP------FEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
I + P ++ L F G++ N+ D+ T KGF +V + +
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66
Score = 40.5 bits (95), Expect = 4e-05
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++ L F G++ N+ D+ T KGF +V
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECG 62
>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 = 50.2 bits (120), Expect = 2e-08
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK--GFGYVNFKAEEEE 193
+ I +P+ E++ F C + I GK G + E++
Sbjct: 9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEM-ESEQD 67
Query: 194 LRKAFESCGEIDNVRLIR 211
++KA E R +
Sbjct: 68 VQKALEKHRMYMGQRYVE 85
Score = 36.8 bits (85), Expect = 0.001
Identities = 8/46 (17%), Positives = 21/46 (45%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
I + + +A + ++ + V+KALE + + + + V +
Sbjct: 44 IHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEI 89
Score = 34.1 bits (78), Expect = 0.009
Identities = 7/43 (16%), Positives = 13/43 (30%), Gaps = 2/43 (4%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGK--GFGYVNFK 227
+ E++ F C + I GK G + +
Sbjct: 21 WSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEME 63
>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 = 49.5 bits (118), Expect = 3e-08
Identities = 16/105 (15%), Positives = 38/105 (36%), Gaps = 12/105 (11%)
Query: 123 HTIRVDKALTTTKSNSHSIFIGN--IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK 180
HT+ + + T + S+ + N + +L E CG +D + + K
Sbjct: 10 HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NK 63
Query: 181 GFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 225
+ + ++ EE + + ++ ++ D I +V
Sbjct: 64 PYSFARYRTTEE----SKRAYVTLNGKEVVDDLGQKITLYLNFVE 104
Score = 30.7 bits (69), Expect = 0.13
Identities = 9/65 (13%), Positives = 21/65 (32%), Gaps = 24/65 (36%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+ + G V+ + P K ++ R++ E ++A +
Sbjct: 47 VLEKCGLVDALLM---------PPNKPY--------------SFARYRTTEESKRAYVTL 83
Query: 116 NGHVI 120
NG +
Sbjct: 84 NGKEV 88
>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 = 48.6 bits (116), Expect = 6e-08
Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 135 KSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+ + + + + +P ++L+ G++ + RD G G V F +E++
Sbjct: 12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF-VRKEDM 63
Query: 195 RKA 197
A
Sbjct: 64 TYA 66
Score = 29.4 bits (66), Expect = 0.38
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 7/44 (15%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++L+ G++ + RD G G V F
Sbjct: 21 SGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF 57
Score = 28.2 bits (63), Expect = 1.1
Identities = 5/33 (15%), Positives = 9/33 (27%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
V F E + A+ ++ H
Sbjct: 53 GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI 85
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 48.4 bits (116), Expect = 6e-08
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 138 SHSIFIGNIPFEAEEEELRKA----FESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
+H+I+I N+ + +++EL+K+ F G+I ++ + R +G +V FK E
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK-EVSS 63
Query: 194 LRKAFES 200
A S
Sbjct: 64 ATNALRS 70
Score = 35.7 bits (83), Expect = 0.002
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 184 YV---NFKAEEEELRKA----FESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
Y+ N K +++EL+K+ F G+I ++ + R +G +V FK
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 59
Score = 31.4 bits (72), Expect = 0.061
Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 25/90 (27%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA 112
S+ ++F +G++ DI + R + A+V FK + S A
Sbjct: 28 SLHAIFSRFGQIL----------DILVSR----------SLKMRGQAFVIFKEVSSATNA 67
Query: 113 L-EMNGHVIDEHTIRVDKALTTTKSNSHSI 141
L M G + +R+ A K++S I
Sbjct: 68 LRSMQGFPFYDKPMRIQYA----KTDSDII 93
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 48.3 bits (115), Expect = 7e-08
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S I I +P + E E+ G++ N+ +++ K ++ EE
