RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2983
(370 letters)
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 211 bits (539), Expect = 1e-67
Identities = 47/195 (24%), Positives = 90/195 (46%), Gaps = 3/195 (1%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
M + ++ + + + + F+ G ++ + + + T + KG
Sbjct: 13 MGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGF 72
Query: 61 AYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYI 119
A++E++ PE+ LA+ +N L G I V + + R+Y+
Sbjct: 73 AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA--QPIIDQLAEEARAFNRIYV 130
Query: 120 GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
S+H ++++D ++ +FE FGKI + L DP TG+ KGYGFI + A ++ A +N F
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190
Query: 180 ELAGRPMKVGTVTDR 194
+L G+ ++VG
Sbjct: 191 DLGGQYLRVGKAVTP 205
Score = 110 bits (276), Expect = 1e-28
Identities = 31/94 (32%), Positives = 52/94 (55%), Gaps = 1/94 (1%)
Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
Q +G M +Y+GS+++ + ED +R F PFG I +I + D T + KG+ F+
Sbjct: 17 SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
+ + A+ A EQ+N L GR +KVG ++ +
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110
>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 = 206 bits (527), Expect = 3e-66
Identities = 43/185 (23%), Positives = 78/185 (42%), Gaps = 17/185 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
E +F L+ +L+ S + D+ ++ +T + Y++F+ E
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAE 65
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
+ A+ L G K+ G I ++ + ++ L +L FNITED
Sbjct: 66 DLEKALELTGLKVFGNEIKLEKPKGRDSKKVR-----------AARTLLAKNLSFNITED 114
Query: 130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
L+ +FE +I + G+SKG +I F S DA+K E+ G E+ GR + +
Sbjct: 115 ELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169
Query: 190 TVTDR 194
++
Sbjct: 170 YTGEK 174
Score = 99.2 bits (248), Expect = 5e-25
Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 2/93 (2%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
P L+IG+L+ N + L+ +++ ++ D TG ++ +G++ F SA+D +KA
Sbjct: 12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 70
Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPSNL 205
E L G ++ G +K+ R+ L
Sbjct: 71 LE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTL 102
>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 = 205 bits (523), Expect = 2e-65
Identities = 37/194 (19%), Positives = 77/194 (39%), Gaps = 12/194 (6%)
Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDPES 70
AR ++ + I + +FF++ ++ + N + + K A++EF+ +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 71 VPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTG-------GPMRLYIGSLH 123
AM +G G + ++ + G + +L+IG L
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123
Query: 124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
+ +D ++ + FG + L+ D TG SKGY F + + +A LNG +L
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 184 RPMKVGTVTDRNES 197
+ + V + ++
Sbjct: 184 KKLLVQRASVGAKN 197
Score = 93.6 bits (233), Expect = 1e-22
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 7/99 (7%)
Query: 112 GGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQL-----MVDPDTGRSKGYGFITFHS 165
G R LY+G++ F ITE+ + F ++ + ++ + K + F+ F S
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
D+ +A +G G+ +K+ D G +
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENP 98
Score = 63.9 bits (156), Expect = 3e-12
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
+ A +F L + ++E +S G ++ L+ + T KG A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIVQ-PTQAEKN 97
+ E+ D A+ GLNG +L ++VQ + KN
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
>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 = 186 bits (475), Expect = 2e-58
Identities = 38/179 (21%), Positives = 74/179 (41%), Gaps = 18/179 (10%)
Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDPES 70
AR ++ + I + +FF++ ++ + N + + K A++EF+ +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 71 VPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
AM +G G + + R + + G +L+IG L + +D
Sbjct: 64 TTQAMAFDGIIFQGQSLKI-------RRPHD------YQPLPGAHKLFIGGLPNYLNDDQ 110
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
++ + FG + L+ D TG SKGY F + + +A LNG +L + + V
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169
Score = 96.1 bits (240), Expect = 5e-24
Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 13/107 (12%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQL-----MVDPDTGRSKGYGFITFHSADDAK 170
RLY+G++ F ITE+ + F ++ + ++ + K + F+ F S D+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNES-------VGGGPSNLDTDEM 210
+A +G G+ +K+ D +GG P+ L+ D++
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 111
Score = 61.5 bits (150), Expect = 1e-11
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
A +F L + ++E +S G ++ L+ + T KG A+ E+ D
Sbjct: 89 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 148
Query: 71 VPLAM-GLNGQKLLGIPIIVQ 90
A+ GLNG +L ++VQ
Sbjct: 149 TDQAIAGLNGMQLGDKKLLVQ 169
>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 = 168 bits (428), Expect = 1e-51
Identities = 48/183 (26%), Positives = 84/183 (45%), Gaps = 22/183 (12%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT--RRFKGIAYIEFKDPESVP 72
DA +F Q+ + +DL E F G V ++ ++ + KG ++ F ++
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 73 LAM-GLNGQKLLG---IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
A L+ K+L PI ++P +EKN A +L+IG + TE
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED------------RKLFIGMISKKCTE 109
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG---FELAGRP 185
+ +R +F FG+I+ +++ PD G S+G F+TF + A+ A + ++ E P
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168
Query: 186 MKV 188
M V
Sbjct: 169 MVV 171
Score = 91.9 bits (229), Expect = 2e-22
Identities = 20/113 (17%), Positives = 46/113 (40%), Gaps = 13/113 (11%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG--RSKGYGFITFHSADDAK 170
+++++G + +E LR +FE +G + I ++ D +SKG F+TF++ A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNES-----------VGGGPSNLDTDEMER 212
+AQ L+ ++ + + +G +++
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 114
Score = 43.8 bits (104), Expect = 2e-05
Identities = 16/94 (17%), Positives = 41/94 (43%), Gaps = 5/94 (5%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +D + R +F +S++ D+ FSS G++ + R++ +G
Sbjct: 80 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGC 138
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGI---PIIVQ 90
A++ F A+ ++ + + P++V+
Sbjct: 139 AFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172
>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 = 153 bits (389), Expect = 2e-46
Identities = 69/105 (65%), Positives = 83/105 (79%)
Query: 92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
+ + N +G+ GPMRLY+GSLHFNITEDMLRGIFEPFG+I++IQLM+D +
Sbjct: 4 HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE 63
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
TGRSKGYGFITF ++ AKKA EQLNGFELAGRPMKVG VT+R +
Sbjct: 64 TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 56.2 bits (136), Expect = 3e-10
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
M A +++L ++ L I L F G++ ++L+ ++T R KG
Sbjct: 11 MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
+I F D E A+ LNG +L G P+ V
Sbjct: 71 GFITFSDSECAKKALEQLNGFELAGRPMKV 100
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 146 bits (370), Expect = 2e-43
Identities = 32/113 (28%), Positives = 52/113 (46%), Gaps = 4/113 (3%)
Query: 80 QKLLGIPIIVQPTQAEKNR----AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
+ L +P V T G+ LY+G L + + +L F
Sbjct: 25 EILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAF 84
Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +N EL GR ++V
Sbjct: 85 IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
Score = 62.1 bits (151), Expect = 4e-12
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
R ++ L++ + + L F G + D+++ +T + +G A++EF+ E
Sbjct: 57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 70 SVPLAM-GLNGQKLLGIPIIV 89
A+ +N +L G I V
Sbjct: 117 DAAAAIDNMNESELFGRTIRV 137
>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 = 142 bits (360), Expect = 2e-41
Identities = 44/174 (25%), Positives = 89/174 (51%), Gaps = 13/174 (7%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
R ++ L + I L+++F G + +++++ +K + A++E+ +A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMI-DKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 76 GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
LNG+++ + + N A + Q + L++G L+ N+ ++ LR F
Sbjct: 60 TLNGKQIENNIVKI-------NWAFQS----QQSSSDDTFNLFVGDLNVNVDDETLRNAF 108
Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
+ F + +M D TG S+GYGF++F S DDA+ A + + G +L GRP+++
Sbjct: 109 KDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
>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 = 139 bits (352), Expect = 3e-41
Identities = 69/95 (72%), Positives = 79/95 (83%), Gaps = 1/95 (1%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G LY+GSLHFNITEDMLRGIFEPFGKIDNI LM D DTGRSKGYGFITF ++ A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++A EQLNGFELAGRPM+VG VT+R + G GPS+
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDG-GSGPSS 94
Score = 57.9 bits (141), Expect = 5e-11
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ ++ L I L F GK+ ++ L+ + T R KG +I F D E A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 75 M-GLNGQKLLGIPIIV 89
+ LNG +L G P+ V
Sbjct: 64 LEQLNGFELAGRPMRV 79
>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 = 139 bits (352), Expect = 4e-41
Identities = 67/96 (69%), Positives = 82/96 (85%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+ +RR KGIAY+EF
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNT 102
+ +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR
Sbjct: 76 EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGP 111
Score = 92.0 bits (229), Expect = 3e-23
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
++ L I L F GK+ +++++ D ++ RSKG ++ F A L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGL 86
Query: 177 NGFELAGRPMKV 188
G L G P+ V
Sbjct: 87 TGQRLLGVPIIV 98
>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 = 143 bits (362), Expect = 2e-40
Identities = 40/189 (21%), Positives = 71/189 (37%), Gaps = 27/189 (14%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
+ + R+ R I L + +++ + S L C ++KG A
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE------LKYC-FVDKYKGTA 60
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
++ + E A+ + +L + V LQP L +
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSV---------------QLQPTDA----LLCVA 101
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
+L ++T+ + PFG ++ L+ TG+SKGYGF + D A +A+ L G
Sbjct: 102 NLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP 161
Query: 181 LAGRPMKVG 189
L R + V
Sbjct: 162 LGPRTLYVH 170
Score = 139 bits (352), Expect = 5e-39
Identities = 35/174 (20%), Positives = 62/174 (35%), Gaps = 13/174 (7%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
+ L + + EE G + L+ +T + KG + E+ +S A
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE-DMLRGIF 135
L G+ L + V T A + L + L + D L
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLHSR----------CLCVDRLPPGFNDVDALCRAL 206
Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
QL G+ KG+ + + +A+ A++AQ+Q +G L G ++V
Sbjct: 207 SAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 259
>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 = 138 bits (349), Expect = 2e-39
Identities = 55/229 (24%), Positives = 95/229 (41%), Gaps = 28/229 (12%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
P S + S +++ L + L E FS G + +R+ TRR G AY
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPIIV----QPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
+ F+ P A+ +N + G P+ + + K+ GN +
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN---------------I 106
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
+I +L +I L F FG I + +++ D SKGYGF+ F + + A++A E++N
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 178 GFELAGRPMKVGTVT---DRNESVGGGPSNLDTDEMERAGVDLGATGRL 223
G L R + VG +R +G ++ G++GR+
Sbjct: 165 GMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYA---GSSGRI 210
>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 = 135 bits (342), Expect = 8e-39
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 16/175 (9%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ L Q + R+L F ++G + R++ KT G A+++F A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 76 GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
LNG + + V + +T LY+ +L IT+D L IF
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDT-------------NLYVTNLPRTITDDQLDTIF 110
Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKV 188
+G I ++ D TGR +G F+ ++ ++A++A LN G +P+ V
Sbjct: 111 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 106 bits (268), Expect = 5e-28
Identities = 29/104 (27%), Positives = 49/104 (47%), Gaps = 7/104 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L ++T+ L +F G I+ ++M D TG S GY F+ F S D+++A + L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 177 NGFELAGRPMKVGTVTDRNES-------VGGGPSNLDTDEMERA 213
NG + + +KV ES V P + D+++
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 109
Score = 50.6 bits (122), Expect = 6e-08
Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 4/92 (4%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ E ++ L + I L+ F G + ++ T R +G+
Sbjct: 75 LKVSYAR-PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 133
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLG--IPIIV 89
A++ + E A+ LN G P+ V
Sbjct: 134 AFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
>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 = 134 bits (340), Expect = 1e-38
Identities = 43/174 (24%), Positives = 77/174 (44%), Gaps = 16/174 (9%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
+ L Q + + F S+G++ +L+ T + G ++ + DP+ A+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
LNG +L I V + + LY+ L +T+ L +F
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRDA-------------NLYVSGLPKTMTQKELEQLFS 110
Query: 137 PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKV 188
+G+I +++VD TG S+G GFI F +A++A + LNG + +G P+ V
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
Score = 104 bits (261), Expect = 4e-27
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 3/95 (3%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L N+T++ R +F G+I++ +L+ D TG+S GYGF+ + DA+KA L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 177 NGFELAGRPMKVGTVTDRNESVGGGP---SNLDTD 208
NG L + +KV + S+ S L
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 99
Score = 50.3 bits (121), Expect = 1e-07
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ S ++ L + + ++LE+ FS G++ R++ T +G+
Sbjct: 74 IKVSYAR-PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGI--PIIV 89
+I F A+ GLNGQK G PI V
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 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 = 135 bits (342), Expect = 2e-38
Identities = 46/195 (23%), Positives = 78/195 (40%), Gaps = 8/195 (4%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
E R +F LS L F G + D ++ T+R +G ++ + E
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
V AM K+ G + E RA + + +P ++++G + + E
Sbjct: 67 EVDAAMNARPHKVDGRVV-------EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
LR FE +GKI+ I++M D +G+ +G+ F+TF D K Q + G +V
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178
Query: 190 TVTDRNESVGGGPSN 204
+ E S
Sbjct: 179 KALSKQEMASASSSQ 193
Score = 89.7 bits (223), Expect = 2e-21
Identities = 30/118 (25%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
P+ +L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNES-------------VGGGPSNLDTDEME 211
++ A ++ GR ++ R +S VGG + + +
Sbjct: 66 EEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 122
>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 = 130 bits (328), Expect = 2e-37
Identities = 31/105 (29%), Positives = 58/105 (55%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + Q + T +++G L IT + ++ F PFG+I + +++ D TG+SKGYG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
F++F + DA+ A +Q+ G L GR ++ T + + +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105
Score = 57.0 bits (138), Expect = 2e-10
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
+F LS I T D++ F+ G++ D R++ T + KG ++ F + A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
+ GQ L G I K A + + +G
Sbjct: 77 MGGQWLGGRQIRTNWAT-RKPPAPKSTYESNTKQSGPS 113
>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 = 126 bits (318), Expect = 3e-36
Identities = 31/92 (33%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 114 PMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
P R +Y+GS+ ++ TE+ + + G + N+++M DP TGRSKGY FI F + + A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
LNG++L R +K G ++ + S +
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92
Score = 61.9 bits (151), Expect = 2e-12
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
+R ++ + + + S+VG V +++++ +T R KG A+IEF+D ES A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 76 -GLNGQKLLGIPIIVQPTQAEKNRAGN 101
LNG +L + + +
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGVS 88
>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 = 125 bits (317), Expect = 3e-36
Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDA 169
+ P +++IG L N+T+D + IF +GKI I + V+ SKGY ++ F + D+A
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNE 196
+KA + ++G ++ G+ + V
Sbjct: 61 EKALKHMDGGQIDGQEITATAVLAPWP 87
Score = 61.8 bits (151), Expect = 1e-12
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDPESVPLAM- 75
+ +L++ + + E FS+ GK++ + + KG AY+EF++P+ A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
++G ++ G I A R
Sbjct: 66 HMDGGQIDGQEITATAVLAPWPR 88
>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 = 127 bits (320), Expect = 5e-36
Identities = 30/120 (25%), Positives = 57/120 (47%), Gaps = 4/120 (3%)
Query: 90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
Q Q ++ + + P L + + + E LR +FE +G I++++++ D
Sbjct: 18 QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77
Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE----SVGGGPSNL 205
+T +S+GYGF+ F S A++A LNGF + + +KV ++ + G N
Sbjct: 78 RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137
Score = 64.4 bits (157), Expect = 8e-13
Identities = 24/120 (20%), Positives = 47/120 (39%), Gaps = 8/120 (6%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
+ ++PE R + + + L + F G + V+++ +TR+ +G
Sbjct: 27 QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYI 119
+++F+ S A+ GLNG +L + V + R G G G Y+
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA-------GAVGDGNGYL 139
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 130 bits (328), Expect = 2e-35
Identities = 27/182 (14%), Positives = 63/182 (34%), Gaps = 22/182 (12%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
++ R+ T+ L + + ++F G + V + ++ A IEF
Sbjct: 32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFA 89
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
+ A+ + + IIV + L++ + +
Sbjct: 90 RYDGALAAITKTHKVVGQNEIIV-------SHLTEC-------------TLWMTNFPPSY 129
Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
T+ +R + + + + S+ + +I S +DA+ E+LNG ++ G +
Sbjct: 130 TQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL 189
Query: 187 KV 188
Sbjct: 190 VT 191
Score = 126 bits (319), Expect = 4e-34
Identities = 34/175 (19%), Positives = 68/175 (38%), Gaps = 10/175 (5%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
T++ R++ + + V + + + AYI+ E +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 76 GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT-EDMLRGI 134
LNG K+ G ++ + + + L+ R + I +L + E++LR
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR------EIMIRNLSTELLDENLLRES 231
Query: 135 FEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
FE FG I+ I + + + F+ F + D A++A + +N L R + V
Sbjct: 232 FEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISV 285
Score = 93.5 bits (233), Expect = 5e-22
Identities = 12/95 (12%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+ + +L + ++ + F+ G I ++ + ++ + I F D A A +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITKT 101
Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEME 211
+ + + V +T+ + P + +
Sbjct: 102 HK-VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIR 135
Score = 54.6 bits (132), Expect = 1e-08
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 2/76 (2%)
Query: 17 RTIFCMQLSQRIRT-RDLEEFFSSVGKVRDVRLITCNK-TRRFKGIAYIEFKDPESVPLA 74
R I LS + L E F G + + + K A++ F++ +S A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 75 MGLNGQKLLGIPIIVQ 90
+ +N L I V
Sbjct: 271 LQMNRSLLGNREISVS 286
>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 = 123 bits (311), Expect = 2e-35
Identities = 26/79 (32%), Positives = 40/79 (50%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G LYI L T+ L + +P+GKI + + ++D T + KGYGF+ F S A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 170 KKAQEQLNGFELAGRPMKV 188
+KA L + + K
Sbjct: 61 QKAVTALKASGVQAQMAKQ 79
Score = 48.7 bits (117), Expect = 7e-08
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 1/71 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ ++ L +DL + GK+ + I T + KG +++F P + A
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 75 M-GLNGQKLLG 84
+ L +
Sbjct: 64 VTALKASGVQA 74
>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 = 123 bits (311), Expect = 3e-35
Identities = 29/84 (34%), Positives = 48/84 (57%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
G +++G L IT + F PFG+I + +++ D TG+SKGYGF++F + DA+
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 171 KAQEQLNGFELAGRPMKVGTVTDR 194
A +Q+ G L GR ++ T +
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWATRK 86
Score = 53.7 bits (130), Expect = 1e-09
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F LS I T + F+ G++ D R++ T + KG ++ F + A+ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 78 NGQKLLGIPIIV 89
GQ L G I
Sbjct: 69 GGQWLGGRQIRT 80
>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 = 123 bits (311), Expect = 6e-35
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 1/98 (1%)
Query: 92 TQAEKNRAGNTLPNLQPRGTGGP-MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
+ +P G P LY+ +L +TE L +F F + +
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61
Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
TGR +G FITF + + A +A +NG++L G+ + +
Sbjct: 62 MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI 99
Score = 62.3 bits (152), Expect = 2e-12
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ ++ LS R+ RDL F+ + + + T R +G A+I F + E A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
+NG KL G ++++ + +K R
Sbjct: 86 LVNGYKLYGKILVIEFGKNKKQR 108
>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 = 124 bits (315), Expect = 6e-35
Identities = 43/183 (23%), Positives = 81/183 (44%), Gaps = 17/183 (9%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
+++ +F L+ +L E+F G V D++++ T R +G ++ F+ P SV
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 74 AMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLR 132
+ L G I + RA PR +++G + ++
Sbjct: 61 VVK-TQHILDGKVI-------DPKRA-------IPRDEQDKTGKIFVGGIGPDVRPKEFE 105
Query: 133 GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT 192
F +G I + QLM+D DTG+S+G+GF+T+ SAD + + + R +++
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAE 164
Query: 193 DRN 195
R+
Sbjct: 165 PRH 167
Score = 62.2 bits (152), Expect = 7e-12
Identities = 16/79 (20%), Positives = 32/79 (40%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
E+ IF + +R ++ EEFFS G + D +L+ T + +G ++ + ++
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 71 VPLAMGLNGQKLLGIPIIV 89
V I +
Sbjct: 142 VDRVCQNKFIDFKDRKIEI 160
>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 = 122 bits (308), Expect = 1e-34
Identities = 28/97 (28%), Positives = 51/97 (52%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G+ G RL++ +L + +E+ L +F +G + + +D T + KG+ F+TF +
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
A KA +++G GR + V T + E+ GPS+
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
Score = 61.8 bits (151), Expect = 2e-12
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 1/91 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + +F LS DLE+ FS+ G + ++ + T++ KG A++ F PE
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
A ++GQ G + V P+ +K +
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92
>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 = 121 bits (306), Expect = 1e-34
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 108 PRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
R P L + L TE LR +F +G I ++ ++ D + RS+G+ F+ F +
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
DDAK+A+E+ NG EL GR ++V
Sbjct: 68 DDAKEAKERANGMELDGRRIRV 89
Score = 59.1 bits (144), Expect = 2e-11
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
+ LS RDL E FS G + DV ++ ++RR +G A++ F++ +
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQA 94
A NG +L G I V +
Sbjct: 70 AKEAKERANGMELDGRRIRVSGPSS 94
>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 = 120 bits (302), Expect = 6e-34
Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 3/97 (3%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSA 166
G+ G L+I +L+F+ TE+ L+G+F G I + + + S G+GF+ +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ A+KA +QL G + G ++V + G S
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97
Score = 51.9 bits (125), Expect = 7e-09
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 4/90 (4%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT---CNKTRRFKGIAYIEFKDPESV 71
+ +F L+ L+ FS VG ++ + G ++E+K PE
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 72 PLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
A+ L G + G + V+ ++ A
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISERATKPAS 93
>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 = 120 bits (303), Expect = 6e-34
Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 1/106 (0%)
Query: 89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
+ + +N + L R G L++ S+H ED ++ F +G+I NI L +
Sbjct: 2 IHSYERVRNEDDDELEPGPQRSVEG-WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60
Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
D TG SKGY + + + A A+E LNG E+ G+ ++V +
Sbjct: 61 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106
Score = 59.6 bits (145), Expect = 2e-11
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ +F + + + +++E F G+++++ L +T KG A +E++ + A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 75 M-GLNGQKLLGIPIIV 89
LNG +++G I V
Sbjct: 85 KEALNGAEIMGQTIQV 100
>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 = 119 bits (300), Expect = 1e-33
Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
L +L FNITED L+ +FE +I + G+SKG +I F S DA+K
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 68
Query: 172 AQEQLNGFELAGRPMKVGTVTDRNESVG 199
E+ G E+ GR + + ++ + G
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTGEKGGTRG 96
Score = 63.8 bits (156), Expect = 4e-13
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 6/92 (6%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + R ART+ LS I +L+E F ++R V + + KGIAYIEFK
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA 64
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
+ G ++ G + + T + G
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 120 bits (302), Expect = 1e-33
Identities = 27/113 (23%), Positives = 49/113 (43%), Gaps = 3/113 (2%)
Query: 84 GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN 143
G + P + + + + G +L + +L F +++ ++ +F FG +
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGG--GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK 64
Query: 144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
+ D +GRS G + F DA KA +Q G L GRPM + V + +
Sbjct: 65 AAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116
Score = 52.4 bits (126), Expect = 8e-09
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
L + D++E F+ G ++ + +++ R G A + F+ AM G L
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDY-DRSGRSLGTADVHFERRADALKAMKQYKGVPL 101
Query: 83 LGIPIIVQPTQAEKNR 98
G P+ +Q ++ +
Sbjct: 102 DGRPMDIQLVASQIDL 117
>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 = 118 bits (297), Expect = 2e-33
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 5/81 (6%)
Query: 113 GPM-----RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G M LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 168 DAKKAQEQLNGFELAGRPMKV 188
DA A + +N EL GR ++V
Sbjct: 61 DAAAAIDNMNESELFGRTIRV 81
Score = 60.2 bits (147), Expect = 6e-12
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
R ++ L++ + + L F G + D+++ +T + +G A++EF+ E
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 71 VPLAM-GLNGQKLLGIPIIV 89
A+ +N +L G I V
Sbjct: 62 AAAAIDNMNESELFGRTIRV 81
>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 = 118 bits (298), Expect = 4e-33
Identities = 29/90 (32%), Positives = 46/90 (51%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ +N EL GR ++V G S
Sbjct: 72 DNMNESELFGRTIRVNLAKPMRIKESGPSS 101
Score = 60.3 bits (147), Expect = 7e-12
Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S S R ++ L++ + + L F G + D+++ +T + +G A++EF
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
+ E A+ +N +L G I V + + +
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97
>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 = 118 bits (298), Expect = 4e-33
Identities = 32/104 (30%), Positives = 59/104 (56%), Gaps = 2/104 (1%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + P RL++ ++ F + LR +F FGKI +++++ + SKG+G
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFG 58
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
F+TF ++ DA +A+E+L+G + GR ++V T R + G S
Sbjct: 59 FVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102
Score = 55.0 bits (133), Expect = 6e-10
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 3/94 (3%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S S + + + + R R DL + F GK+ DV +I R KG ++ F
Sbjct: 5 SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTF 62
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
++ A L+G + G I V A
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARVMT 96
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 118 bits (298), Expect = 4e-33
Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 107 QPRGTGGPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGF 160
Q GP R L++ +H TE+ + F +G+I NI L +D TG KGY
Sbjct: 10 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 161 ITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
+ + + +A+ A E LNG +L G+P+ V R
Sbjct: 70 VEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
Score = 60.0 bits (146), Expect = 1e-11
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ +F + + D+ + F+ G+++++ L +T KG +E++ + A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 75 M-GLNGQKLLGIPIIV 89
M GLNGQ L+G PI V
Sbjct: 82 MEGLNGQDLMGQPISV 97
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 118 bits (297), Expect = 6e-33
Identities = 30/109 (27%), Positives = 60/109 (55%), Gaps = 5/109 (4%)
Query: 89 VQPTQAEKNRAGNTLP---NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQ 145
+ + + + +P ++ P RL++ ++ F + LR +F FGKI +++
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 60
Query: 146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
++ + SKG+GF+TF ++ DA +A+E+L+G + GR ++V T R
Sbjct: 61 IIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 52.7 bits (127), Expect = 5e-09
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
+ P S + + + + + R R DL + F GK+ DV +I R KG
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGF 71
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
++ F++ A L+G + G I V
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEV 101
>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 = 116 bits (294), Expect = 1e-32
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G +L + +L F +++ ++ +F FG + + D +GRS G + F
Sbjct: 23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKA 81
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVT 192
DA KA +Q NG L GRPM + VT
Sbjct: 82 DALKAMKQYNGVPLDGRPMNIQLVT 106
Score = 48.4 bits (116), Expect = 1e-07
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
L + D++E F+ G ++ + +++ R G A + F+ AM NG L
Sbjct: 37 LDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQYNGVPL 95
Query: 83 LGIPIIVQ 90
G P+ +Q
Sbjct: 96 DGRPMNIQ 103
>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 = 114 bits (289), Expect = 5e-32
Identities = 39/96 (40%), Positives = 52/96 (54%), Gaps = 2/96 (2%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADD 168
G+ G ++IG+L I E +L F FG I ++M DPDTG SKGY FI F S D
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ A E +NG L RP+ V ++ G GPS+
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYAFKKDSK-GSGPSS 95
Score = 46.8 bits (112), Expect = 4e-07
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKV-RDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
IF L I + L + FS+ G + + +++ T KG A+I F ++ A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
+NGQ L PI V + ++
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
>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 = 115 bits (289), Expect = 5e-32
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+Y+ +L F++T + L IF +GK+ + +M D DT +SKG FI F D A+
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 175 QLNGFELAGRPMKV 188
+N +L GR +K
Sbjct: 77 AINNKQLFGRVIKA 90
Score = 61.9 bits (151), Expect = 2e-12
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 1/87 (1%)
Query: 4 AYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
S T++ L + DL FS GKV V ++ TR+ KG+A+I
Sbjct: 4 GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63
Query: 64 EFKDPESVPLAM-GLNGQKLLGIPIIV 89
F D +S +N ++L G I
Sbjct: 64 LFLDKDSAQNCTRAINNKQLFGRVIKA 90
>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 = 115 bits (289), Expect = 6e-32
Identities = 31/94 (32%), Positives = 49/94 (52%), Gaps = 4/94 (4%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
++L+IG + N+ E L+ +FE FGKI + ++ D TG KG F+T+ + A KAQ
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Query: 174 EQLNG---FELAGRPMKVGTVTDRNESVGGGPSN 204
L+ RP++V + G GPS+
Sbjct: 73 SALHEQKTLPGMNRPIQVKPADSESR-GGSGPSS 105
Score = 59.3 bits (144), Expect = 2e-11
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 4/95 (4%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
++ DA +F Q+ + + +DL+ F GK+ ++ ++ T KG A++ + + E
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66
Query: 70 SVPLAM-GLNGQKLL---GIPIIVQPTQAEKNRAG 100
S A L+ QK L PI V+P +E
Sbjct: 67 SALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101
>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 = 114 bits (287), Expect = 8e-32
Identities = 28/79 (35%), Positives = 47/79 (59%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L++G L+ N+ ++ LR F+ F + +M D TG S+GYGF++F S DDA+ A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 176 LNGFELAGRPMKVGTVTDR 194
+ G +L GRP+++
Sbjct: 63 MQGQDLNGRPLRINWAAKL 81
Score = 52.9 bits (128), Expect = 2e-09
Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F L+ + L F ++ +T +G ++ F + AM +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 78 NGQKLLGIPIIV 89
GQ L G P+ +
Sbjct: 64 QGQDLNGRPLRI 75
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 116 bits (292), Expect = 8e-32
Identities = 28/130 (21%), Positives = 46/130 (35%), Gaps = 2/130 (1%)
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
L Q + P + Q + N + +Y+GS + T+ L +
Sbjct: 18 LYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIR 77
Query: 137 PFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
G D ++ + G+SKGY + S + K E L G L G + V T +
Sbjct: 78 SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
Query: 195 NESVGGGPSN 204
N S +
Sbjct: 138 NLSQFEAQAR 147
Score = 55.3 bits (133), Expect = 1e-09
Identities = 19/111 (17%), Positives = 35/111 (31%), Gaps = 3/111 (2%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFK 58
PA S ++ S + L + S+G V +++ + K
Sbjct: 40 KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99
Query: 59 GIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQP 108
G A + SV + L G+ L G + V+P + +
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE 150
>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 = 113 bits (286), Expect = 2e-31
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
G + L + +L ++ TE+ L+ +FE I + G+SKGY FI F S
Sbjct: 7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFAS 62
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+DAK+A N E+ GR +++ R G S
Sbjct: 63 FEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100
Score = 54.6 bits (132), Expect = 8e-10
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S +++T+ LS L+E F ++ + N+ + KG A+IEF E
Sbjct: 9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFE 64
Query: 70 SVPLAM-GLNGQKLLGIPIIV 89
A+ N +++ G I +
Sbjct: 65 DAKEALNSCNKREIEGRAIRL 85
>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 = 113 bits (286), Expect = 2e-31
Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 3/105 (2%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + R + + +L + E L+ +F PFG I I L D TG+SKG+
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
FI+FH +DA +A ++GF + V S GPS+
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS---GPSS 102
Score = 61.9 bits (151), Expect = 2e-12
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 1/92 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
+ D TI LS+ R DL+E F G + + L T + KG A+I F E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
A+ G++G + + V+ + N
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPSTNSGP 100
>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 = 113 bits (284), Expect = 4e-31
Identities = 27/96 (28%), Positives = 49/96 (51%), Gaps = 1/96 (1%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G + L + +L + + D LR +FE +G++ ++ + +P T +G+ F+ FH
Sbjct: 7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
DA+ A+ ++G EL GR ++V GPS
Sbjct: 67 DAQDAEAAMDGAELDGRELRVQVARYGRRD-LSGPS 101
Score = 64.2 bits (157), Expect = 3e-13
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 3/97 (3%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
P+ T+ L+ R L F G+V DV + T+ +G A++ F D
