BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy3016
(305 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 157 bits (397), Expect = 6e-39, Method: Compositional matrix adjust.
Identities = 70/85 (82%), Positives = 79/85 (92%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT HQGYGF+EF+ EEDADYAI
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNL 118
KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 75 KIMDMIKLYGKPIRVNKASAHNKNL 99
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 47/91 (51%), Gaps = 30/91 (32%)
Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP---------------------- 152
++N D A +++G LD +V E LL++ F G ++ T
Sbjct: 11 ERNQD--ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 153 ------KIMNMIKLYGKPIRVNKASSHQKNL 177
KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 144 bits (362), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 74/123 (60%), Positives = 84/123 (68%), Gaps = 38/123 (30%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+ IFIGNLDPE+DEKLLYDTFSAFGVILQT
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQT------------------------------ 35
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
P+IMRDPDTGNSKG+AFIN+ASF+ASDA+I+AM+GQYLCNRPI+VSYAFKKD
Sbjct: 36 --------PKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD 87
Query: 242 SKG 244
SKG
Sbjct: 88 SKG 90
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDADY 91
G + I++G LD ++ E L+++ F G ++ + +D T +GY FI F + +D
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
AI+ MN L +PI V+ A
Sbjct: 64 AIEAMNGQYLCNRPITVSYA 83
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 63/221 (28%), Positives = 107/221 (48%), Gaps = 45/221 (20%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
A++YVG L V+E +++E F +GP++++ + +D +T+ GY ++ F DA+ A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 95 IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
MN + GKP+R+ ++ + VG NIFI NLD +D K LYDTFSAFG IL
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVG-NIFIKNLDKSIDNKALYDTFSAFGNILSCK 129
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
+ D SKG+ F+++ +
Sbjct: 130 VVC-----------------------------------------DENGSKGYGFVHFETQ 148
Query: 213 EASDASIDAMHGQYLCNRPISV-SYAFKKDSKGDRHGSAAE 252
EA++ +I+ M+G L +R + V + +K+ + + A E
Sbjct: 149 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 189
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 3/91 (3%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G I++ LD + +++ F G +++ + D +GYGF+ F +E A+ A
Sbjct: 97 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 154
Query: 93 IKIMNMIKLYGKPIRVNK-ASSHQKNLDVGA 122
I+ MN + L + + V + S ++ ++GA
Sbjct: 155 IEKMNGMLLNDRKVFVGRFKSRKEREAELGA 185
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 63/221 (28%), Positives = 107/221 (48%), Gaps = 45/221 (20%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
A++YVG L V+E +++E F +GP++++ + +D +T+ GY ++ F DA+ A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 95 IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
MN + GKP+R+ ++ + VG NIFI NLD +D K LYDTFSAFG IL
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVG-NIFIKNLDKSIDNKALYDTFSAFGNILSCK 134
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
+ D SKG+ F+++ +
Sbjct: 135 VVC-----------------------------------------DENGSKGYGFVHFETQ 153
Query: 213 EASDASIDAMHGQYLCNRPISV-SYAFKKDSKGDRHGSAAE 252
EA++ +I+ M+G L +R + V + +K+ + + A E
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 194
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 3/91 (3%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G I++ LD + +++ F G +++ + D +GYGF+ F +E A+ A
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 159
Query: 93 IKIMNMIKLYGKPIRVNK-ASSHQKNLDVGA 122
I+ MN + L + + V + S ++ ++GA
Sbjct: 160 IEKMNGMLLNDRKVFVGRFKSRKEREAELGA 190
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 80.9 bits (198), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 98/205 (47%), Gaps = 41/205 (20%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+YVG LD ++E ++ + F GP+ N+ + D+ + Y F+E+ DA+ A++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 96 MNMIKLYGKPIRVNKA-SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
+N ++ +++N A S Q + D N+F+G+L+ VD++ L + F F L
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL----- 115
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
S H +M D TG+S+G+ F+++ S +
Sbjct: 116 ----------------SGH------------------VMWDMQTGSSRGYGFVSFTSQDD 141
Query: 215 SDASIDAMHGQYLCNRPISVSYAFK 239
+ ++D+M GQ L RP+ +++A K
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
S D ++VG L+ V + + F ++ H+ D T + +GYGF+ F ++DA
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 90 DYAIKIMNMIKLYGKPIRVNKAS 112
A+ M L G+P+R+N A+
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWAA 165
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 73.9 bits (180), Expect = 1e-13, Method: Composition-based stats.