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEA 64
Score = 32.5 bits (74), Expect = 0.028
Identities = 5/44 (11%), Positives = 15/44 (34%), Gaps = 6/44 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ E E+ G++ N+ +++ K ++
Sbjct: 22 RKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEM 59
Score = 27.1 bits (60), Expect = 2.5
Identities = 15/94 (15%), Positives = 27/94 (28%), Gaps = 30/94 (31%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
V S+ P+G+V + L K A++ E+ +
Sbjct: 33 VISLGLPFGKVTNLLM---------LKGKNQ--------------AFIEMNTEEAANTMV 69
Query: 114 E---MNGHVIDEHTIRVD----KALTTTKSNSHS 140
V+ I + K L T S + +
Sbjct: 70 NYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 103
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 49.8 bits (118), Expect = 9e-08
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
S++I P +A +++++ E G++ N+++ R H KG +V F E +K
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFD-SIESAKKFV 167
Query: 199 E 199
E
Sbjct: 168 E 168
Score = 39.4 bits (91), Expect = 4e-04
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
A +++++ E G++ N+++ R H KG +V F
Sbjct: 121 ATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFD 158
Score = 39.0 bits (90), Expect = 4e-04
Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 18/82 (21%)
Query: 46 SKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKN 105
+ L + + G+V ++ R + K + +V F +
Sbjct: 118 PTDATLDDIKEWLEDKGQVLNIQMR------------------RTLHKAFKGSIFVVFDS 159
Query: 106 LESVEKALEMNGHVIDEHTIRV 127
+ES +K +E G E + +
Sbjct: 160 IESAKKFVETPGQKYKETDLLI 181
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 48.0 bits (114), Expect = 1e-07
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S I I +P + E E+ G++ N+ +++ K ++ EE
Sbjct: 31 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEA 79
Score = 31.8 bits (72), Expect = 0.074
Identities = 5/45 (11%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ E E+ G++ N+ +++ K ++
Sbjct: 36 IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEM 74
Score = 28.7 bits (64), Expect = 0.83
Identities = 14/94 (14%), Positives = 27/94 (28%), Gaps = 30/94 (31%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
V S+ P+G+V + + K A++ E+ +
Sbjct: 48 VISLGLPFGKVTNLLM--------------------LKGKN---QAFIEMNTEEAANTMV 84
Query: 114 E---MNGHVIDEHTIRVD----KALTTTKSNSHS 140
V+ I + K L T S + +
Sbjct: 85 NYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 118
>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 = 47.9 bits (114), Expect = 1e-07
Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
++ + + + + +P ++L+ G++ + RD G G V F +E+
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF-VRKED 63
Query: 194 LRKA 197
+ A
Sbjct: 64 MTYA 67
Score = 28.6 bits (64), Expect = 0.84
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 7/44 (15%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++L+ G++ + RD G G V F
Sbjct: 22 SGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEF 58
Score = 27.9 bits (62), Expect = 1.5
Identities = 5/33 (15%), Positives = 9/33 (27%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
V F E + A+ ++ H
Sbjct: 54 GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI 86
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 47.0 bits (112), Expect = 1e-07
Identities = 9/57 (15%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S S I + N+P ++ +E+ + ++ + + K +V E+
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQ 52
Score = 28.9 bits (65), Expect = 0.43
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 87 MNKVHEKRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+ + R A+V N E + A++ + + + V
Sbjct: 31 LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 8/59 (13%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++++ LR AF G I ++ + + +V ++ E
Sbjct: 35 APRKGNTLYVYGEDMT--PTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMES 85
Score = 42.8 bits (101), Expect = 9e-06
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 7/44 (15%)