Sbjct: 7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPN 105
A ++G +L G + VQ A R + P+
Sbjct: 67 DAQDAEAAMDGAELDGRELRVQ--VARYGRRDLSGPS 101
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 111 bits (281), Expect = 6e-31
Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 2/91 (2%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G ++++ +L F+ T ML+ F G + + ++ G+SKG G + F S + A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
++A +NG +L+GR + V + + G
Sbjct: 62 ERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
Score = 49.5 bits (119), Expect = 3e-08
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S A IF L + L++ F+ G V + + + KG ++F+ PE
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPE 59
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQ-AEKNRAG 100
A +NG KL G I V+ + A +G
Sbjct: 60 VAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
>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 = 112 bits (283), Expect = 8e-31
Identities = 31/93 (33%), Positives = 51/93 (54%), Gaps = 1/93 (1%)
Query: 97 NRAGNTLPNLQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRS 155
+ G ++ R P L + L TE LR +F +G I ++ ++ D + RS
Sbjct: 28 QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 87
Query: 156 KGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+G+ F+ F + DDAK+A+E+ NG EL GR ++V
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 60.9 bits (148), Expect = 9e-12
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 3/99 (3%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
R + + LS RDL E FS G + DV ++ ++RR +G A
Sbjct: 32 RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
++ F++ + A NG +L G I V + R
Sbjct: 92 FVYFENVDDAKEAKERANGMELDGRRIRVD--FSITKRP 128
>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 = 111 bits (280), Expect = 1e-30
Identities = 24/93 (25%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
+ + P L+IG+L+ N + L+ +++ ++ D TG ++ +G++ F SA
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 68
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVG 199
+D +KA E L G ++ G +K+ R+ + G
Sbjct: 69 EDLEKALE-LTGLKVFGNEIKLEKPKGRDGTRG 100
Score = 68.4 bits (168), Expect = 9e-15
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 1/92 (1%)
Query: 9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
E +F L+ +L+ S + D+ ++ +T + Y++F+
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESA 68
Query: 69 ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
E + A+ L G K+ G I ++ + G
Sbjct: 69 EDLEKALELTGLKVFGNEIKLEKPKGRDGTRG 100
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 111 bits (280), Expect = 1e-30
Identities = 15/79 (18%), Positives = 36/79 (45%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G + L+ N+ E L+ + +G+++ +++++ P T + G + F S A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 170 KKAQEQLNGFELAGRPMKV 188
K+ + L+ + G +
Sbjct: 62 KETVKNLHLTSVMGNIIHA 80
Score = 69.3 bits (170), Expect = 5e-15
Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 9/103 (8%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ + +L+ +R L++ G+V +V ++ +TR+ G+A + F +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 76 GLNGQKLLGIPIIVQ--------PTQAEKNRAGNTLPNLQPRG 110
L+ ++G I Q E G+ P P G
Sbjct: 67 NLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPTG 109
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 110 bits (278), Expect = 2e-30
Identities = 30/90 (33%), Positives = 52/90 (57%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
+L++G L F+ E L +F +G+I + ++ D +T RS+G+GF+TF + DDAK A
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+NG + GR ++V +++ G S
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
Score = 58.4 bits (142), Expect = 4e-11
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S S D +F LS + LE+ FS G++ +V ++ +T+R +G ++ F
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
++ + AM +NG+ + G I V
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRV 86
>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 = 111 bits (279), Expect = 3e-30
Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 7/110 (6%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + P ++I +L F+ E+ L + + FG + +++++ PDT SKG
Sbjct: 1 GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
Query: 160 FITFHSADDAKKAQEQLN------GFELAGRPMKVGTVTDRNESVGGGPS 203
F F + + A+K + G +L GR +KV R+E+ GPS
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA-ASGPS 109
Score = 58.5 bits (142), Expect = 5e-11
Identities = 23/101 (22%), Positives = 36/101 (35%), Gaps = 7/101 (6%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S L + + +T+F LS L E G ++ VR++ T KG A+ +F
Sbjct: 5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64
Query: 66 KDPESVPLAM-------GLNGQKLLGIPIIVQPTQAEKNRA 99
E+ + G KL G + V A
Sbjct: 65 MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105
>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 = 112 bits (282), Expect = 3e-30
Identities = 28/137 (20%), Positives = 52/137 (37%), Gaps = 1/137 (0%)
Query: 53 KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTG 112
+ KG E D + + +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 113 GPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
M L + +L + + D LR +FE +G++ ++ + D T S+G+ F+ FH DA+
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 172 AQEQLNGFELAGRPMKV 188
A + ++G L GR ++V
Sbjct: 128 AMDAMDGAVLDGRELRV 144
Score = 62.6 bits (152), Expect = 4e-12
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 1/92 (1%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
+ ++ L+ R L F G+V DV + T+ +G A++ F D
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
AM ++G L G + VQ + + +
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156
>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 = 112 bits (282), Expect = 3e-30
Identities = 28/106 (26%), Positives = 49/106 (46%)
Query: 89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
+ + P+ + L++ S+H ED ++ F +G+I NI L +
Sbjct: 47 AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 106
Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
D TG SKGY + + + A A+E LNG E+ G+ ++V +
Sbjct: 107 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152
Score = 61.0 bits (148), Expect = 2e-11
Identities = 17/88 (19%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ +F + + + +++E F G+++++ L +T KG A +E++ + A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 75 M-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
LNG +++G I V + +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVK 158
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 115 bits (289), Expect = 4e-30
Identities = 41/208 (19%), Positives = 74/208 (35%), Gaps = 30/208 (14%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
++ +F L I D + F G+ +V + R +G
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFG 61
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
+I + +A L+G L P+ + G L +
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRI---------------RFATHGA----ALTVK 102
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN-GF 179
+L ++ ++L F FG ++ ++VD D GR+ G GF+ F + A+KA E+ G
Sbjct: 103 NLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGA 161
Query: 180 ELAGRPMKVGTVT--DRNESVGGGPSNL 205
L + V ++ + G P L
Sbjct: 162 FLLTTTPRPVIVEPMEQFDDEDGLPEKL 189
Score = 92.4 bits (230), Expect = 9e-22
Identities = 27/99 (27%), Positives = 52/99 (52%), Gaps = 7/99 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++G+L +ITE+ + +FE +G+ + + R +G+GFI S A+ A+ +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESRTLAEIAKAE 77
Query: 176 LNGFELAGRPMKVGTVT-DRNESVGGGPSNLDTDEMERA 213
L+G L RP+++ T +V + + +E+A
Sbjct: 78 LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQA 116
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 112 bits (281), Expect = 5e-30
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G +L + +L F +++ ++ +F FG + + D +GRS G + F
Sbjct: 82 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRA 140
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
DA KA +Q G L GRPM + V + +
Sbjct: 141 DALKAMKQYKGVPLDGRPMDIQLVASQID 169
Score = 53.3 bits (128), Expect = 1e-08
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
L + D++E F+ G ++ + +++ R G A + F+ AM G L
Sbjct: 96 LDFGVSDADIQELFAEFGTLKKAAVDY-DRSGRSLGTADVHFERRADALKAMKQYKGVPL 154
Query: 83 LGIPIIVQPTQAEKNR 98
G P+ +Q ++ +
Sbjct: 155 DGRPMDIQLVASQIDL 170
>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 = 108 bits (273), Expect = 2e-29
Identities = 29/98 (29%), Positives = 54/98 (55%), Gaps = 7/98 (7%)
Query: 110 GTGGPMR-------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
G+ GP+ +Y+G L ++E +L +F G + N + D TG+ +GYGF+
Sbjct: 4 GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
F S +DA A + ++ +L G+P++V + N+++ G
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 64.6 bits (158), Expect = 3e-13
Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 1/90 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
E T++ L +++ L E F G V + + T + +G ++EF E
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ ++ KL G PI V A
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKN 98
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 109 bits (275), Expect = 2e-29
Identities = 27/98 (27%), Positives = 50/98 (51%)
Query: 91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
T ++ G+ P G L + +L + + D LR +FE +G++ ++ + D
Sbjct: 24 MTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83
Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
T S+G+ F+ FH DA+ A + ++G L GR ++V
Sbjct: 84 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
Score = 61.3 bits (149), Expect = 7e-12
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 1/92 (1%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
P+ ++ L+ R L F G+V DV + T+ +G A++ F D
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
AM ++G L G + VQ + + +
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 108 bits (271), Expect = 4e-29
Identities = 26/100 (26%), Positives = 46/100 (46%)
Query: 89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
P + A + L+I L T+ L F PFG + + ++ +
Sbjct: 15 TSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI 74
Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
D T SK +GF++F + D A+ A + +NGF++ + +KV
Sbjct: 75 DKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114
Score = 49.3 bits (118), Expect = 9e-08
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F L Q DL F G V ++ +T K ++ F +P+S +A+ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 78 NGQKLLGIPIIVQ 90
NG ++ + VQ
Sbjct: 103 NGFQVGTKRLKVQ 115
>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 = 111 bits (279), Expect = 4e-29
Identities = 36/160 (22%), Positives = 58/160 (36%), Gaps = 9/160 (5%)
Query: 64 EFKDPESVPL------AMGLNGQKLLGIPIIVQPTQAEKNRAGNTL-PNLQPRGTGGPMR 116
E+ + + L NG + + G PN+ TG +
Sbjct: 11 EYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA 70
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
LYIG+L + T++ L G D I+ + G+SKG+ + S +KK +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAG 214
L EL G+ V V + S S T + +G
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSG 170
Score = 54.7 bits (131), Expect = 7e-09
Identities = 21/160 (13%), Positives = 41/160 (25%), Gaps = 7/160 (4%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKG 59
+ A + + ++ L+ DL E S+G + +++ + KG
Sbjct: 54 KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
Query: 60 IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-- 116
A + S M L ++L G +V P + +
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGK 173
Query: 117 --LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR 154
GS + P + G
Sbjct: 174 AGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGG 213
>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 = 107 bits (269), Expect = 5e-29
Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 3/89 (3%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P G P +++G + + E +R F +G + ++++ D TG SKGYGF++F++
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
D +K E + G+ +K+G +
Sbjct: 62 DVQKIVE--SQINFHGKKLKLGPAIRKQN 88
Score = 48.4 bits (116), Expect = 1e-07
Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 6/100 (6%)
Query: 11 PEERD-ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
PE + T+F + R+ ++ FF+ G V++V++IT ++T KG ++ F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDV 61
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPR 109
V + + G + + P ++N + ++QPR
Sbjct: 62 DVQKIV-ESQINFHGKKLKLGPAIRKQNLSTY---HVQPR 97
>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 = 106 bits (268), Expect = 6e-29
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 1/91 (1%)
Query: 99 AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
+ + P +++G+L + E++L +F G + + + D + G+ K +
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSF 59
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
GF+ F + A LNG L GRP+ V
Sbjct: 60 GFVCFKHPESVSYAIALLNGIRLYGRPINVS 90
Score = 63.4 bits (155), Expect = 5e-13
Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
S +E RT+F L R+R L E F G + V + ++ + K +
Sbjct: 3 SGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICK-DREGKPKSFGF 61
Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPIIV 89
+ FK PESV A+ LNG +L G PI V
Sbjct: 62 VCFKHPESVSYAIALLNGIRLYGRPINV 89
>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 = 107 bits (269), Expect = 9e-29
Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 6/101 (5%)
Query: 110 GTGGPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
GP R L++ +H TE+ + F +G+I NI L +D TG KGY + +
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 164 HSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ +A+ A E LNG +L G+P+ V R G
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGG 112
Score = 59.7 bits (145), Expect = 3e-11
Identities = 25/103 (24%), Positives = 44/103 (42%), Gaps = 3/103 (2%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
+ +F + + D+ + F+ G+++++ L +T KG +E++ + A
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 75 M-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
M GLNGQ L+G PI V G R + P R
Sbjct: 81 MEGLNGQDLMGQPISVDWCFVRGPPKGKRRGG--RRRSRSPDR 121
>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 = 106 bits (266), Expect = 1e-28
Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G +LYIG+L +T D LR +F + GY F+ + + A
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWA 57
Query: 170 KKAQEQLNG-FELAGRPMKVGTVTDRNESVGGGPSN 204
+A E L+G EL G+ M+V + GPS+
Sbjct: 58 IRAIETLSGKVELHGKIMEVDYSVSKKLR-SSGPSS 92
Score = 49.9 bits (120), Expect = 3e-08
Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 8/86 (9%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
++ LS + DL + F + G A++++ D A+
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE 62
Query: 76 GLNGQ-KLLGIPIIVQPTQAEKNRAG 100
L+G+ +L G + V + ++K R+
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLRSS 88
>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 = 106 bits (266), Expect = 1e-28
Identities = 24/110 (21%), Positives = 47/110 (42%), Gaps = 6/110 (5%)
Query: 94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG 153
+ N ++ + + +Y G + +T+ ++R F PFG+I I++ +
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---- 60
Query: 154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
KGY F+ F + + A A +NG + G +K + + G S
Sbjct: 61 --KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108
Score = 48.1 bits (115), Expect = 2e-07
Identities = 20/112 (17%), Positives = 46/112 (41%), Gaps = 15/112 (13%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
+ D ++ T++C ++ + + + + FS G++ ++R+ KG ++
Sbjct: 12 LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSF 65
Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGG 113
+ F ES A+ +NG + G + K G P++ + G
Sbjct: 66 VRFSTHESAAHAIVSVNGTTIEGHVV--------KCYWGKESPDMTSGPSSG 109
>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 = 106 bits (266), Expect = 4e-28
Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 10/111 (9%)
Query: 88 IVQPTQAEKNRAG----NTLPNLQPRGTGGP-MRLYIGSLHFNITEDMLRGIFEPFGKID 142
+ + EK R TL + G P R+Y+ +L ++ E L+ IF +
Sbjct: 14 CISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFS 73
Query: 143 NIQLMVDPD-----TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ + D GR KG FI + A KA ++ NG+ L G+PM V
Sbjct: 74 SETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124
Score = 53.7 bits (129), Expect = 5e-09
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKV-----RDVRLITCNKTRRFKGIAYIEFKDPESV 71
I+ L++ ++ +DL+ F R + I K R KG A+I + ++
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 72 PLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ NG L G P++VQ ++ + +
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSARPK 133
>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 = 104 bits (262), Expect = 4e-28
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 2/84 (2%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+ LYIG+L + T++ L G D I+ + G+SKG+ + S +KK
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 173 QEQLNGFELAGRPMKVGTVTDRNE 196
+ L EL G+ V
Sbjct: 62 MDLLPKRELHGQNPVVTPSNKLEH 85
Score = 50.3 bits (121), Expect = 2e-08
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 3/70 (4%)
Query: 32 DLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII 88
DL E S+G + +++ + KG A + S M L ++L G +
Sbjct: 17 DLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPV 76
Query: 89 VQPTQAEKNR 98
V P+ ++
Sbjct: 77 VTPSNKLEHH 86
>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 = 104 bits (261), Expect = 6e-28
Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 6/104 (5%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + + RL++G+L +ITE+ +R +FE +GK + + + KG+G
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFG 54
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
FI + A+ A+ +L+ L G+ ++V G S
Sbjct: 55 FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98
Score = 46.5 bits (111), Expect = 5e-07
Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 7/85 (8%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S +F L I ++ + F GK +V + + KG +I
Sbjct: 5 SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRL 58
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
+ +A L+ L G + V
Sbjct: 59 ETRTLAEIAKVELDNMPLRGKQLRV 83
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 103 bits (258), Expect = 2e-27
Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 15/111 (13%)
Query: 79 GQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF 138
G + +G+P V P + + + + PR T YIG++ TE L +F+ F
Sbjct: 1 GSQTIGLPPQVNPQAVD-----HIIRSAPPRVT----TAYIGNIPHFATEADLIPLFQNF 51
Query: 139 GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
G I + + + KG FI + + + A L F GR ++ G
Sbjct: 52 GFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96
Score = 46.5 bits (111), Expect = 6e-07
Identities = 13/86 (15%), Positives = 25/86 (29%), Gaps = 7/86 (8%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
A + T + + DL F + G + D + KG +
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCF 67
Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPI 87
I++ E + + L G +
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 103 bits (259), Expect = 2e-27