Identities = 34/82 (41%), Positives = 55/82 (67%), Gaps = 1/82 (1%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+ D T++VG L+ +V E +++ELF+Q+GP+ V + KDR + + +GF+ F E Y
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP-KSFGFVCFKHPESVSY 72
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
AI ++N I+LYG+PI V+ SS
Sbjct: 73 AIALLNGIRLYGRPINVSGPSS 94
Score = 34.7 bits (78), Expect = 0.061, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 27/76 (35%)
Query: 124 IFIGNLDPEVDEKLLYDTF-------------------SAFG-VILQTPK-------IMN 156
+F+GNL+ V E++LY+ F +FG V + P+ ++N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 157 MIKLYGKPIRVNKASS 172
I+LYG+PI V+ SS
Sbjct: 79 GIRLYGRPINVSGPSS 94
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 61/224 (27%), Positives = 99/224 (44%), Gaps = 53/224 (23%)
Query: 24 LEGGGESGDGDAT-----------IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT 72
+ GG + G G A +YVG + ++ E + + F GP+ ++ M D VT
Sbjct: 7 MTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 66
Query: 73 QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE 132
H+G+ F+E+ E A A++ MN + L G+ I+V + S+ IG P
Sbjct: 67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN------------IGQAQPI 114
Query: 133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLD 189
+D+ L + AF R+ AS HQ + D ++F G +
Sbjct: 115 IDQ--LAEEARAFN-------------------RIYVASVHQDLSDDDIKSVFEAFGKIK 153
Query: 190 PEIM-RDPDTGNSKGFAFINYASFEASDASIDAMH-----GQYL 227
+ RDP TG KG+ FI Y ++S ++ +M+ GQYL
Sbjct: 154 SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 52/111 (46%), Gaps = 8/111 (7%)
Query: 1 MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGP 60
+ +GR G + P + L+ E IYV + +S+ + +F G
Sbjct: 100 IKVGRPSNIGQAQPIIDQLA--------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGK 151
Query: 61 VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ + + +D T H+GYGFIE+ + + A+ MN+ L G+ +RV KA
Sbjct: 152 IKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 28/132 (21%), Positives = 50/132 (37%), Gaps = 39/132 (29%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G+ + A+ Q L + + +++G++ E+ E + F+ FG I
Sbjct: 10 GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPI-------------- 55
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
K++D+ D T KGFAF+ Y EA+ +++ M
Sbjct: 56 ------------KSIDMS-------------WDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 223 HGQYLCNRPISV 234
+ L R I V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 56/200 (28%), Positives = 92/200 (46%), Gaps = 42/200 (21%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVG + ++ E + + F GP+ ++ M D VT H+G+ F+E+ E A A++ M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
N + L G+ I+V + S+ IG P +D+ L + AF
Sbjct: 76 NSVMLGGRNIKVGRPSN------------IGQAQPIIDQ--LAEEARAFN---------- 111
Query: 157 MIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLDP-EIMRDPDTGNSKGFAFINYASF 212
R+ AS HQ + D ++F G + + RDP TG KG+ FI Y
Sbjct: 112 ---------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
Query: 213 EASDASIDAMH-----GQYL 227
++S ++ +M+ GQYL
Sbjct: 163 QSSQDAVSSMNLFDLGGQYL 182
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 52/108 (48%), Gaps = 2/108 (1%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
GR I+ G P +Q ++ E IYV + +S+ + +F G + +
Sbjct: 82 GRNIKVG--RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 139
Query: 64 VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ +D T H+GYGFIE+ + + A+ MN+ L G+ +RV KA
Sbjct: 140 CTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 26/123 (21%), Positives = 46/123 (37%), Gaps = 39/123 (31%)
Query: 112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAS 171
+ Q+ L + +++G++ E+ E + F+ FG I
Sbjct: 4 AQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPI----------------------- 40
Query: 172 SHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
K++D+ D T KGFAF+ Y EA+ +++ M+ L R
Sbjct: 41 ---KSIDMS-------------WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRN 84
Query: 232 ISV 234
I V
Sbjct: 85 IKV 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF EDA AI
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 96 MNMIKLYGKPIRVNKA 111
MN +L+G+ IRVN A
Sbjct: 74 MNESELFGRTIRVNLA 89
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++G L EVD+K+L+ F FG I
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 40
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 41 -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF EDA AI
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 96 MNMIKLYGKPIRVNKA 111
MN +L+G+ IRVN A