Query: 184 YV-NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV LR AF G I ++ + + +V +
Sbjct: 43 YVYGEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTY 80
Score = 39.3 bits (92), Expect = 2e-04
Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 24/74 (32%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-EMN 116
F P+G + + P + C A+V ++ +ES ++A+ E+N
Sbjct: 58 FSPFGNIIDLSM---------DPPRNC--------------AFVTYEKMESADQAVAELN 94
Query: 117 GHVIDEHTIRVDKA 130
G ++ ++V+ A
Sbjct: 95 GTQVESVQLKVNIA 108
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 47.1 bits (112), Expect = 2e-07
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ S + I +P E E E+ G++ N+ +++ GK ++ EE
Sbjct: 11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELATEEA 63
Score = 31.3 bits (71), Expect = 0.079
Identities = 6/44 (13%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ + E E+ G++ N+ +++ GK ++
Sbjct: 21 RKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLEL 58
Score = 27.5 bits (61), Expect = 1.6
Identities = 13/92 (14%), Positives = 26/92 (28%), Gaps = 30/92 (32%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
V ++ P+G+V + L K A++ E+ +
Sbjct: 32 VIALGLPFGKVTNILM---------LKGKNQ--------------AFLELATEEAAITMV 68
Query: 114 E---MNGHVIDEHTIRVD----KALTTTKSNS 138
+ I + K L T+ +S
Sbjct: 69 NYYSAVTPHLRNQPIYIQYSNHKELKTSGPSS 100
>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 = 47.9 bits (114), Expect = 2e-07
Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEID-----NVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ I++ N+ +E++L+ F + + IR KG ++ E+
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104
Score = 35.2 bits (81), Expect = 0.007
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 184 YV---NFKAEEEELRKAFESCGEID-----NVRLIRDQHTNIGKGFGYVNFK 227
YV +E++L+ F + + IR KG ++
Sbjct: 49 YVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP 100
Score = 31.7 bits (72), Expect = 0.10
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-E 114
+F Y + + + DI L + E R A++ N ++ KAL E
Sbjct: 64 YIFGRYVDFSS--ETQRIMFDIRLMK----------EGRMKGQAFIGLPNEKAAAKALKE 111
Query: 115 MNGHVIDEHTIRVDKA 130
NG+V+ + V A
Sbjct: 112 ANGYVLFGKPMVVQFA 127
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 8/59 (13%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++++ + LR AF G I ++ + + +V ++ E
Sbjct: 11 APRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMES 61
Score = 40.7 bits (96), Expect = 3e-05
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 7/44 (15%)
Query: 184 YV-NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
YV LR AF G I ++ + + +V +
Sbjct: 19 YVYGEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTY 56
Score = 38.0 bits (89), Expect = 3e-04
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 24/75 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-EM 115
F P+G + + P + C A+V ++ +ES ++A+ E+
Sbjct: 33 AFSPFGNIIDLS---------MDPPRNC--------------AFVTYEKMESADQAVAEL 69
Query: 116 NGHVIDEHTIRVDKA 130
NG ++ ++V+ A
Sbjct: 70 NGTQVESVQLKVNIA 84
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 46.4 bits (110), Expect = 3e-07
Identities = 9/60 (15%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 133 TTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ +++GN+P +A +L++A G + +RL + ++++
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGP----RRRAFLHYPDSAA 68
Score = 32.9 bits (75), Expect = 0.019
Identities = 7/33 (21%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
A++ + + + ++A+ + G + T+RV A
Sbjct: 59 AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
Score = 28.6 bits (64), Expect = 0.51
Identities = 6/39 (15%), Positives = 16/39 (41%), Gaps = 5/39 (12%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
A +L++A G + +RL + ++++
Sbjct: 31 ARVSDLKRALRELGSVP-LRLTWQGP----RRRAFLHYP 64
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 45.9 bits (109), Expect = 5e-07
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 6/55 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S + I + E +L +A + G I V ++ K V F+