Identities = 28/115 (24%), Positives = 53/115 (46%), Gaps = 10/115 (8%)
Query: 99 AGNTLPNLQPRGTGGPMR---------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
+ L + G L+I L + L +F PFG + + ++ +D
Sbjct: 1 GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60
Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
T SK +GF+++ + A+ A + +NGF++ + +KV +N+S GPS+
Sbjct: 61 KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS-KSGPSS 114
Score = 49.6 bits (119), Expect = 6e-08
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F L Q +DL + F G V ++ +T K ++ + +P S A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 78 NGQKLLGIPIIVQPTQAEKNR 98
NG ++ + VQ +++ +
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDS 108
>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 = 102 bits (256), Expect = 6e-27
Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 1/89 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
P +L+IG L+ E ML+ +F G I + L+ D T +S+G+ FITF + DAK A
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAA 65
Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGP 202
+ +NG L G+ +KV + GG
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94
Score = 58.1 bits (141), Expect = 6e-11
Identities = 24/111 (21%), Positives = 46/111 (41%), Gaps = 5/111 (4%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
E +F L++ + L+ F G + +V LI ++T + +G A+I F++P
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK-DRTSKSRGFAFITFENPADA 61
Query: 72 PLAM-GLNGQKLLGIPIIV---QPTQAEKNRAGNTLPNLQPRGTGGPMRLY 118
A +NG+ L G I V + + + + R G + +
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHH 112
>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 = 101 bits (254), Expect = 7e-27
Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 5/93 (5%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+++G++ + TE+ L+ IF G + + +L+ D +TG+ KGYGF + + A A
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 175 QLNGFELAGRPMKVGTVTDR-----NESVGGGP 202
LNG E +GR ++V +S+G G
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101
Score = 67.7 bits (166), Expect = 2e-14
Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 6/103 (5%)
Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
+R R++F + L++ FS VG V RL+ +T + KG + E++D E+
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 73 LAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
AM LNG++ G + V +EKN+ L+ GTG P
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKNK-----EELKSLGTGAP 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 = 101 bits (254), Expect = 1e-26
Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 1/90 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
P LYI +L ++ E L + +PFG++ + +++ D +G S+G GF S + +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
NG + P G S
Sbjct: 84 GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113
Score = 48.4 bits (116), Expect = 1e-07
Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
+E+D ++ L + ++LE G+V R++ + + +G+ + + E
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEK 78
Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQ 93
+ NG+ + P + PT+
Sbjct: 79 CEAVIGHFNGKFIKTPPGVSAPTE 102
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 100 bits (252), Expect = 1e-26
Identities = 17/90 (18%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 99 AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
+ + + + +L+I L F+ T++ L I + G + +++L+ + G+ KG
Sbjct: 2 SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGL 60
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
++ + + A +A +++G + +KV
Sbjct: 61 AYVEYENESQASQAVMKMDGMTIKENIIKV 90
Score = 63.8 bits (156), Expect = 4e-13
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 2/89 (2%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
+ +F L +LEE + G V+D+RL+T N+ + KG+AY+E+++
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVT-NRAGKPKGLAYVEYENESQ 70
Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ ++G + I V + + +
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAISNSGPSS 99
>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 = 103 bits (257), Expect = 3e-26
Identities = 30/200 (15%), Positives = 59/200 (29%), Gaps = 31/200 (15%)
Query: 15 DARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
D+ + L ++ + F G V V+ +K G A +E D +V
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVK-FMKSK----PGAAMVEMADGYAVDR 57
Query: 74 AM-GLNGQKLLGIPIIV---------------QPTQAEKNRAGNTLPNLQPRGTGGPMR- 116
A+ LN + G + V + + + N + +
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117
Query: 117 --------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
L+ + +TE+ I + G + V G + + S D
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177
Query: 169 AKKAQEQLNGFELAGRPMKV 188
A + LN +++
Sbjct: 178 ALETLGFLNHYQMKNPNGPY 197
Score = 64.3 bits (156), Expect = 2e-12
Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 6/74 (8%)
Query: 117 LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L + L + D + +F +G ++ ++ M G + +A
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61
Query: 176 LNGFELAGRPMKVG 189
LN + G+ M V
Sbjct: 62 LNNNFMFGQKMNVC 75
Score = 46.2 bits (109), Expect = 4e-06
Identities = 6/73 (8%), Positives = 19/73 (26%), Gaps = 1/73 (1%)
Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
+ + + + + E +G R + + +E+
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
Query: 73 LAM-GLNGQKLLG 84
+ LN ++
Sbjct: 180 ETLGFLNHYQMKN 192
>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 = 99 bits (250), Expect = 3e-26
Identities = 33/90 (36%), Positives = 54/90 (60%), Gaps = 3/90 (3%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+ LY+ +L I ++ LR F PFG I + ++M++ GRSKG+GF+ F S ++A KA
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++NG +A +P+ V + E GPS+
Sbjct: 74 EMNGRIVATKPLYVALAQRKEER-QSGPSS 102
Score = 44.1 bits (105), Expect = 4e-06
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
++ L I L + FS G + +++ + R KG ++ F PE A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 78 NGQKLLGIPIIVQPTQA-EKNRAGNT 102
NG+ + P+ V Q E+ ++G +
Sbjct: 76 NGRIVATKPLYVALAQRKEERQSGPS 101
>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 = 99.7 bits (249), Expect = 5e-26
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 2/106 (1%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD-TGRSKGY 158
G++ + Q ++ + ++ F + +R +F FG++ ++L TG +G+
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 159 GFITFHSADDAKKAQEQL-NGFELAGRPMKVGTVTDRNESVGGGPS 203
GF+ F + DAKKA L + L GR + + G S
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
Score = 58.1 bits (141), Expect = 6e-11
Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 3/92 (3%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDP 68
P+++ I + + R++ E FS+ G+++ VRL T +G +++F
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 69 ESVPLAMG--LNGQKLLGIPIIVQPTQAEKNR 98
+ A + L G ++++ +E
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100
>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 = 99.3 bits (248), Expect = 5e-26
Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 4/101 (3%)
Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
+ P P + L++ L + TE+ L+ E F +++ D +TG SKG+GF+
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVD 60
Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
F+S +DAK A+E + E+ G + + + E G S
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
Score = 49.6 bits (119), Expect = 5e-08
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 4/85 (4%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S + + ++T+F LS+ L+E F R++T +T KG +++F
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDF 61
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
E A + ++ G + +
Sbjct: 62 NSEEDAKAAKEAMEDGEIDGNKVTL 86
>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 = 99.0 bits (247), Expect = 9e-26
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LYI +L + IT + + IF +G I I++ +T ++G ++ + DAK A + L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 177 NGFELAGRPMKVG 189
+GF ++ R + V
Sbjct: 68 SGFNVSNRYLVVL 80
Score = 68.6 bits (168), Expect = 1e-14
Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 6/93 (6%)
Query: 8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD 67
L PE R ++ L +I ++ + F G +R +R+ T +G AY+ ++D
Sbjct: 2 RLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYED 56
Query: 68 PESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
A+ L+G + ++V A +
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQ 89
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 98.1 bits (245), Expect = 2e-25
Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 9/97 (9%)
Query: 93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT 152
+ G+ + + Q G RL++ ++ E L IF PFG + ++++
Sbjct: 11 SSGLVPRGSHMHHRQ-EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64
Query: 153 GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
G+ F+ F A+ A KA E+++G A +P++V
Sbjct: 65 ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
Score = 61.5 bits (150), Expect = 3e-12
Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 11/100 (11%)
Query: 2 RPAYSDDLSPEERDA--RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
P S +E + +F ++ +L E F G +++V+++ G
Sbjct: 15 VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NG 66
Query: 60 IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A++EF++ ES A+ ++G+ P+ V ++ R
Sbjct: 67 FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 97.9 bits (244), Expect = 2e-25
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 8/99 (8%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHS 165
+++ L N+T + + F+ G I I L D +TG+ KG ++F
Sbjct: 7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
AK A + +G E +G P+KV T R + GG +
Sbjct: 67 PPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105
Score = 65.5 bits (160), Expect = 2e-13
Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 11/101 (10%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYI 63
+ D TIF L + + + ++F +G ++ + L T +T + KG A +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 64 EFKDPESVPLAM-GLNGQKLLGIPIIVQPTQ--AEKNRAGN 101
F DP S A+ +G++ G PI V A+ NR G
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGG 103
>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 = 97.3 bits (243), Expect = 3e-25
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 116 RLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
+YI +L+ I +D L+ IF FG+I +I + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSATN 66
Query: 172 AQEQLNGFELAGRPMKV 188
A + GF +PM++
Sbjct: 67 ALRSMQGFPFYDKPMRI 83
Score = 59.2 bits (144), Expect = 2e-11
Identities = 21/93 (22%), Positives = 47/93 (50%), Gaps = 8/93 (8%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D+ + ++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFK 59
Query: 67 DPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
+ S A+ + G P+ +Q + + +
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
>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 = 96.9 bits (242), Expect = 4e-25
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 3/105 (2%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + G P LY+G+L ++TE ++ +F G + +++ + + Y
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YC 58
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
F+ F+ DA A +NG ++ G+ +KV T + GPS+
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ-KSGPSS 102
Score = 55.7 bits (135), Expect = 4e-10
Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 3/90 (3%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
++ RT++ LS+ + + + FS +G + ++IT + + ++EF +
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHR 66
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ +NG+K+LG + V ++
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATTPSSQ 96
>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 = 97.6 bits (243), Expect = 9e-25
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
LY+G+L F TE+ + +F G I I + +D + G+ F+ ++S DA+ A
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 176 LNGFELAGRPMKV 188
+NG L R ++
Sbjct: 101 INGTRLDDRIIRT 113
Score = 58.3 bits (141), Expect = 1e-10
Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 3/89 (3%)
Query: 2 RPAYSDDLSPEER--DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
+ D+ E+ + T++ LS + E FS G ++ + + + G
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 60 IAYIEFKDPESVPLAM-GLNGQKLLGIPI 87
++E+ AM +NG +L I
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRII 111
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 96.0 bits (239), Expect = 1e-24
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
I S + + L +F GK+ N++ +D TG++KG+ F+ S +DAKK + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 178 GFELAGRP-MKVGTVTD 193
G L + + + T+ D
Sbjct: 76 GKRLDLKHRLFLYTMKD 92
Score = 47.8 bits (114), Expect = 2e-07
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLG 84
L FS GKV ++ T + KG ++E + +G++L
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL 81
>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 = 95.3 bits (238), Expect = 1e-24
Identities = 21/74 (28%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+Y+G+L ++ T + ++ +F FGK+ N++L+ D +T + KG+GF+ + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 175 QLNGFELAGRPMKV 188
+L+ + GR ++V
Sbjct: 61 KLDNTDFMGRTIRV 74
Score = 54.9 bits (133), Expect = 5e-10
Identities = 21/85 (24%), Positives = 39/85 (45%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
R I+ L + ++E FS GKV +V+LI +T++ KG ++E ++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGN 101
L+ +G I V +K+ +
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLEHH 86
>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 = 94.5 bits (236), Expect = 2e-24
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+Y+G++ + T + L F G ++ + ++ D +G KG+ +I F + + +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66
Query: 176 LNGFELAGRPMKV 188
L+ GR +KV
Sbjct: 67 LDESLFRGRQIKV 79
Score = 77.6 bits (192), Expect = 4e-18
Identities = 29/88 (32%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
E DAR+I+ + +LE F G V V ++ + KG AYIEF D ESV
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 73 LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
++ L+ G I V NR G
Sbjct: 63 TSLALDESLFRGRQIKV--IPKRTNRPG 88
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 94.6 bits (236), Expect = 3e-24
Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
T P Y+G+L FN + + IF+ I +++L+ D DT + KG+ ++ F D K
Sbjct: 12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+A +G L R ++V R + G S
Sbjct: 71 EALT-YDGALLGDRSLRVDIAEGRKQDKSGPSS 102
Score = 61.5 bits (150), Expect = 3e-12
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 1/85 (1%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
T + L D++ F + +R VRL+ T +FKG Y+EF + +S+ A+
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGN 101
+G L + V + K
Sbjct: 75 YDGALLGDRSLRVDIAEGRKQDKSG 99
>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 = 94.3 bits (235), Expect = 5e-24
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 1/88 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+++ +L + + L+ +F G + ++ D D G+S+G G +TF + +A +A
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISM 75
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
NG L RPM V P
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGDFFPP 103
Score = 51.9 bits (125), Expect = 1e-08
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 3/110 (2%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S R T+F L ++ + L+E FS G V ++ +K + +GI + F
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILE-DKDGKSRGIGTVTF 63
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
+ A+ NGQ L P+ V+ + G+ P +P+ +G
Sbjct: 64 EQSIEAVQAISMFNGQLLFDRPMHVKMDE-RALPKGDFFPPERPQQSGPS 112
>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 = 94.8 bits (236), Expect = 5e-24
Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 1/99 (1%)
Query: 90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
+ T + + + +Y+G++ + T L F G I+ I ++ D
Sbjct: 12 KMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD 71
Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+G KGY +I F + A ++ GR +KV
Sbjct: 72 KFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKV 109
Score = 75.9 bits (187), Expect = 4e-17
Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 2/99 (2%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
P +E D R+++ + +DLE FSS G + + ++ + KG A
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 62 YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
YIEF + SV A+ ++ G I V P N G
Sbjct: 82 YIEFAERNSVDAAVAMDETVFRGRTIKVLP--KRTNMPG 118
>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 = 96.9 bits (241), Expect = 5e-24
Identities = 34/197 (17%), Positives = 68/197 (34%), Gaps = 34/197 (17%)
Query: 17 RTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
+ L+ +R+ + L F G V+ V+++ K A ++ D LAM
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAM 58
Query: 76 -GLNGQKLLGIPIIVQP----------------------TQAEKNRAGNTLPNLQPRGTG 112
LNG KL G PI + + +R
Sbjct: 59 SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
L++ ++ +++E+ L+ +F G + + + I S ++A +A
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQA 174
Query: 173 QEQLNGFELA-GRPMKV 188
L+ +L ++V
Sbjct: 175 LIDLHNHDLGENHHLRV 191
Score = 71.1 bits (174), Expect = 9e-15
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 117 LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L + +L+ +T L +F +G + ++++ + K + + A+ A
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 176 LNGFELAGRPMKVG 189
LNG +L G+P+++
Sbjct: 61 LNGHKLHGKPIRIT 74
>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 = 94.2 bits (235), Expect = 6e-24
Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G G ++I +L +I L F FG I + +++ D SKGYGF+ F + + A
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAA 58
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNES 197
++A E++NG L R + VG R E
Sbjct: 59 ERAIEKMNGMLLNDRKVFVGRFKSRKER 86
Score = 61.9 bits (151), Expect = 3e-12
Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 8/112 (7%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
IF L + I + L + FS+ G + +++ KG ++ F+ E+ A+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 65
Query: 78 NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
NG L + V ++ K R L T +YI + T
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAE-LGARAKEFT----NVYIKNFGPGSTRA 112
>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 = 93.5 bits (233), Expect = 6e-24
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L++G L + E+ + F G + +++++ + TG GY F+ F A+K +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 176 LNGFELAG----RPMKVGTVTDRNESVGGGPSN 204
+NG L G + K+ N + GPS+
Sbjct: 72 INGKPLPGATPAKRFKL------NYATYSGPSS 98
Score = 50.0 bits (120), Expect = 3e-08
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDP 68
S A +++ L + + F+++G V V++I T G ++EF D
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62
Query: 69 ESVPLAM-GLNGQKLLGIPIIVQ 90
+ + +NG+ L G +
Sbjct: 63 ATAEKCLHKINGKPLPGATPAKR 85
>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 = 93.5 bits (233), Expect = 8e-24