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLG 69
Score = 32.0 bits (73), Expect = 0.044
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ E +L +A + G I V ++ K V F
Sbjct: 26 IRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEF 64
Score = 25.1 bits (55), Expect = 9.7
Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 26/78 (33%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ + +G + V +P+K A V F+++ A+
Sbjct: 38 LVEALQEFGPISYVVV---------MPKKRQ--------------ALVEFEDVLGACNAV 74
Query: 114 E---MNGHVIDEHTIRVD 128
N I H V+
Sbjct: 75 NYAADNQIYIAGHPAFVN 92
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 45.2 bits (107), Expect = 1e-06
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 6/55 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
S + + + E +L +A E G I V ++ K V F+ +
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDS 63
Score = 30.1 bits (68), Expect = 0.21
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ E +L +A E G I V ++ K V F
Sbjct: 23 LCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEF 58
Score = 28.6 bits (64), Expect = 0.77
Identities = 10/92 (10%), Positives = 24/92 (26%), Gaps = 30/92 (32%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ + +G + V A V F+N++S ++ +
Sbjct: 32 LVEALEKFGTICYVMMM-----------------------PFKRQALVEFENIDSAKECV 68
Query: 114 E---MNGHVIDEHTIRVD----KALTTTKSNS 138
I + K +T ++
Sbjct: 69 TFAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100
>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 = 47.2 bits (111), Expect = 1e-06
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 138 SHSIFIGNIPFEAEEEELRKA----FESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+H+I+I N+ + +++EL+K+ F G+I ++ + R + +G +V FK
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSS 64
Score = 40.2 bits (93), Expect = 3e-04
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
H +F+ N+P E E L F VRL+ + +V F E +
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQ 256
Score = 34.9 bits (79), Expect = 0.017
Identities = 20/103 (19%), Positives = 36/103 (34%), Gaps = 23/103 (22%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-EM 115
+F +G++ + + +L + A+V FK + S AL M
Sbjct: 33 IFSQFGQILDI------LVSRSLKMRGQ--------------AFVIFKEVSSATNALRSM 72
Query: 116 NGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKA 158
G + +R+ A T S+ + G + E RK
Sbjct: 73 QGFPFYDKPMRIQYA--KTDSDIIAKMKGTFVERDRKREKRKP 113
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 44.1 bits (105), Expect = 2e-06
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 141 IFIGNIPFE-AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIGN+P + +E+L + F G I + + FG++ F +
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQS 57
Score = 31.0 bits (71), Expect = 0.090
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+L + F G I + + FG++ F
Sbjct: 22 NVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQF 52
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 44.9 bits (106), Expect = 2e-06
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 138 SHSIFIGNIPFEAEEEELRKA----FESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
S + I NI E +E+L+ S G+I ++ + G Y+ F +E
Sbjct: 29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN---SGKAYIVFA-TQES 84
Query: 194 LRKAFESC 201
+ E+
Sbjct: 85 AQAFVEAF 92
Score = 31.8 bits (72), Expect = 0.075
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 186 NFKAEEEELRKA----FESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
N + +E+L+ S G+I ++ + G Y+ F
Sbjct: 38 NPEVPKEKLQALLYALASSQGDILDIVVDLSDDN---SGKAYIVFA 80
Score = 30.6 bits (69), Expect = 0.16
Identities = 9/85 (10%), Positives = 24/85 (28%), Gaps = 21/85 (24%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA 112
+ ++ G++ + + AY+ F ES +
Sbjct: 49 LLYALASSQGDILDIVVD--------------------LSDDNSGKAYIVFATQESAQAF 88
Query: 113 LE-MNGHVIDEHTIRVDKALTTTKS 136
+E G+ + + + + T
Sbjct: 89 VEAFQGYPFQGNPLVITFSETPQSQ 113
>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 = 44.3 bits (105), Expect = 2e-06
Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 123 HTIRVDKALTTTKSNSHS----IFIGNIPFE-AEEEELRKAFESCGEIDNVRLIRDQHTN 177
++++ + T K++ S +FIGN+ ++ ++ F G + +
Sbjct: 8 MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH------ 61
Query: 178 IGKGFGYVNFKAEEE 192
KG+ +V + E
Sbjct: 62 --KGYAFVQYSNERH 74
Score = 30.4 bits (69), Expect = 0.16
Identities = 5/39 (12%), Positives = 14/39 (35%), Gaps = 8/39 (20%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ ++ F G + + KG+ +V +
Sbjct: 39 LVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQY 69
Score = 30.0 bits (68), Expect = 0.22
Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 26/76 (34%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE- 114
++F YG VA ++ K A+V++ N A+
Sbjct: 47 TIFSKYG----------RVAGCSVH-KGY--------------AFVQYSNERHARAAVLG 81
Query: 115 MNGHVIDEHTIRVDKA 130
NG V+ T+ ++ A
Sbjct: 82 ENGRVLAGQTLDINMA 97
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 44.0 bits (104), Expect = 2e-06
Identities = 12/61 (19%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRK 196
+ I + N+P ++L+ +T G G + F EE L +
Sbjct: 27 KRYRITMKNLPEGCSWQDLKDLARENS---LETTFSSVNTRDFDGTGALEF-PSEEILVE 82
Query: 197 A 197
A
Sbjct: 83 A 83
Score = 34.8 bits (80), Expect = 0.005
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRV 127
V+ + + + F + E + +ALE +N I V
Sbjct: 60 SVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
>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 = 43.7 bits (103), Expect = 3e-06
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESC---GEIDNVRLIRDQHTNIGK---GFGYVNFKAEEEEL 194
+F+ + + E+ K E G+I V + + YV + E+ L
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 195 R 195
R
Sbjct: 78 R 78
Score = 42.9 bits (101), Expect = 8e-06
Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 20/103 (19%)
Query: 39 MNPSLTKSKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN 98
++ L + + F +G++ + + + + + +
Sbjct: 23 LSQRLA---DPEVLKRPEYFGKFGKIH----------KVVINNS----TSYAGSQGPSAS 65
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNSHS 140
AYV + E +A++ +N V+D T++ TTK S+S
Sbjct: 66 AYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG--TTKYCSYS 106
Score = 32.1 bits (73), Expect = 0.045
Identities = 8/51 (15%), Positives = 17/51 (33%), Gaps = 6/51 (11%)
Query: 183 GYVNFKAEEEELRKAFESC---GEIDNVRLIRDQHTNIGK---GFGYVNFK 227
++ + + E+ K E G+I V + + YV +
Sbjct: 21 VGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 41.6 bits (98), Expect = 1e-05
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 141 IFIGNIP------FEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
I + N+P E + + K F G+I N + KG+ ++ + +
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59
Score = 32.4 bits (74), Expect = 0.022
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + K F G+I N + KG+ ++ +
Sbjct: 21 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYA 55
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 42.4 bits (100), Expect = 1e-05
Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 8/58 (13%)
Query: 141 IFIGNIPFEAEE------EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
I + N+P + + K F G+I N + KG+ ++ + +
Sbjct: 18 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73
Score = 31.6 bits (72), Expect = 0.068
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ + K F G+I N + KG+ ++ +
Sbjct: 35 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYA 69
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 12/78 (15%)
Query: 116 NGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFE-AEEEELRKAFESCGEIDNVRLIRDQ 174
+ H H+ + +FIGN+P + +E+L + F G I + +
Sbjct: 3 SSHHHHHHS---SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--- 56
Query: 175 HTNIGKGFGYVNFKAEEE 192
FG++ F +
Sbjct: 57 -----NAFGFIQFDNPQS 69
Score = 28.8 bits (65), Expect = 0.46
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+L + F G I + + FG++ F
Sbjct: 34 NVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQF 64
>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 = 41.4 bits (96), Expect = 2e-04
Identities = 36/279 (12%), Positives = 82/279 (29%), Gaps = 84/279 (30%)