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 4/92 (4%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + G +L++G L+ +E+ + +F+PFG ID ++ PD G SKG
Sbjct: 1 GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCA 59
Query: 160 FITFHSADDAKKAQEQLNG---FELAGRPMKV 188
F+ F S +A+ A L+G A + V
Sbjct: 60 FVKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91
Score = 48.8 bits (117), Expect = 9e-08
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 5/98 (5%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S R +F L+++ D+ F G + + ++ KG A+++F
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKF 63
Query: 66 KDPESVPLAM-GLNGQKLL---GIPIIVQPTQAEKNRA 99
A+ L+G + + ++V+ +K
Sbjct: 64 SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG 101
>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 = 97.0 bits (241), Expect = 1e-23
Identities = 35/212 (16%), Positives = 71/212 (33%), Gaps = 34/212 (16%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
+ L+ R+ + L F G V+ V+++ K
Sbjct: 20 HMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----EN 74
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG---TGGPMR 116
A ++ D LAM LNG KL G PI + ++ + + Q P+
Sbjct: 75 ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134
Query: 117 -------------------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
L++ ++ +++E+ L+ +F G + + +
Sbjct: 135 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRK 190
Query: 158 YGFITFHSADDAKKAQEQLNGFELA-GRPMKV 188
I S ++A +A L+ +L ++V
Sbjct: 191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222
Score = 68.1 bits (166), Expect = 2e-13
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 107 QPRGTGGPMR-LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
P G L + +L+ +T L +F +G + ++++ + K +
Sbjct: 26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMA 80
Query: 165 SADDAKKAQEQLNGFELAGRPMKVG 189
+ A+ A LNG +L G+P+++
Sbjct: 81 DGNQAQLAMSHLNGHKLHGKPIRIT 105
>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 = 92.6 bits (231), Expect = 1e-23
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 8/95 (8%)
Query: 109 RGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
G+ G ++L+IG+L TE +R +FE +GK+ ++ K YGF+
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
A+ A L+ ++L G + V +++++ G S
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSS 89
Score = 60.3 bits (147), Expect = 5e-12
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 9/92 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S +F L + +++ F GKV + +I K ++ +D
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
+ A+ L+ KL G+ I V+ ++ + +
Sbjct: 54 AAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85
>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 = 92.3 bits (230), Expect = 2e-23
Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 3/91 (3%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHS 165
P ++G+L +++TE+ ++ F I ++L +P + R KG+G+ F
Sbjct: 12 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 70
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
D A LN L R ++V +
Sbjct: 71 LDSLLSALS-LNEESLGNRRIRVDVADQAQD 100
Score = 63.8 bits (156), Expect = 5e-13
Identities = 23/97 (23%), Positives = 37/97 (38%), Gaps = 2/97 (2%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR-RFKGI 60
+ + T F L + ++EFF + + VRL R KG
Sbjct: 5 HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63
Query: 61 AYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKN 97
Y EF+D +S+ A+ LN + L I V ++
Sbjct: 64 GYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQD 100
>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 = 91.6 bits (228), Expect = 3e-23
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 17/98 (17%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L++ +L +TE++L F FGK++ ++ + K Y FI F D A KA E+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEE 64
Query: 176 LNGFELAGRPMKVG---------TVTDRNESVGGGPSN 204
+NG +L G +++ GPS+
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102
Score = 51.9 bits (125), Expect = 8e-09
Identities = 25/106 (23%), Positives = 41/106 (38%), Gaps = 11/106 (10%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + +F L+ + LE+ FS GK+ V+ + K A+I F + +
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD 56
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
AM +NG+ L G I + A+ Q + GP
Sbjct: 57 GAVKAMEEMNGKDLEGENIEI--VFAKPPDQKRKERKAQRQAASGP 100
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 91.2 bits (227), Expect = 4e-23
Identities = 16/78 (20%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGK--IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+ + ++ + D + P+ ++NI+L+ D T +++G+ F+ SA DA + +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 175 QLNG----FELAGRPMKV 188
L ++ G+ + V
Sbjct: 72 ILQSLHPPLKIDGKTIGV 89
Score = 43.5 bits (103), Expect = 5e-06
Identities = 11/72 (15%), Positives = 24/72 (33%), Gaps = 3/72 (4%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGK--VRDVRLITCNKTRRFKGIAYIEFKDPE 69
TI ++ + S V ++RLI +T++ +G A+++
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 70 SVPLAM-GLNGQ 80
+ L
Sbjct: 65 DASQLLQILQSL 76
>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 = 91.2 bits (227), Expect = 6e-23
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 3/98 (3%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHS 165
P ++G+L +++TE+ ++ F I ++L +P + R KG+G+ F
Sbjct: 8 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
D A LN L + ++V + G S
Sbjct: 67 LDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103
Score = 65.4 bits (160), Expect = 1e-13
Identities = 24/100 (24%), Positives = 40/100 (40%), Gaps = 2/100 (2%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIA 61
+ S + T F L + ++EFF + + VRL + R KG
Sbjct: 2 SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60
Query: 62 YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGN 101
Y EF+D +S+ A+ LN + L I V +++
Sbjct: 61 YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100
>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 = 90.8 bits (226), Expect = 6e-23
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSAD 167
+++ L N+T + + F+ G I I L D +TG+ KG ++F
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 168 DAKKAQEQLNGFELAGRPMKV 188
AK A + +G E +G P+KV
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKV 95
Score = 66.9 bits (164), Expect = 3e-14
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 9/95 (9%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRF 57
D TIF L + + + ++F +G ++ + L T +T +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 58 KGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQP 91
KG A + F DP S A+ +G++ G PI V
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 91.1 bits (226), Expect = 1e-22
Identities = 16/103 (15%), Positives = 39/103 (37%), Gaps = 7/103 (6%)
Query: 90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQ 145
+ E+ + P T + I +++ + ++ L+ + G I +I
Sbjct: 5 AAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV 64
Query: 146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ + + G +I F + + A+ E G+ G P+ +
Sbjct: 65 VD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI 104
Score = 60.7 bits (147), Expect = 1e-11
Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 8/95 (8%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRR 56
M P ++ + ++ + L+ SS G + D+ + +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDD 70
Query: 57 FKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
G AYI F ES + G G P+++
Sbjct: 71 NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT 105
>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 = 89.6 bits (223), Expect = 2e-22
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ +L + +E+M+ F ++ + + Y F+ F + +DA +A + L
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71
Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPS 203
NG L G P++V ++ G S
Sbjct: 72 NGKVLDGSPIEVTLAKPVDKDSSGPSS 98
Score = 50.4 bits (121), Expect = 2e-08
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ ++ L +E+ F+++ R ++ + A++ F + E AM
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMK 69
Query: 76 GLNGQKLLGIPIIV 89
LNG+ L G PI V
Sbjct: 70 ALNGKVLDGSPIEV 83
>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 = 89.3 bits (222), Expect = 2e-22
Identities = 19/89 (21%), Positives = 37/89 (41%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + G GP + + ++ F ++ D + F + I + + G G
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ F S D+A A LN + R +K+
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKL 89
Score = 53.8 bits (130), Expect = 1e-09
Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 1/85 (1%)
Query: 4 AYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
+ S S + I + + ++ +FF + + N+ G A +
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 64 EFKDPESVPLAM-GLNGQKLLGIPI 87
F+ + A+ LN + + +
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKV 87
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 89.3 bits (222), Expect = 3e-22
Identities = 19/89 (21%), Positives = 37/89 (41%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + G GP + + ++ F ++ D + F + I + + G G
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ F S D+A A LN + R +K+
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKL 89
Score = 52.7 bits (127), Expect = 4e-09
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 1/75 (1%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
I + + ++ +FF + + N+ G A + F+ + A+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 77 LNGQKLLGIPIIVQP 91
LN + + + +
Sbjct: 77 LNDRPIGSRKVKLVL 91
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 88.3 bits (219), Expect = 5e-22
Identities = 18/82 (21%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L I ++ ++ ++L + +G +++ + + +T +T+ S D A++A ++
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQARQALDK 73
Query: 176 LNGFELAGRPMKVGTVTDRNES 197
LNGF+L +KV + D +
Sbjct: 74 LNGFQLENFTLKVAYIPDEMAA 95
Score = 56.3 bits (136), Expect = 2e-10
Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 4/81 (4%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
P+ + R + + ++ L+ G V + T + + + +
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQ 66
Query: 71 VPLAM-GLNGQKLLGIPIIVQ 90
A+ LNG +L + V
Sbjct: 67 ARQALDKLNGFQLENFTLKVA 87
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 88.0 bits (219), Expect = 8e-22
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 1/88 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G + N E LR F+ FG + + ++ D + R +G+GFITF +A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ ++ G+ ++V R+ G S
Sbjct: 72 -HFHDIMGKKVEVKRAEPRDSKSSGPSS 98
Score = 51.0 bits (123), Expect = 1e-08
Identities = 18/75 (24%), Positives = 35/75 (46%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
+ IF + +L E+F G V +V +I + +R +G +I F+D +
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Query: 70 SVPLAMGLNGQKLLG 84
SV A+ ++ ++G
Sbjct: 64 SVDQAVNMHFHDIMG 78
>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 = 88.2 bits (219), Expect = 1e-21
Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 8/112 (7%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI--------DNIQLMVDPD 151
G++ + P +Y+ L+ ++T D L F+ G + I + +D +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
TG+ KG +++ AK A E +G + G +KV + G S
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
Score = 63.2 bits (154), Expect = 1e-12
Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 9/98 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIA 61
E+ D I+ L+ + DL +FF G V+ + + +T + KG A
Sbjct: 9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
+ ++DP + A+ +G+ G + V + +
Sbjct: 69 TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>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 = 87.9 bits (218), Expect = 2e-21
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
LY+ ++T +LRG F PFG I ++ + + F+T+ + A +A +
Sbjct: 41 TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAE 92
Query: 176 LNGFELAGRPMKV 188
LNG ++ +KV
Sbjct: 93 LNGTQVESVQLKV 105
Score = 46.3 bits (110), Expect = 9e-07
Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 9/91 (9%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
R + S R T++ + L FS G + D+ + +
Sbjct: 24 FRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD------PPRNC 75
Query: 61 AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
A++ ++ ES A+ LNG ++ + + V
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQLKVN 106
>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 = 87.0 bits (216), Expect = 2e-21
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ ++T +LRG F PFG I ++ + + F+T+ + A +A +L
Sbjct: 18 LYVY--GEDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAEL 69
Query: 177 NGFELAGRPMKV 188
NG ++ +KV
Sbjct: 70 NGTQVESVQLKV 81
Score = 41.5 bits (98), Expect = 3e-05
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 9/82 (10%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
R T++ + L FS G + D+ + A++ ++ E
Sbjct: 9 RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDL------SMDPPRNCAFVTYEKME 60
Query: 70 SVPLAM-GLNGQKLLGIPIIVQ 90
S A+ LNG ++ + + V
Sbjct: 61 SADQAVAELNGTQVESVQLKVN 82
>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 = 88.4 bits (219), Expect = 2e-21
Identities = 28/140 (20%), Positives = 52/140 (37%), Gaps = 9/140 (6%)
Query: 53 KTRRFKGIAYIEFKDPESVPLAMG--LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG 110
+ KG E D + N + G T+ G+ +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR 67
Query: 111 TGGPM--RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
P+ ++Y+G+L N + L F +G + ++ + +P G+ F+ F D
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRD 122
Query: 169 AKKAQEQLNGFELAGRPMKV 188
A A +L+G L G ++V
Sbjct: 123 AADAVRELDGRTLCGCRVRV 142
Score = 64.9 bits (158), Expect = 7e-13
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
++ L +LE F G +R V + R G A++EF+DP
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEFEDPRDAAD 125
Query: 74 AM-GLNGQKLLGIPIIVQPTQAEK 96
A+ L+G+ L G + V+ + EK
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEK 149
>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 = 86.1 bits (214), Expect = 3e-21
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
+G ++++G++ T LR +FE G++ ++ K Y F+ DAK
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGP 202
A QLNG E+ G+ + V T + G
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89
Score = 58.8 bits (143), Expect = 2e-11
Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 9/92 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + IF +S +++L F G+V + ++ K A++ +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
A+ LNG+++ G I V+ + + ++G
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
>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 = 85.0 bits (211), Expect = 8e-21
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 8/91 (8%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+L++G++ T LR FE +G + ++ K Y F+ A+DA +A
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEA 60
Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
L+ E G+ M V T R + G S
Sbjct: 61 IRGLDNTEFQGKRMHVQLSTSRLRTASGPSS 91
Score = 58.0 bits (141), Expect = 4e-11
Identities = 17/106 (16%), Positives = 36/106 (33%), Gaps = 21/106 (19%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
+ + + +S ++L F G V + ++ K A++ + E
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAE 55
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
A+ GL+ + G + VQ + + + R GP
Sbjct: 56 DAVEAIRGLDNTEFQGKRMHVQLSTS------------RLRTASGP 89
>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 = 84.7 bits (210), Expect = 2e-20
Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 3/91 (3%)
Query: 98 RAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
+ ++ R+Y+G+L +I + +F +G I +I L
Sbjct: 6 SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPP 62
Query: 158 YGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ F+ F DA+ A +G++ G ++V
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93
Score = 67.3 bits (165), Expect = 3e-14
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 4/90 (4%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
P + I+ L IRT+D+E+ F G +RD+ L R A++EF+DP
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPR 72
Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ G +G G + V+ ++ +
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102
>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 = 82.9 bits (206), Expect = 2e-20
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L + E+ +R F FG++++I+L +D T + +G+ FITF + KK E+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 176 LNGFELAGRPMKV 188
+ ++
Sbjct: 61 -KYHNVGLSKCEI 72
Score = 48.3 bits (116), Expect = 6e-08
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
IF LS + E+F G+V + L NKT + +G +I FK+ E V M
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 GQKLLG 84
+
Sbjct: 62 YHNVGL 67
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 82.9 bits (206), Expect = 3e-20
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L N T + ++ FE FGK+D+ LM D T R +G+GF+TF S D +K E
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 176 LNGFELAGRPMKV 188
+ E+ + ++
Sbjct: 61 -HFHEINNKMVEC 72
Score = 48.2 bits (116), Expect = 7e-08
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
LS D++ +F GKV D L+ T R +G ++ F+ + V ++ ++
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN 66
Query: 84 G 84
Sbjct: 67 N 67
>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 = 83.9 bits (208), Expect = 4e-20
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L ++ T+ LR FE FG I+ ++ D TG+S+GYGF+T A++A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 176 LNGFELAGRPMKV 188
N + GR V
Sbjct: 79 PNP-IIDGRKANV 90
Score = 47.7 bits (114), Expect = 3e-07
Identities = 19/111 (17%), Positives = 36/111 (32%), Gaps = 10/111 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S ++ IF L L ++F G + + +IT +T + +G ++ D
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
+ A + G V N A +PR + +
Sbjct: 71 AAERACKDPNPIIDGRKANV-------NLA---YLGAKPRSLQTGFAIGVS 111
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 83.1 bits (206), Expect = 5e-20
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
M++Y+G+L + L F +G + + + +P G+ F+ F DA+ A
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR 55
Query: 175 QLNGFELAGRPMKV 188
L+G + G ++V
Sbjct: 56 GLDGKVICGSRVRV 69
Score = 60.8 bits (148), Expect = 5e-12
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 15/99 (15%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
++ L +LE FS G +R V + R G A++EF+DP A+ GL
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGL 57
Query: 78 NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
+G+ + G + V+ + R R P R
Sbjct: 58 DGKVICGSRVRVELSTGMPRR---------SRFDRPPAR 87
>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 = 83.0 bits (206), Expect = 5e-20
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 2/104 (1%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + R L + L + TE L+ F FG++ +Q+ D TG SKG+G
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
F+ F + K Q + + GR + G S
Sbjct: 61 FVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPSS 102