Query: 14 PTQNRN-LMSKLKV-----FLNIWKMALKLKMNPSLT--------KS--KNHALSSVTSM 57
N N + +K V +L + + L+L+ ++ K+ S
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177
Query: 58 FKPYGEVE--TVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEM 115
K ++ ++ + P + + +K +++ R++ ++ ++ + S++ L
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL-RIHSIQAELRR 236
Query: 116 --------NG-----HVIDEHTIRV-D---KALTTTKSNSHSIFIGN-----IPFEA--- 150
N +V + + K L TT+ + F+ I +
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 151 --EEEELRKAFESCGEIDNVRL------------------IRDQHTNIGKGFGYVNFKA- 189
+E++ + L IRD + +VN
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD-GLATWDNWKHVNCDKL 355
Query: 190 -----------EEEELRKAFESCGEIDNVRLIRDQHTNI 217
E E RK F+ + +I
Sbjct: 356 TTIIESSLNVLEPAEYRKMFDRLS-------VFPPSAHI 387
Score = 36.0 bits (82), Expect = 0.010
Identities = 25/184 (13%), Positives = 51/184 (27%), Gaps = 62/184 (33%)
Query: 3 IIKNFL--SLTMIPTQNRNLMSKLKVFLNIWKMALKLKMNPSLTKSKNHALSSVTSMFKP 60
F ++ T+ + + L ++L + +LT + +L
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSA-ATTTHISLD-HHSMTLTPDEVKSLLL------- 308
Query: 61 YGEVETVRFRSVPVADITLPRKAC------IKMNKVHEKRTNMNAYVRFKNLESVEKALE 114
++ D LPR+ + + + E + A + N + V
Sbjct: 309 -------KYLDCRPQD--LPREVLTTNPRRLSI--IAESIRDGLA--TWDNWKHVNC--- 352
Query: 115 MNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQ 174
LTT +S ++ E E RK F+ +
Sbjct: 353 --------------DKLTTIIESSLNVL--------EPAEYRKMFDRLS-------VFPP 383
Query: 175 HTNI 178
+I
Sbjct: 384 SAHI 387
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 40.5 bits (94), Expect = 2e-04
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 15/65 (23%)
Query: 137 NSHSIFIGNIPF---------EAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ ++++G I E +R F G+ID +R + K G+V F
Sbjct: 133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKF 186
Query: 188 KAEEE 192
K +
Sbjct: 187 KYQAN 191
Score = 38.2 bits (88), Expect = 0.001
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 24/72 (33%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F G+++ +R+ + K C +V+FK + E A E M
Sbjct: 163 VFSRLGDIDRIRY---------VESKNC--------------GFVKFKYQANAEFAKEAM 199
Query: 116 NGHVIDEHTIRV 127
+ + + +
Sbjct: 200 SNQTLLLPSDKE 211
Score = 34.8 bits (79), Expect = 0.016
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++ E +R F G+ID +R + K G+V FK
Sbjct: 148 SKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFK 187
>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 = 34.1 bits (78), Expect = 0.008
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 7/66 (10%)
Query: 128 DKALTTTKSNSHSIFIGNIPFEA-EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 186
D+ + I + N+P + + K E G+I N L+R K ++
Sbjct: 15 DQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIE 68
Query: 187 FKAEEE 192
+ E+
Sbjct: 69 METRED 74
Score = 25.7 bits (56), Expect = 7.2
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 6/36 (16%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ + K E G+I N L+R K ++
Sbjct: 40 DSAVLKLAEPYGKIKNYILMR------MKSQAFIEM 69
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 32.2 bits (73), Expect = 0.040
Identities = 7/55 (12%), Positives = 18/55 (32%), Gaps = 3/55 (5%)
Query: 93 KRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIP 147
+R + F+ E+ L H + + + A + + + +P
Sbjct: 44 QRLGCGGVLTFREPADAERVLAQADHELHGAQLSLRPAPPRAPAR---LLLQGLP 95
Score = 31.8 bits (72), Expect = 0.048
Identities = 8/57 (14%), Positives = 20/57 (35%), Gaps = 13/57 (22%)
Query: 140 SIFIGNIPFEAEEEELRKAFESC-----GEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++ + +P +E L FE+ G + + + + G + F+
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPA 58
>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 = 32.8 bits (74), Expect = 0.070
Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 8/72 (11%)
Query: 123 HTIRVDKALTTTKSNSHSIFIGN--IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK 180
HT+ + + T + S+ + N + +L E CG +D + K
Sbjct: 3 HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNK 56
Query: 181 GFGYVNFKAEEE 192
+ + ++ EE
Sbjct: 57 PYSFARYRTTEE 68
Score = 27.0 bits (59), Expect = 5.4
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 11/51 (21%)
Query: 177 NIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
N G G G +L E CG +D + K + + ++
Sbjct: 25 NGGLGNG-----VSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYR 64
>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 = 30.2 bits (68), Expect = 0.17
Identities = 7/60 (11%), Positives = 16/60 (26%), Gaps = 7/60 (11%)
Query: 134 TKSNSHSIFIGNIPFE-AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ I + +L + E G I N ++ ++ E+
Sbjct: 11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTED 64
>2x7v_A Probable endonuclease 4; DNA repair protein, metal-binding,
hydrolase, DNA damage, DN; 2.30A {Thermotoga maritima
MSB8} PDB: 2x7w_A*
Length = 287
Score = 31.0 bits (70), Expect = 0.33
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 153 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE-EELRKAFESCGEIDNVRLI- 210
E+L+K + R+ T G GY K E E L ES ++ +++I
Sbjct: 158 EQLKKIRDLVD--QRDRVAITYDTCHGFDSGYDITKKEGVEALLNEIESLFGLERLKMIH 215
Query: 211 -----------RDQHTNIGKGF 221
+D+H IG GF
Sbjct: 216 LNDSKYPLGAAKDRHERIGSGF 237
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 29.2 bits (65), Expect = 0.64
Identities = 5/52 (9%), Positives = 15/52 (28%), Gaps = 4/52 (7%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
I + N+ + + L + F G + + + + +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ----FQALLQYADPVS 78
Score = 26.5 bits (58), Expect = 5.5
Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 24/75 (32%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F +G V + K A +++ + S + A +
Sbjct: 48 IFSKFGTVLKIITF---------------------TKNNQFQALLQYADPVSAQHAKLSL 86
Query: 116 NGHVI--DEHTIRVD 128
+G I T+R+D
Sbjct: 87 DGQNIYNACCTLRID 101
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.88
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 11/40 (27%)
Query: 47 KNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIK 86
K AL + + K Y + S P I KA ++
Sbjct: 19 KQ-ALKKLQASLKLYAD------DSAPALAI----KATME 47
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 28.1 bits (62), Expect = 1.1
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 91 HEKRTNMN-AYVRFKNLESVEKALEMNGHVIDEHTI 125
H N ++R+++ KAL +G + E +
Sbjct: 53 HVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIM 88
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 28.2 bits (62), Expect = 1.2
Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 5/80 (6%)
Query: 49 HALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN-AYVRFKNLE 107
+ V + F+ +G + V ++ + + + + + N
Sbjct: 18 TMANQVIAYFQEFGTI----LEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPA 73
Query: 108 SVEKALEMNGHVIDEHTIRV 127
S AL NG V + + V
Sbjct: 74 SAVDALLENGAVFNGVLLGV 93
>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 = 27.8 bits (61), Expect = 2.0
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALE-MNGHVI--DEHTIRVD 128
+ K A +++ + S + A ++G I T+R+D
Sbjct: 73 VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID 119
>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 = 28.5 bits (63), Expect = 2.5
Identities = 36/218 (16%), Positives = 67/218 (30%), Gaps = 72/218 (33%)
Query: 8 LSLT--------MIPTQNRNLMSKLKVFLNIWKMALKLKMNPSLTKSKNHALSSVTSMFK 59
L+L+ ++PT + +A +L+ K + +
Sbjct: 9 LTLSHGSLEHVLLVPT-------------ASFFIASQLQ--EQFNKILPEPTEGFAADDE 53
Query: 60 PYGEVE-TVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE---M 115
P E +F V+ V + V L E +
Sbjct: 54 PTTPAELVGKFLGY-VSS------------LVEPSKVGQFDQV----LNLCLTEFENCYL 96
Query: 116 NGHVIDEHTI--RVDKALTTTKSNSHSIF--------IGNIPFEAEEE-ELRKAFESCGE 164
G+ D H + ++ + TT + + + PF+ + L F + GE
Sbjct: 97 EGN--DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL---FRAVGE 151
Query: 165 IDNVRLIRDQHTNIGKGFGYVN--FKAEEEELRKAFES 200
N +L+ G G G + F EELR +++
Sbjct: 152 -GNAQLV----AIFG-GQGNTDDYF----EELRDLYQT 179
>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 = 27.0 bits (60), Expect = 3.1