Score = 46.8 bits (112), Expect = 4e-07
Identities = 17/70 (24%), Positives = 33/70 (47%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S + + + + L + +DL+E+FS+ G+V V++ KT KG ++ F
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 66 KDPESVPLAM 75
+ E+ M
Sbjct: 65 TEYETQVKVM 74
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 82.7 bits (205), Expect = 7e-20
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 116 RLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
L++G L ++ + ML F + + ++++D TG SKGYGF+ F + K+A
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69
Query: 175 QLNG-FELAGRPMKVGTVT---DRNESVGGGPSN 204
+ G L +P+++ R + V GPS+
Sbjct: 70 ECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103
>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 = 81.9 bits (203), Expect = 2e-19
Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F TE+ LR +E +GK+ + +M DP + RS+G+GF+TF S + A
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ GR ++ R ES G S
Sbjct: 89 -RPHSIDGRVVEPKRAVAREESGSGPSS 115
Score = 48.0 bits (115), Expect = 2e-07
Identities = 16/75 (21%), Positives = 29/75 (38%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
E+ R +F LS L ++ GK+ D ++ ++R +G ++ F
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80
Query: 70 SVPLAMGLNGQKLLG 84
V AM + G
Sbjct: 81 EVDAAMAARPHSIDG 95
>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 = 80.9 bits (200), Expect = 2e-19
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 113 GPM----RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM-----VDPDTGRSKGYGFITF 163
GP+ RLY+G++ F ITE+ + F ++ + + + K + F+ F
Sbjct: 1 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
Query: 164 HSADDAKKAQEQLNGFELAGRPMKVG 189
S D+ +A +G G+ +K+
Sbjct: 61 RSVDETTQAM-AFDGIIFQGQSLKIR 85
Score = 52.8 bits (127), Expect = 3e-09
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 5/81 (6%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDP 68
AR ++ + I + +FF++ ++ + N + + K A++EF+
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 69 ESVPLAMGLNGQKLLGIPIIV 89
+ AM +G G + +
Sbjct: 64 DETTQAMAFDGIIFQGQSLKI 84
>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 = 80.0 bits (198), Expect = 4e-19
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA-QEQ 175
LY+G L ITE LR F FG+I I ++ + FI F + A+ A ++
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 176 LNGFELAGRPMKVG 189
N + GR + V
Sbjct: 69 FNKLIVNGRRLNVK 82
Score = 45.3 bits (108), Expect = 1e-06
Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S E++ T++ L I DL F G++R + ++ + + A+I+F +
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQ 59
Query: 70 SVPLAM--GLNGQKLLGIPIIVQ 90
+ +A N + G + V+
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVK 82
>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 = 79.3 bits (196), Expect = 1e-18
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 104 PNLQPRGTGGPMRLYIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
L PRG+ RL+IG+L N++++ L IF P+G I I + +GFI
Sbjct: 12 SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQ 63
Query: 163 FHSADDAKKAQEQLNGFELAGRPMKV 188
F + + A E + G+ + +
Sbjct: 64 FDNPQSVRDAIEXESQEMNFGKKLIL 89
Score = 53.9 bits (130), Expect = 1e-09
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 6 SDDLSPEERDART-IFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
S L P ++ +F L + + DL FS G + + + +I
Sbjct: 11 SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFI 62
Query: 64 EFKDPESVPLAM-GLNGQKLLGIPIIVQP 91
+F +P+SV A+ + + G +I++
Sbjct: 63 QFDNPQSVRDAIEXESQEMNFGKKLILEV 91
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 78.3 bits (194), Expect = 1e-18
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+++IG L + T++ LR F FG++ +M DP T RS+G+GF+TF K Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 176 LNGFELAGR 184
+ EL +
Sbjct: 62 -SRHELDSK 69
Score = 45.6 bits (109), Expect = 6e-07
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
LS + L E+F G+V++ ++ T+R +G ++ F D V + + +L
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67
Query: 84 G 84
Sbjct: 68 S 68
>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 = 79.2 bits (196), Expect = 1e-18
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++G L N + L F+ FG I I D + + +I + S D A+ A +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSFAYIQYESLDAAQAACAK 72
Query: 176 LNGFELAGRPMKV 188
+ GF L G ++
Sbjct: 73 MRGFPLGGPDRRL 85
Score = 45.7 bits (109), Expect = 9e-07
Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 9/86 (10%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
++ L L F G +R + + + AYI+++ ++ A
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71
Query: 76 GLNGQKLLG--IPIIVQPTQAEKNRA 99
+ G L G + V ++ +
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSSG 97
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L ++ ++ L+ F FG++ + + +DP+TGRS+G+GFI F A +K +Q
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 176 LNGFELAGRPMKV 188
L GR +
Sbjct: 73 KEH-RLDGRVIDP 84
Score = 51.0 bits (123), Expect = 9e-09
Identities = 24/75 (32%), Positives = 36/75 (48%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S E DA +F LS +DL+++F+ G+V D + T R +G +I FKD
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64
Query: 70 SVPLAMGLNGQKLLG 84
SV + +L G
Sbjct: 65 SVEKVLDQKEHRLDG 79
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 79.0 bits (195), Expect = 2e-18
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
+G ++++ IF FGKI N + G++KGY F+ + S A A + +
Sbjct: 25 QVGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 82
Query: 178 GFELAGR-PMKVGTVTD 193
G++L + +V TD
Sbjct: 83 GYKLDKQHTFRVNLFTD 99
Score = 44.7 bits (106), Expect = 3e-06
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLG 84
+ + FS GK+ + + + KG ++E+ P A+ +G KL
Sbjct: 36 NVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88
>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 = 78.8 bits (195), Expect = 2e-18
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G L ++ T++ LR F +G++ + +M D T +S+G+GF+ F +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
L GR + T R G S
Sbjct: 78 -RPHTLDGRNIDPKPCTPRGMQPSGPSS 104
Score = 48.4 bits (116), Expect = 1e-07
Identities = 17/75 (22%), Positives = 30/75 (40%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
+ + +F L L +FS G+V D ++ T + +G +++FKDP
Sbjct: 10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
Query: 70 SVPLAMGLNGQKLLG 84
V + L G
Sbjct: 70 CVGTVLASRPHTLDG 84
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 78.2 bits (193), Expect = 4e-18
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+YI + T D ++ E G++ NIQ+ KG F+ F S + AKK E
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET- 71
Query: 177 NGFELAGRPMKVGTVTDRNE 196
G + + + D
Sbjct: 72 PGQKYKETDLLILFKDDYFA 91
Score = 72.8 bits (179), Expect = 3e-16
Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
+ R+++ D++E+ G+V ++++ + FKG ++ F ES
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESA 65
Query: 72 PLAMGLNGQKLLGIPIIVQPTQ---AEKNR 98
+ GQK +++ A+KN
Sbjct: 66 KKFVETPGQKYKETDLLILFKDDYFAKKNE 95
>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 = 77.7 bits (192), Expect = 5e-18
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 108 PRGTGGPMR---LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
PRG+ ++IG L + T++ LR F FG++ +M DP T RS+G+GF+TF
Sbjct: 16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Query: 165 SADDAKKAQEQLNGFELAGR 184
K Q + EL +
Sbjct: 76 DQAGVDKVLAQ-SRHELDSK 94
Score = 49.2 bits (118), Expect = 8e-08
Identities = 16/75 (21%), Positives = 31/75 (41%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S +F LS + L E+F G+V++ ++ T+R +G ++ F D
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
Query: 70 SVPLAMGLNGQKLLG 84
V + + +L
Sbjct: 79 GVDKVLAQSRHELDS 93
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 83.7 bits (206), Expect = 6e-18
Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 1/100 (1%)
Query: 90 QPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
+ Q + P+ P G + L++ ++++ TE LR FE +G I I ++
Sbjct: 77 RRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+G+ +GY FI + D A + +G ++ GR + V
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 55.2 bits (132), Expect = 1e-08
Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 3/141 (2%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
+T+F +++ L F G ++ + ++ ++ + +G A+IE++ + A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 77 -LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
+G+K+ G ++V P G GG R + D
Sbjct: 163 HADGKKIDGRRVLVD--VERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220
Query: 136 EPFGKIDNIQLMVDPDTGRSK 156
E G D D R +
Sbjct: 221 ERPGPSPLPHRDRDRDRERER 241
>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 = 77.6 bits (191), Expect = 7e-18
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 13/108 (12%)
Query: 109 RGTGGPMR------LYIGSLHFNIT-EDMLRG--IFEPFGKIDNIQLMVDPDTGRSK--- 156
+G +R +++ L + ++L+ F FGKI + + S+
Sbjct: 4 GSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPS 63
Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++T+ ++DA +A + +N + GR +K T + S GPS+
Sbjct: 64 ASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCS-YSGPSS 110
Score = 44.1 bits (104), Expect = 5e-06
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 18 TIFCMQLSQRIRTRDL---EEFFSSVGKVRDVRLI---TCNKTRRFKGIAYIEFKDPESV 71
+F + LSQR+ ++ E+F GK+ V + + ++ AY+ + E
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 72 PLAM-GLNGQKLLGIPI 87
A+ +N + G +
Sbjct: 77 LRAIQCVNNVVVDGRTL 93
>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 = 77.1 bits (190), Expect = 1e-17
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQ 173
RL+IG + + + + + ++ + D +++G+ F+ + S A A+
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 174 EQLN--GFELAGRPMKV 188
+L +L G + V
Sbjct: 70 RKLMPGRIQLWGHQIAV 86
Score = 47.5 bits (113), Expect = 3e-07
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 5/81 (6%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLIT-CNKTRRFKGIAYIEFKDPESV 71
+F + + + ++ E + V + V DV + + +G A++E++ +
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 72 PLA---MGLNGQKLLGIPIIV 89
+A + +L G I V
Sbjct: 66 AMARRKLMPGRIQLWGHQIAV 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 = 75.9 bits (187), Expect = 2e-17
Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 8/95 (8%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G + + +L + + + + + + R+K F+T + + A
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ A + + + G+ + V + + + GPS+
Sbjct: 54 QNAIQMFHQYSFRGKDLIV-QLQPTDALLCSGPSS 87
Score = 40.5 bits (95), Expect = 5e-05
Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 8/78 (10%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
+ I L Q +++ + ++ + R K A++ + E
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYD----LKYCYVD---RNKRTAFVTLLNGEQAQN 55
Query: 74 AM-GLNGQKLLGIPIIVQ 90
A+ + G +IVQ
Sbjct: 56 AIQMFHQYSFRGKDLIVQ 73
>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 = 76.3 bits (188), Expect = 2e-17
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHS 165
+ + +I ++ F+IT+ + E + + ++VD + G+ G + F +
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN-GQGLGQALVQFKN 66
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRN 195
DDA+K++ L+ +L GR V VT +
Sbjct: 67 EDDARKSER-LHRKKLNGREAFVHVVTLED 95
Score = 71.7 bits (176), Expect = 8e-16
Identities = 19/115 (16%), Positives = 36/115 (31%), Gaps = 3/115 (2%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
S + + I D+ +F + + + + + G A
Sbjct: 2 SSGSSGEGDVNS-AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60
Query: 62 YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
++FK+ + + L+ +KL G V E R N +G GP
Sbjct: 61 LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMRE--IEKNPPAQGKSGPSS 113
>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 = 80.3 bits (197), Expect = 2e-17
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 12/89 (13%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYG 159
P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 4 PETRPNHT-----IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQA 55
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 56 FVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Score = 64.5 bits (156), Expect = 6e-12
Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 6/123 (4%)
Query: 68 PESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT 127
P +P + L I ++ G P L++ +L
Sbjct: 161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETN 220
Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL-AGRPM 186
E ML +F F ++L+ F+ F + A A++ L GF++ M
Sbjct: 221 ELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275
Query: 187 KVG 189
K+
Sbjct: 276 KIS 278
Score = 56.4 bits (135), Expect = 3e-09
Identities = 27/175 (15%), Positives = 59/175 (33%), Gaps = 13/175 (7%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
PE R TI+ L+++I+ +L++ FS G++ D+ +++ + +G A++ F
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIL---VSRSLKMRGQAFVIF 59
Query: 66 KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
K+ S A+ + G P+ +Q + + + R R
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKR-----KPK 114
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
+ + + G + + P G + G
Sbjct: 115 SQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGM 169
Score = 39.9 bits (92), Expect = 8e-04
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
+F L + L F+ ++VRL+ IA++EF + A
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-----PGRHDIAFVEFDNEVQAGAARDA 263
Query: 77 LNGQKLL-GIPIIVQ 90
L G K+ + +
Sbjct: 264 LQGFKITQNNAMKIS 278
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 75.3 bits (186), Expect = 3e-17
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 116 RLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
RL+IG+L N++++ L IF P+G I I + +GFI F + + A E
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 63
Query: 175 QLNGFELAGRPMKV 188
+ G+ + +
Sbjct: 64 CESQEMNFGKKLIL 77
Score = 54.9 bits (133), Expect = 6e-10
Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 25 SQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLL 83
+ + DL FS G + + + +I+F +P+SV A+ + +
Sbjct: 20 LKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNF 71
Query: 84 GIPIIVQPTQAEKNRAGN 101
G +I++ + + +
Sbjct: 72 GKKLILEVSSSNARPQFD 89
>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 = 75.1 bits (185), Expect = 4e-17
Identities = 24/114 (21%), Positives = 46/114 (40%), Gaps = 11/114 (9%)
Query: 91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVD 149
+ K +A N P+ R++IG+L+ + + + IF +G++ +
Sbjct: 6 SGMSLKLQASNVTNKNDPKSINS--RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-- 61
Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
KGY F+ + + A+ A NG LAG+ + + + G S
Sbjct: 62 ------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109
Score = 55.1 bits (133), Expect = 6e-10
Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 10/100 (10%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
++ + + + + +F L+ ++ D+E FS G+V + KG
Sbjct: 12 LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KG 63
Query: 60 IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A++++ + A+ G NG+ L G + + K
Sbjct: 64 YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD 103
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 72.0 bits (177), Expect = 3e-16
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 119 IGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
+G ++++ IF FGKI N + G++KGY F+ + S A A + +G
Sbjct: 12 VGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 69
Query: 179 FELAGR 184
++L +
Sbjct: 70 YKLDKQ 75
Score = 43.5 bits (103), Expect = 4e-06
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
+ + FS GK+ + + + KG ++E+ P A+ +G KL
Sbjct: 24 IHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72
>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 = 72.7 bits (178), Expect = 5e-16
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 120 GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
G L ++ + L + E G +D + ++ P+ K Y F + + +++K+A LNG
Sbjct: 33 GGLGNGVSRNQLLPVLEKCGLVDAL--LMPPN----KPYSFARYRTTEESKRAYVTLNGK 86
Query: 180 ELAG 183
E+
Sbjct: 87 EVVD 90
Score = 34.9 bits (80), Expect = 0.009
Identities = 10/74 (13%), Positives = 22/74 (29%), Gaps = 7/74 (9%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+ L + L G V + + K ++ ++ E A L
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYVTL 83
Query: 78 NGQKLLGIPIIVQP 91
NG++++
Sbjct: 84 NGKEVVDDLGQKIT 97
>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 = 70.3 bits (173), Expect = 1e-15
Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G +++G ++TED LR F +G + ++ + + + F+TF A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIA 55
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ + + G + + ++ S G S
Sbjct: 56 QSLCGE--DLIIKGISVHISNAEPKHNSNSGPSS 87
Score = 43.4 bits (103), Expect = 5e-06
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
+ +F + + + +L EFFS G V DV + + F+ A++ F D +
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQS 57
Query: 74 AMGLNGQKLLGIPIIV 89
G + GI + +
Sbjct: 58 LCG-EDLIIKGISVHI 72
>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 = 69.7 bits (171), Expect = 4e-15
Identities = 28/40 (70%), Positives = 32/40 (80%)
Query: 266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
P+ATQCF L+NMF+P TE WD EI+DDVIEECNKHG
Sbjct: 3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHG 42
Score = 35.8 bits (83), Expect = 0.004
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 9/65 (13%)
Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG--FELAG 183
I +D+ G + +I + + G ++ S A A L+G F AG
Sbjct: 30 IKDDV-IEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHGRWF--AG 82
Query: 184 RPMKV 188
+ +
Sbjct: 83 KMITA 87
Score = 26.9 bits (60), Expect = 5.3
Identities = 9/49 (18%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNG 79
D+ E + G V + + + + G Y++ + A+ L+G
Sbjct: 33 DVIEECNKHGGVIHIYV--DKNSAQ--GNVYVKCPSIAAAIAAVNALHG 77
>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 = 69.1 bits (169), Expect = 7e-15
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 9/88 (10%)
Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
+ +++ L ++ E L E FG I + +M K +
Sbjct: 4 GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVE 57
Query: 163 FHSADDAKKAQE--QLNGFELAGRPMKV 188
F + D AK+ +AG+
Sbjct: 58 FENIDSAKECVTFAADVPVYIAGQQAFF 85
Score = 45.6 bits (108), Expect = 1e-06
Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 10/93 (10%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ L + + DL E G + V + FK A +EF++ +S +
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVT 69
Query: 76 --GLNGQKLLGIPIIVQP-TQAEKNRAGNTLPN 105
+ G T R GN+ P+
Sbjct: 70 FAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102
>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 = 69.1 bits (169), Expect = 8e-15
Identities = 11/72 (15%), Positives = 23/72 (31%), Gaps = 6/72 (8%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+ +L ++ F FG + + L + F +A+KA L
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66
Query: 177 NGFELAGRPMKV 188
+ P+ +
Sbjct: 67 AYSKFHHVPLYL 78
Score = 52.1 bits (125), Expect = 8e-09