Identities = 5/30 (16%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALE-MNG 117
+ ++ + A V F++ E + ++ ++G
Sbjct: 57 LLFDRHPDGVASVSFRDPEEADYCIQTLDG 86
>1g61_A EIF-6, translation initiation factor 6; alpha-beta-barrel velcro
closure subdomain, structural genomics, PSI; 1.30A
{Methanocaldococcus jannaschii} SCOP: d.126.1.1
Length = 228
Score = 27.2 bits (60), Expect = 4.4
Identities = 8/43 (18%), Positives = 21/43 (48%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG 179
N + + + I + E + ++ + NV +I+ ++T +G
Sbjct: 66 NKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALG 108
>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 = 26.0 bits (57), Expect = 5.3
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 98 NAYVRFKNLESVEKALE-MNGHVIDEHTIRVD 128
N YV+F+ E EKA+ +N + I +
Sbjct: 70 NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
>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 = 25.8 bits (57), Expect = 7.2
Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALE-MNG 117
V + N YV+ ++ + A+ ++G
Sbjct: 48 YVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77
>3tsz_A Tight junction protein ZO-1; PDZ3-SH3-GUK, scaffolding, JAM, tight
junction, cell adhesio; 2.50A {Homo sapiens} PDB: 3tsw_A
3lh5_A
Length = 391
Score = 26.7 bits (58), Expect = 7.8
Identities = 11/98 (11%), Positives = 32/98 (32%), Gaps = 12/98 (12%)
Query: 80 PRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSH 139
P I ++ + T+ + L ++++ ++ + H + + T L +
Sbjct: 254 PDIYQIAKSEPRDAGTDQRSS-GIIRLHTIKQIIDQDKHALLDVTPNAVDRLNYAQWYPI 312
Query: 140 SIFI-----------GNIPFEAEEEELRKAFESCGEID 166
+F+ + RK +E ++
Sbjct: 313 VVFLNPDSKQGVKTMRMRLCPESRKSARKLYERSHKLR 350
>3fk4_A Rubisco-like protein; structural genomics, target 9463A, PSI-2,
protein structure initiative; 2.00A {Bacillus cereus
atcc 14579}
Length = 414
Score = 26.5 bits (58), Expect = 8.4
Identities = 4/17 (23%), Positives = 7/17 (41%)
Query: 149 EAEEEELRKAFESCGEI 165
E ++ L A + G
Sbjct: 392 EVDDINLHSALQIWGNP 408
>3aam_A Endonuclease IV, endoiv; DNA repair, base excision repair, BER, TIM
barrel, endonucle hydrolase, structural genomics,
NPPSFA; 1.58A {Thermus thermophilus}
Length = 270
Score = 26.3 bits (58), Expect = 8.7
Identities = 7/51 (13%), Positives = 18/51 (35%), Gaps = 13/51 (25%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLI------------RDQHTNIGKGF 221
GY + + + A + ++ V ++ D H ++ +G
Sbjct: 177 GY-DVAEDPLGVLDALDRAVGLERVPVVHLNDSVGGLGSRVDHHAHLLQGK 226
>3shw_A Tight junction protein ZO-1; PDZ-SH3-GUK supramodule, cell
adhesion; 2.90A {Homo sapiens}
Length = 468
Score = 26.4 bits (57), Expect = 9.1
Identities = 21/161 (13%), Positives = 50/161 (31%), Gaps = 26/161 (16%)
Query: 31 WKMALKLKMNPSLTKSKNHALSSVTSMFKPYGEVETV---RFRSV----PVADIT----- 78
L+ ++ + V + F Y V R V P+AD+
Sbjct: 183 RFRGLRSSKRNLRKSREDLSAQPVQTKFPAYERVVLREAGFLRPVTIFGPIADVAREKLA 242
Query: 79 --LPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKS 136
P I ++ + T+ + L ++++ ++ + H + + T L +
Sbjct: 243 REEPDIYQIAKSEPRDAGTDQRSS-GIIRLHTIKQIIDQDKHALLDVTPNAVDRLNYAQW 301
Query: 137 NSHSIFIGNIPFE-----------AEEEELRKAFESCGEID 166
+F+ + + RK +E ++
Sbjct: 302 YPIVVFLNPDSKQGVKTMRMRLCPESRKSARKLYERSHKLR 342
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 25.3 bits (55), Expect = 10.0
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 142 FIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
F G++ + E+L F + GEI + +R G G + FK + +E
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGK 72
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
0.319 0.133 0.376
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: 3,503,207
Number of extensions: 202845
Number of successful extensions: 1479
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1159
Number of HSP's successfully gapped: 556
Length of query: 239
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 148
Effective length of database: 4,160,982
Effective search space: 615825336
Effective search space used: 615825336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)