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 7/82 (8%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
R I L +++E FS G + V L A +EF +P
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPL 57
Query: 70 SVPLAM-GLNGQKLLGIPIIVQ 90
A L K +P+ ++
Sbjct: 58 EARKAFRHLAYSKFHHVPLYLE 79
>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 = 68.6 bits (168), Expect = 9e-15
Identities = 17/94 (18%), Positives = 40/94 (42%), Gaps = 1/94 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
SP+ + + L ++ +FFS + V + + + R G A+++F E
Sbjct: 9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68
Query: 70 SVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNT 102
A+ + +++ I + ++AE +G +
Sbjct: 69 IAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPS 102
Score = 66.3 bits (162), Expect = 6e-14
Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 1/104 (0%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + T + + L F +++ + F + N + GRS G
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
F+ F S + A+KA + + + R +++ + G S
Sbjct: 61 FVQFASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVRTSGPSS 103
>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 = 68.2 bits (167), Expect = 1e-14
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 3/94 (3%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
+ + + + F+ E+ +R F ++D + L+ D GR+ G G + F S D
Sbjct: 13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTF 70
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+A + N + R ++V T+R GG
Sbjct: 71 EALK-RNRMLMIQRYVEVSPATERQWVAAGGHIT 103
Score = 64.8 bits (158), Expect = 3e-13
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 3/97 (3%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
P D + + D+ +FF + +V V L+ + R G ++F P+
Sbjct: 10 LPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQ 67
Query: 70 SVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPN 105
A+ N ++ + V P T+ + AG + +
Sbjct: 68 DTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITS 104
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 67.9 bits (166), Expect = 1e-14
Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 8/74 (10%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
++I L + E L + FG I + +M K + F A A
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77
Query: 177 --NGFELAGRPMKV 188
N +AG P V
Sbjct: 78 ADNQIYIAGHPAFV 91
Score = 45.9 bits (109), Expect = 8e-07
Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 9/77 (11%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
+ L + DL E G + V ++ K A +EF+D A+
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVN 75
Query: 76 --GLNGQKLLGIPIIVQ 90
N + G P V
Sbjct: 76 YAADNQIYIAGHPAFVN 92
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 68.0 bits (166), Expect = 2e-14
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
G+G P R ++I L ++TE + + PFGK+ N+ ++ + K FI ++
Sbjct: 8 HHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 61
Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
+ A L G+P+ +
Sbjct: 62 EEAANTMVNYYTSVTPVLRGQPIYI 86
Score = 47.9 bits (114), Expect = 2e-07
Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 9/93 (9%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
MR ++ +R I +L + ++ GKV ++ ++ + K
Sbjct: 1 MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQ 54
Query: 61 AYIEFKDPESVPLAM---GLNGQKLLGIPIIVQ 90
A+IE E+ + L G PI +Q
Sbjct: 55 AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 87
>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 = 68.0 bits (166), Expect = 2e-14
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
R G P R ++I L ++TE + + PFGK+ N+ ++ + K FI ++
Sbjct: 23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 76
Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
+ A L G+P+ +
Sbjct: 77 EEAANTMVNYYTSVTPVLRGQPIYI 101
Score = 48.4 bits (115), Expect = 2e-07
Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 9/92 (9%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
R ++ D +R I +L + ++ GKV ++ ++ + K A
Sbjct: 17 RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 70
Query: 62 YIEFKDPESVPLAM---GLNGQKLLGIPIIVQ 90
+IE E+ + L G PI +Q
Sbjct: 71 FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102
>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 = 68.3 bits (167), Expect = 3e-14
Identities = 14/95 (14%), Positives = 36/95 (37%), Gaps = 3/95 (3%)
Query: 94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG 153
+ + + + +++ L + TE+ + F P + + + PD G
Sbjct: 26 GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-G 83
Query: 154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
R G + F + ++A A + + R +++
Sbjct: 84 RVTGEADVEFATHEEAVAAMS-KDRANMQHRYIEL 117
Score = 58.7 bits (142), Expect = 7e-11
Identities = 21/110 (19%), Positives = 37/110 (33%), Gaps = 3/110 (2%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
R + + + + + L + D+ FFS + VR V I R G A
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VH-IEIGPDGRVTGEA 89
Query: 62 YIEFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRG 110
+EF E AM + + I + + + + +Q G
Sbjct: 90 DVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGMG 139
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 67.5 bits (165), Expect = 3e-14
Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 3/93 (3%)
Query: 96 KNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRS 155
+ + + R+ + +L + L+ + +T
Sbjct: 10 HSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDF 66
Query: 156 KGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
G G + F S + +A E+LN E G + V
Sbjct: 67 DGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 41.0 bits (96), Expect = 7e-05
Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 4/81 (4%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S I L + +DL++ + TR F G +EF E
Sbjct: 22 SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN---TRDFDGTGALEFPSEE 78
Query: 70 SVPLAMG-LNGQKLLGIPIIV 89
+ A+ LN + G I V
Sbjct: 79 ILVEALERLNNIEFRGSVITV 99
>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 = 67.2 bits (164), Expect = 5e-14
Identities = 18/116 (15%), Positives = 39/116 (33%), Gaps = 3/116 (2%)
Query: 75 MGLNGQKL-LGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLR 132
MG + ++ + + G + + + L F T++ +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIV 60
Query: 133 GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F + N + G+ G F+ F S + A+KA + + R ++V
Sbjct: 61 QFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV 115
Score = 61.8 bits (150), Expect = 4e-12
Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 1/90 (1%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + + + L ++ +FFS + V + + + + G A+++F E
Sbjct: 36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95
Query: 70 SVPLAMGLNGQKLLGIPIIVQP-TQAEKNR 98
A+G + +++ I V +Q E
Sbjct: 96 LAEKALGKHKERIGHRYIEVFKSSQEEVRS 125
>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 = 66.3 bits (162), Expect = 5e-14
Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
+ +++ L + TE+ + F P + + + PD GR G + F +
Sbjct: 8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATH 65
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+DA A + + R +++ + + G GPS+
Sbjct: 66 EDAVAAMA-KDKANMQHRYVEL-FLNSTAGTSGSGPSS 101
Score = 55.9 bits (135), Expect = 3e-10
Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 3/96 (3%)
Query: 6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
S S + + L R D+ FFS + V + R G A +EF
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEF 62
Query: 66 KDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAG 100
E AM + + + + + A + +G
Sbjct: 63 ATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSG 98
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 67.2 bits (164), Expect = 6e-14
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
+Y+ L F + F+ +++ + G++ G GF+ F + D K A
Sbjct: 25 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84
Query: 174 EQLNGFELAGRPMKVGTVTDRN 195
+ + R ++V +T +
Sbjct: 85 C-RHKQYMGNRFIQVHPITKKG 105
Score = 66.0 bits (161), Expect = 1e-13
Identities = 14/92 (15%), Positives = 29/92 (31%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
++ L + + +FF + V D I + G ++EF+
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
+ A+ + Q + I V P +
Sbjct: 76 NEADYKAALCRHKQYMGNRFIQVHPITKKGML 107
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 65.4 bits (160), Expect = 1e-13
Identities = 13/81 (16%), Positives = 29/81 (35%), Gaps = 6/81 (7%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G+ G +++ + L F FG + ++ ++D D G + +
Sbjct: 2 SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVG 56
Query: 168 DAKKAQEQLNGFELAGRPMKV 188
+ Q + L G ++V
Sbjct: 57 AREAVLSQ-SQHSLGGHRLRV 76
Score = 57.7 bits (140), Expect = 4e-11
Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S R++F + + + L E+F + G V V + F A +E D
Sbjct: 2 SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK--DKGVF---AIVEMGDVG 56
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG 110
+ + + L G + V+P + ++ ++ + P+G
Sbjct: 57 AREAVLSQSQHSLGGHRLRVRPREQKEFQSP---ASKSPKG 94
>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 = 64.8 bits (158), Expect = 2e-13
Identities = 15/99 (15%), Positives = 29/99 (29%), Gaps = 10/99 (10%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P R+ + L + + L+ G + + G G + F +
Sbjct: 9 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKE 61
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVT---DRNESVGGGPS 203
D A +L+ + + + D S G S
Sbjct: 62 DMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRS 100
Score = 42.5 bits (100), Expect = 1e-05
Identities = 14/80 (17%), Positives = 23/80 (28%), Gaps = 8/80 (10%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
P R + L +DL++ G V + G +EF E
Sbjct: 10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKED 62
Query: 71 VPLAM-GLNGQKLLGIPIIV 89
+ A+ L+ K
Sbjct: 63 MTYAVRKLDNTKFRSHEGET 82
>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 = 63.9 bits (156), Expect = 4e-13
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+ + FN+TE + P K I+++ + G GY F+ F + ++ K+A +
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALK-C 69
Query: 177 NGFELAGRPMKV 188
N + GR ++V
Sbjct: 70 NREYMGGRYIEV 81
Score = 55.0 bits (133), Expect = 4e-10
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 3/84 (3%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
T+ + +++ EF + + K +R++ N G +++F + E V A
Sbjct: 9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQA 66
Query: 75 MGLNGQKLLGIPIIVQP-TQAEKN 97
+ N + + G I V +
Sbjct: 67 LKCNREYMGGRYIEVFREKSGPSS 90
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 63.7 bits (155), Expect = 4e-13
Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)
Query: 108 PRGTGGPM--RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
P G G P+ +Y+G+L + L+ G + + + F+ +
Sbjct: 11 PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFLHYPD 65
Query: 166 ADDAKKAQEQLNGFELAGRPMKV 188
+ A++A L G L ++V
Sbjct: 66 SAAAQQAVSCLQGLRLGTDTLRV 88
Score = 52.1 bits (125), Expect = 6e-09
Identities = 16/88 (18%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
A ++ L + R DL+ +G V +RL + + A++ + D +
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRL----TWQGPRRRAFLHYPDSAAA 69
Query: 72 PLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
A+ L G +L + V + ++++
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQQRDK 97
>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 = 63.7 bits (155), Expect = 4e-13
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 9/85 (10%)
Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
+ G P R L+I L +TE + + PFGK+ NI ++ + K F+ +
Sbjct: 7 GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELAT 60
Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
+ A L +P+ +
Sbjct: 61 EEAAITMVNYYSAVTPHLRNQPIYI 85
Score = 44.4 bits (105), Expect = 3e-06
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 9/77 (11%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
R + +L + ++ GKV ++ ++ + K A++E E+ +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69
Query: 76 --GLNGQKLLGIPIIVQ 90
L PI +Q
Sbjct: 70 YYSAVTPHLRNQPIYIQ 86
>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 = 64.1 bits (156), Expect = 4e-13
Identities = 11/96 (11%), Positives = 27/96 (28%), Gaps = 7/96 (7%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P R+ + L + + L+ G + + G G + F +
Sbjct: 10 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKE 62
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
D A +L+ + + + + +
Sbjct: 63 DMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 98
Score = 43.7 bits (103), Expect = 7e-06
Identities = 14/89 (15%), Positives = 23/89 (25%), Gaps = 8/89 (8%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
P R + L +DL++ G V + G
Sbjct: 2 GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTG 54
Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
+EF E + A+ L+ K
Sbjct: 55 VVEFVRKEDMTYAVRKLDNTKFRSHEGET 83
>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 = 63.0 bits (153), Expect = 1e-12
Identities = 21/109 (19%), Positives = 36/109 (33%), Gaps = 5/109 (4%)
Query: 9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFKGIAYIEF 65
L PE + + L D++ F S V V I + R G A++E
Sbjct: 10 LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVEL 68
Query: 66 KDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRGTGG 113
+ + V LA+ + + + I V + E + G
Sbjct: 69 ESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117
Score = 57.2 bits (138), Expect = 1e-10
Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 6/92 (6%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSK 156
G++ L P G G + + + L ++ + + ++ + + + + GR
Sbjct: 4 GSSGMMLGPEGGEGYV-VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQS 61
Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
G F+ S DD K A + + + R ++V
Sbjct: 62 GEAFVELESEDDVKLALK-KDRESMGHRYIEV 92
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 61.5 bits (150), Expect = 2e-12
Identities = 10/81 (12%), Positives = 34/81 (41%), Gaps = 7/81 (8%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G ++T + L+ F +G++ ++ + + + F+TF A+ +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE 67
Query: 176 LNGFELAGRPMKVGTVTDRNE 196
+ G + + ++
Sbjct: 68 --DLIIKGISVHISNAEPKHN 86
Score = 46.8 bits (112), Expect = 4e-07
Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 9/91 (9%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
+F + ++ + +L++FF G+V DV + + F+ A++ F D +
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDK 59
Query: 70 SVPLAMGLNGQKLLGIPIIV---QPTQAEKN 97
G + GI + + +P + N
Sbjct: 60 VAQSLCG-EDLIIKGISVHISNAEPKHNKLN 89
>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 = 62.4 bits (151), Expect = 6e-12
Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
+ G +R+ + +L + +T D+L IF FG + I ++ + +
Sbjct: 36 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQY 91
Query: 164 HSADDAKKAQEQLNGFELAGRPMKV 188
A+ A+ L+G + +
Sbjct: 92 ADPVSAQHAKLSLDGQNIYNACCTL 116
Score = 33.5 bits (76), Expect = 0.043
Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 6/75 (8%)
Query: 3 PAYSDDLSPEERDARTIFC--MQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
A D + + L + L + FS G V ++IT K +F+
Sbjct: 31 AAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIITFTKNNQFQ-- 86
Query: 61 AYIEFKDPESVPLAM 75
A +++ DP S A
Sbjct: 87 ALLQYADPVSAQHAK 101
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 61.2 bits (148), Expect = 8e-12
Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
+ G +R+ + +L + +T D+L IF FG + I ++ + +
Sbjct: 18 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQY 73
Query: 164 HSADDAKKAQEQLNGFELAGRPMKV 188
A+ A+ L+G + +
Sbjct: 74 ADPVSAQHAKLSLDGQNIYNACCTL 98
Score = 31.9 bits (72), Expect = 0.12
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 23 QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
L + L + FS G V ++IT K +F+ A +++ DP S A
Sbjct: 35 NLFYPVTLDVLHQIFSKFGTVL--KIITFTKNNQFQ--ALLQYADPVSAQHAK 83
>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 = 60.8 bits (147), Expect = 1e-11
Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 5/102 (4%)
Query: 2 RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFK 58
S L PE + + L D++ F S V I + R
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREGRQS 88
Query: 59 GIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRA 99
G A++E + V +A+ + + + I V + E +
Sbjct: 89 GEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWV 130
Score = 57.7 bits (139), Expect = 2e-10
Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 5/88 (5%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSKGYGF 160
+ G + + L ++ + + ++ + + + GR G F
Sbjct: 34 SMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAF 92
Query: 161 ITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ S DD K A + + + R ++V
Sbjct: 93 VELGSEDDVKMALK-KDRESMGHRYIEV 119
>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 = 60.1 bits (146), Expect = 1e-11
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 265 APPIATQCFLLANMFDPA-TETNPTWDVEIRDDVIEECNKHG 305
+ + ++ NMF P E +P EIR+D+ EC+K G
Sbjct: 10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFG 51
Score = 36.2 bits (84), Expect = 0.003
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
I ED+ FG+I + L G ++F ++A + L+G GR
Sbjct: 39 IREDLRVE-CSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQTLDGRWFGGRQ 93
Query: 186 MKV 188
+
Sbjct: 94 ITA 96
Score = 28.9 bits (65), Expect = 0.96
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
DL S G++R + L + G+A + F+DPE + L+G+ G I Q
Sbjct: 42 DLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
>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 = 59.5 bits (144), Expect = 2e-11
Identities = 17/97 (17%), Positives = 31/97 (31%), Gaps = 5/97 (5%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFKGIAYI 63
L E D I L D+ FFS + + N+ + +G A I
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALI 60
Query: 64 EFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRA 99
E + + V A+ + + + V + +
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDAL 97
Score = 55.2 bits (133), Expect = 6e-10
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
+ L ++ T + + F + I +++ D G+ +G I S D +KA
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72
Query: 174 EQLNGFELAGRPMKV 188
E + + R ++V
Sbjct: 73 E-KHRMYMGQRYVEV 86
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 59.1 bits (143), Expect = 3e-11
Identities = 24/117 (20%), Positives = 41/117 (35%), Gaps = 14/117 (11%)
Query: 99 AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI----DNIQLMVDPDTGR 154
G + Q + + + L F T + + F I + I + PD GR
Sbjct: 8 GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GR 66
Query: 155 SKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV--------GTVTDRNESVGGGPS 203
G F+ F + A+ A + + L R +++ V +R S G S
Sbjct: 67 PTGDAFVLFACEEYAQNA-LRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122
Score = 56.4 bits (136), Expect = 3e-10
Identities = 17/106 (16%), Positives = 32/106 (30%), Gaps = 4/106 (3%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVR---LITCNKTRRFKGIAYIEFKD 67
+ + + L ++ FF + + L R G A++ F
Sbjct: 18 LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFAC 77
Query: 68 PESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRGTG 112
E A+ + L I + T AE + N + +G
Sbjct: 78 EEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSSG 123
>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 = 59.8 bits (144), Expect = 9e-11
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
R+++ D++E+ G+V ++++ + FKG ++ F ES +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESAKKFVE 168
Query: 77 LNGQKLLGIPIIVQPTQ---AEKN 97
GQK +++ A+KN
Sbjct: 169 TPGQKYKETDLLILFKDDYFAKKN 192
Score = 59.8 bits (144), Expect = 9e-11
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 2/79 (2%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+YI + T D ++ E G++ NIQ+ KG F+ F S + AKK E
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 168
Query: 175 QLNGFELAGRPMKVGTVTD 193
+ + + D
Sbjct: 169 TPGQ-KYKETDLLILFKDD 186
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 55.6 bits (134), Expect = 4e-10
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 270 TQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
T+ L NM P + EI +DV +EC+K+G
Sbjct: 5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYG 40
Score = 41.3 bits (97), Expect = 4e-05
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 126 ITEDMLRGIFEPFGKIDNIQL--MVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
I ED+ R +G + +I++ VD G F+ F S D +KA + L G + A
Sbjct: 28 IVEDV-RDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN 86
Query: 184 RPMKV 188
R +
Sbjct: 87 RVVVT 91
Score = 29.0 bits (65), Expect = 0.84
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 32 DLEEFFSSVGKVRDVRL--ITCNKTRRFKGIAYIEFKDPESVPLAM-GLNG 79
D+ + S G V+ + + G ++EF AM GL G
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
>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 = 55.3 bits (133), Expect = 5e-10
Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 10/96 (10%)
Query: 97 NRAGNTLPNLQPRGTGGPMR-LYIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR 154
+ P+ + R +++ +L H ++ + + EP+GKI N LM R
Sbjct: 7 GKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------R 60
Query: 155 SKGYGFITFHSADDAKKAQE--QLNGFELAGRPMKV 188
K FI + +DA + GR +KV
Sbjct: 61 MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 55.4 bits (133), Expect = 6e-10
Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 11/90 (12%)
Query: 110 GTGGPMR---LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD--TGRSKGYGFITFH 164
G+ G +++G L +I ED + F FG + KGY F+ F
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 165 ---SADDAKKAQEQLNG---FELAGRPMKV 188
S A + +G ++ +K
Sbjct: 61 EESSVQALIDACLEEDGKLYLCVSSPTIKD 90
Score = 41.9 bits (98), Expect = 3e-05
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 2/68 (2%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLI--TCNKTRRFKGIAYIEFKD 67
S +R +F L I ++ F G + KG A++ F++
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 68 PESVPLAM 75
SV +
Sbjct: 62 ESSVQALI 69
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 55.6 bits (133), Expect = 4e-09
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 117 LYIGSLHFNIT---------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
LY+G + + E +R +F G ID I+ + SK GF+ F
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQA 190
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESV 198
+A+ A+E ++ L K +
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGTGL 221
Score = 34.8 bits (79), Expect = 0.029
Identities = 17/122 (13%), Positives = 40/122 (32%), Gaps = 23/122 (18%)
Query: 1 MRPAYSDDLS---PEERDARTIFCMQLSQRIRTR---------DLEEFFSSVGKVRDVRL 48
Y +D+ + +T++ + + ++ + FS +G + +R
Sbjct: 116 KFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY 175
Query: 49 ITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA----GNTL 103
+ K +++FK + A ++ Q LL + E N
Sbjct: 176 VE------SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANED 229
Query: 104 PN 105
P+
Sbjct: 230 PD 231
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 49.8 bits (119), Expect = 6e-08
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 254 NSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
+S+ V + +L NM DP D ++ +V EEC K G
Sbjct: 4 SSARHMVMQKLLRKQESTVMVLRNMVDPKD-----IDDDLEGEVTEECGKFG 50
Score = 34.7 bits (80), Expect = 0.010
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 138 FGKIDNIQLMVDPDTGRSKGYG----FITFHSADDAKKAQEQLNGFELAGRPMKV 188
FG ++ + + + F+ F A + KA + LNG AGR +
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVA 103
>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 = 49.1 bits (117), Expect = 9e-08
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
E++ + E +G+++ + + D G ++ F +DA+KA LN G+P+
Sbjct: 41 EEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 188 V 188
Sbjct: 100 A 100
Score = 30.6 bits (69), Expect = 0.23
Identities = 8/51 (15%), Positives = 13/51 (25%), Gaps = 16/51 (31%)
Query: 271 QCFLLANMFDP----------------ATETNPTWDVEIRDDVIEECNKHG 305
Q L N++ E +D + E K+G
Sbjct: 2 QTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYG 52
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 48.9 bits (116), Expect = 1e-07
Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 10/100 (10%)
Query: 91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
+ R GN P G + L I + + IT D+L + P GK+ I
Sbjct: 5 SSGKRITRPGN---TDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRI-----V 56
Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR--PMKV 188
R+ + F S A+KA+ LNG ++ +K+
Sbjct: 57 IFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI 96
Score = 32.3 bits (73), Expect = 0.081
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 6/67 (8%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+ I L + VGKV+ + + N + A +EF+ A L
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ-----AMVEFESVLCAQKAKAAL 82
Query: 78 NGQKLLG 84
NG +
Sbjct: 83 NGADIYA 89
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 51.6 bits (123), Expect = 3e-07
Identities = 57/323 (17%), Positives = 98/323 (30%), Gaps = 116/323 (35%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI---AYI-------EFKDP 68
I +QL+ + T L F + G++R T +G+ I F
Sbjct: 241 IGVIQLAHYVVTAKLLGF--TPGELRS---YLKGATGHSQGLVTAVAIAETDSWESFF-- 293
Query: 69 ESVPLAM------GLNGQKLLGI----PIIVQ---------PT-----------QAEK-- 96
SV A+ G+ + P I++ P+ Q +
Sbjct: 294 VSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
Query: 97 NRAGNTLPNLQ---------PRG---TGGPMRLYIGSLHFNITEDMLRGIFEPFG----K 140
N+ + LP + + +G P LY N+T LR P G +
Sbjct: 354 NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLY----GLNLT---LRKAKAPSGLDQSR 406
Query: 141 IDNIQLMVDPDTGR----SKGYGFIT--FHS---ADDAKKAQEQL--NGFELAGRPMKV- 188
I P + R S + + FHS + + L N + +++
Sbjct: 407 I--------PFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIP 458
Query: 189 --GTVT--DRNESVGGGPSNLDTDEMERAGVD-----------------LGATGRLQLMF 227
T D G + D + R V GA+G L
Sbjct: 459 VYDTFDGSDLRVLSGSISERI-VDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTH 517
Query: 228 KLAEGTGLELPPAAASALNLAQN 250
+ +GTG+ + A L++ +
Sbjct: 518 RNKDGTGVRV--IVAGTLDINPD 538
Score = 35.4 bits (81), Expect = 0.034
Identities = 64/433 (14%), Positives = 117/433 (27%), Gaps = 160/433 (36%)
Query: 6 SDD--LSPEERDARTI-FCMQLSQRIRTRD--------LEEFFSSVGKVRDV-----RLI 49
+DD +P E + + + L + + L EF + + D+ +L+
Sbjct: 50 ADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 50 TCNKT---RRFKGI-AYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA--EKNRAGNTL 103
N T + + I YI + + P + A GN
Sbjct: 110 QENDTTLVKTKELIKNYIT--------------ARIMAKRPFDKKSNSALFRAVGEGNA- 154
Query: 104 PNLQPRGTGGPMRLYIGSLHF----NITE--DMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
+L F N + + LR +++ + ++V
Sbjct: 155 ------------QLV---AIFGGQGNTDDYFEELRDLYQTY------HVLVGD------- 186
Query: 158 YGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDL 217
I F + ++ + L+ ++ + + + + + P D D + +
Sbjct: 187 --LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT---P---DKDYLLSIPISC 238
Query: 218 GATGRLQL----------------MFKLAEGT---GLELPPAAASA--------LNLAQN 250
G +QL + +G L A A A +
Sbjct: 239 PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRK 298
Query: 251 AI-------LNS--STPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRD------ 295
AI + + P S PP + L E P+ + I +
Sbjct: 299 AITVLFFIGVRCYEAYPNTSL---PPSILEDSL------ENNEGVPSPMLSISNLTQEQV 349
Query: 296 -DVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVN-------------LW--CRHARKQD 339
D + + N H V I L VN L+ RK
Sbjct: 350 QDYVNKTNSHLPAGKQV-----EISL-------VNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 340 NPGH--QRRQSMS 350
P Q R S
Sbjct: 398 APSGLDQSRIPFS 410
Score = 33.5 bits (76), Expect = 0.12
Identities = 49/291 (16%), Positives = 80/291 (27%), Gaps = 118/291 (40%)
Query: 107 QPRGTGGPMRLYIGSLHF-NITEDMLRGIFEPFG----KI--DN-IQLMV--DPDTGRS- 155
Q +G G M LY S ++ + +G I +N + L + + G+
Sbjct: 1627 QEQGMG--MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI 1684
Query: 156 -KGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVG-GGPSNLDTDEMERA 213
+ Y + F + D K E++ F+ + + + S L
Sbjct: 1685 RENYSAMIFETIVDGKLKTEKI--FK---------EINEHSTSYTFRSEKGL-------- 1725
Query: 214 GVDLGATGRLQ--LM------FKLAEGTGLELPPAA-A-------SALNLAQNAILNSST 257
L AT Q L F+ + GL A A +AL
Sbjct: 1726 ---LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAAL------------ 1770
Query: 258 PQVSSSTAPPIATQCFLL------ANMFDPATET----------NP-----TWDVEIRDD 296
S + I + ++ + P E NP ++ E
Sbjct: 1771 --ASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQY 1828
Query: 297 VIEECNKHGVGAST--VCFIYSVIFLKLWSYVQVNLWCRHARKQDN-PGHQ 344
V+E VG T + I VN N Q
Sbjct: 1829 VVER-----VGKRTGWLVEI-------------VN---------YNVENQQ 1852
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 46.0 bits (109), Expect = 8e-07
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
T+ LL NM D ++ + EEC K+G
Sbjct: 4 GKCPTKVVLLRNMVGAGEV-----DEDLEVETKEECEKYG 38
Score = 31.0 bits (70), Expect = 0.16
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 1/62 (1%)
Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGR-SKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
E + E +GK+ + P F+ F + A KA LNG GR +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 187 KV 188
K
Sbjct: 87 KA 88
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 45.2 bits (107), Expect = 2e-06
Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 10/88 (11%)
Query: 105 NLQPRGTGGPMR-LYIGSLHFNI-TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
+ +G R ++I L + EPFG I N ++ FI
Sbjct: 5 SSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIE 58
Query: 163 FHSADDAKKAQE--QLNGFELAGRPMKV 188
+ +DA+ A + + G+P++V
Sbjct: 59 MATTEDAQAAVDYYTTTPALVFGKPVRV 86
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 44.2 bits (104), Expect = 4e-06
Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 7/95 (7%)
Query: 110 GTGGPMRLYIGSLHFNITED----MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
+G + + ++ + ++ +L+ F GK+ +++L D + + +
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMEN 61
Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
DA A L+ +++ + + V T + G
Sbjct: 62 LQDAIGAVNSLHRYKIGSKKILVSLATGASGPSSG 96
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 41.1 bits (96), Expect = 5e-05
Identities = 19/103 (18%), Positives = 38/103 (36%), Gaps = 7/103 (6%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G + + + L + +++L FE + ++ R G +TF DA
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---SWQRLGCGGVLTFREPADA 60
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNES---VGGGPSNLDTDE 209
++ Q + EL G + + R + + G P
Sbjct: 61 ERVLAQAD-HELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPS 102
Score = 37.6 bits (87), Expect = 8e-04
Identities = 11/106 (10%), Positives = 29/106 (27%), Gaps = 6/106 (5%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S + L + L +F + + +++ + + F++P
Sbjct: 2 SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG---GVLTFREPA 58
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQAEKNRA---GNTLPNLQPRGTG 112
+ +L G + ++P P +G
Sbjct: 59 DAERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPSSG 104
>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 = 42.8 bits (100), Expect = 1e-04
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 117 LYI--GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
L + G L ++ + L + E G +D + + +K Y F + + +++K+A
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYV 74
Query: 175 QLNGFELAGRP 185
LNG E+
Sbjct: 75 TLNGKEVVDDL 85
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 39.4 bits (91), Expect = 2e-04
Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
++D+L + + +G++ N+ L + + G + F + A+ A + G L
Sbjct: 28 GYSKDVLLRLLQKYGEVLNLVL-----SSKKPGTAVVEFATVKAAELAVQNEVG--LVDN 80
Query: 185 PMKVGTVTDRNESVGGGPS 203
P+K+ + + + G S
Sbjct: 81 PLKISWLEGQPQDASGPSS 99
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 35.0 bits (80), Expect = 0.005
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 6/84 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G L + +L I LR + G + + ++G + + ++A
Sbjct: 3 MAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP------YLNQGIALCKYTTREEA 56
Query: 170 KKAQEQLNGFELAGRPMKVGTVTD 193
KAQ LN LA + + ++
Sbjct: 57 NKAQMALNNCVLANTTIFAESPSE 80
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 32.8 bits (74), Expect = 0.031
Identities = 7/34 (20%), Positives = 18/34 (52%)
Query: 155 SKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ + F + D A++AQ+++ ++ G + V
Sbjct: 45 TGCSAILRFINQDSAERAQKRMENEDVFGNRIIV 78
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 32.4 bits (73), Expect = 0.062
Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 11/74 (14%)
Query: 125 NITEDMLRGIFE-----PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
++ ++ + I I L+ D I F + A K LNG
Sbjct: 32 KVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGS 85
Query: 180 ELAGRPMKVGTVTD 193
+ G+ ++ GT+ D
Sbjct: 86 QFQGKVIRSGTIND 99
>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 = 30.3 bits (67), Expect = 0.54
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 224 QLMFKLAEGTGLEL-PPAAASALNLAQNAIL 253
Q + KL + + L+L +A AL A A +
Sbjct: 20 QALKKL-QAS-LKLYADDSAPAL--AIKATM 46
Score = 29.5 bits (65), Expect = 1.2
Identities = 8/55 (14%), Positives = 17/55 (30%), Gaps = 29/55 (52%)
Query: 26 QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQ 80
Q ++ L+ +S+ +L Y +S P A+ +
Sbjct: 20 QALKK--LQ---ASL------KL-------------Y----ADDSAP-ALAIKAT 45
>1n69_A Saposin B; lipid binding protein, glycosphingolipid activator
protein; HET: PEH; 2.20A {Homo sapiens} SCOP: a.64.1.3
Length = 81
Score = 28.4 bits (63), Expect = 0.80
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 272 CFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVC--FI--YSVIFLKLWSYVQ 327
C + A TN T+ + + V EEC++ G G + +C +I YS I +++ ++Q
Sbjct: 9 CIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQ 68
Query: 328 VNLWCRHA 335
C
Sbjct: 69 PKEICALV 76
>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 = 30.2 bits (67), Expect = 1.3
Identities = 17/129 (13%), Positives = 36/129 (27%), Gaps = 40/129 (31%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG------ 153
+ L + ++ + +DM + I +ID+I + D +G
Sbjct: 19 KDILSVFEDA--------FVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFW 69
Query: 154 --RSKG---------------YGFIT--FHS-----ADDAKKAQEQLNGFELAGRPMKVG 189
SK Y F+ + + + EQ + +
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129
Query: 190 TVTDRNESV 198
V+ R +
Sbjct: 130 NVS-RLQPY 137
>1yac_A Ycacgp, YCAC gene product; unknown bacterial hydrolase, three layer
alpha-beta-alpha SA topology, ENTB homolog, cshase
homolog; 1.80A {Escherichia coli} SCOP: c.33.1.3
Length = 208
Score = 28.6 bits (64), Expect = 2.6
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 81 KLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
K +P I+ T AE G +P L+ + P
Sbjct: 48 KYFNLPTILT-TSAETGPNGPLVPELKAQFPDAP 80
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 26.5 bits (58), Expect = 5.1
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP 91
+L + F+S G+V +R + + ++ F + S + LNG++LL I +
Sbjct: 31 ELLQQFASFGEVILIRFV--------EDKMWVTFLEGSSALNVLSLNGKELLNRTITIAL 82
>1oao_A CODH, carbon monoxide dehydrogenase/acetyl-COA synthase beta;
oxidoreductase-transferase complex, electron transfer,
oxidoreductase; 1.90A {Moorella thermoacetica} SCOP:
e.26.1.2 PDB: 1mjg_A 2z8y_A 3i01_A 3i04_A
Length = 674
Score = 28.1 bits (62), Expect = 5.3
Identities = 17/127 (13%), Positives = 42/127 (33%), Gaps = 20/127 (15%)
Query: 46 VRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPN 105
R+IT + G +I+++ ++ A I +A K R + P
Sbjct: 369 TRIITTADNAKIPGAYHIDYQTATAIESAK----------TAIRMAIEAFKERKESNRPV 418
Query: 106 LQPRG-----TGGPMRLYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMV---DPDTGRS 155
P+ G + L ++ +R + + G++ + L+ + +
Sbjct: 419 YIPQIKNRVVAGWSLEALTKLLATQNAQNPIRVLNQAILDGELAGVALICGCNNLKGFQD 478
Query: 156 KGYGFIT 162
+ +
Sbjct: 479 NSHLTVM 485
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 27.0 bits (59), Expect = 5.9
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD-----AKKAQEQLNGF 179
NI + ++ F+ +G+I + + DP++ I + S+D AK A +
Sbjct: 17 NIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKH 76
Query: 180 ELAG 183
E +G
Sbjct: 77 ESSG 80
>4dqz_A Methyltransferase type 12; ligase-activating, bacterial PNKP; 2.30A
{Clostridium thermocellum} PDB: 4drf_B 4e6n_B*
Length = 230
Score = 27.4 bits (61), Expect = 7.3
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVD---PDTGRSKGYGFIT 162
P++ I L E+++ +FEP G K+D M+D P+ G+S+ Y ++
Sbjct: 117 PLKAKIMMLPCKGGEEIIYRLFEPLGYKVDVEGYMLDEKFPEWGKSR-YYTVS 168
>1i82_A Xylanase A, endo-1,4-beta-xylanase A; cellobiose complex,
hydrolase; HET: BGC; 1.90A {Thermotoga maritima} SCOP:
b.1.9.2 PDB: 1i8a_A* 1i8u_A
Length = 189
Score = 27.2 bits (60), Expect = 7.3
Identities = 6/48 (12%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
LY+ + + +L + D++++ +D + ++ Y
Sbjct: 53 LYVL---AIVKDPVLNKDNSNPWEQDSVEIFIDENNHKTGYYEDDDAQ 97
>4ehi_A Bifunctional purine biosynthesis protein PURH; structural genomics,
center for structural genomics of infec diseases, csgid;
HET: MSE BTB; 2.28A {Campylobacter jejuni subsp}
Length = 534
Score = 27.5 bits (62), Expect = 8.6
Identities = 6/15 (40%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 293 IRDD-VIEECNKHGV 306
IRDD V++ +++G+
Sbjct: 508 IRDDEVVKAADEYGM 522
>2qgq_A Protein TM_1862; alpha-beta protein, structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; HET: CXS; 2.00A {Thermotoga
maritima MSB8}
Length = 304
Score = 27.1 bits (61), Expect = 8.9
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 3 PAYS--DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDV 46
A++ + + PE R + L I L+ F VGK
Sbjct: 200 VAFNLKEKVDPEMAKRRQEELLLLQAEISNSRLDRF---VGKKLKF 242
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
0.318 0.135 0.398
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,665,765
Number of extensions: 349275
Number of successful extensions: 1471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1194
Number of HSP's successfully gapped: 392
Length of query: 370
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 275
Effective length of database: 4,049,298
Effective search space: 1113556950
Effective search space used: 1113556950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)