Sbjct: 125 MNESELFGRTIRVNLA 140
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++G L EVD+K+L+ F FG I
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 91
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 92 -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 63.9 bits (154), Expect = 9e-11, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF EDA AI M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 97 NMIKLYGKPIRVNKA 111
N +L+G+ IRVN A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++G L EVD+K+L+ F FG I
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 30
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 31 -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 63.9 bits (154), Expect = 1e-10, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF EDA AI M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 97 NMIKLYGKPIRVNKA 111
N +L+G+ IRVN A
Sbjct: 68 NESELFGRTIRVNLA 82
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++G L EVD+K+L+ F FG I
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 33
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 34 -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 63.9 bits (154), Expect = 1e-10, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF EDA AI M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 97 NMIKLYGKPIRVNKA 111
N +L+G+ IRVN A
Sbjct: 70 NESELFGRTIRVNLA 84
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++G L EVD+K+L+ F FG I
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 35
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 36 -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 47/182 (25%), Positives = 76/182 (41%), Gaps = 42/182 (23%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+++GGL+ +E + E F + G V ++ + KD T +G+GF+ F D +K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 95 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
++ L GK I +A + D IF+G + P+V K + FS +G I
Sbjct: 64 TQHI--LDGKVIDPKRAIPRDEQ-DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI------ 114
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
+D ++M D DTG S+GF F+ Y S +A
Sbjct: 115 ---------------------------------IDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 215 SD 216
D
Sbjct: 142 VD 143
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMH 223
D +IM+DP TG S+GF F+++ + D + H
Sbjct: 32 DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D I+VGG+ V E F Q G +++ + D+ T +G+GF+ + + D
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Query: 92 AIKIMNMIKLYGKPIRVNKAS 112
+ I + I + +A
Sbjct: 145 VCQ-NKFIDFKDRKIEIKRAE 164
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 53/200 (26%), Positives = 89/200 (44%), Gaps = 42/200 (21%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVG + ++ E + + F GP+ ++ D VT H+G+ F+E+ E A A++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
N + L G+ I+V + S+ IG P +D+ L + AF
Sbjct: 75 NSVXLGGRNIKVGRPSN------------IGQAQPIIDQ--LAEEARAFN---------- 110
Query: 157 MIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLDP-EIMRDPDTGNSKGFAFINYASF 212
R+ AS HQ + D ++F G + + RDP TG KG+ FI Y
Sbjct: 111 ---------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 161
Query: 213 EASDASIDA-----MHGQYL 227
++S ++ + + GQYL
Sbjct: 162 QSSQDAVSSXNLFDLGGQYL 181
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 51/111 (45%), Gaps = 8/111 (7%)
Query: 1 MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGP 60
+ +GR G + P + L+ E IYV + +S+ + +F G
Sbjct: 84 IKVGRPSNIGQAQPIIDQLA--------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGK 135
Query: 61 VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ + + +D T H+GYGFIE+ + + A+ N+ L G+ +RV KA
Sbjct: 136 IKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 48/207 (23%), Positives = 88/207 (42%), Gaps = 42/207 (20%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + V L +++ + LF G V + + +D+V GYGF+ ++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 93 IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
I +N ++L K I+V+ A + + AN++I L + +K + D FS FG I+ +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRIINS- 118
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
++ D TG S+G AFI +
Sbjct: 119 --------------------------------------RVLVDQTTGLSRGVAFIRFDKR 140
Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
++ +I + +G + PI+V +A
Sbjct: 141 SEAEEAITSFNGHKPPGSSEPITVKFA 167
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA +Y+ GL +++ + ++F + G ++N + D+ T +G FI F +A+ AI
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 94 KIMNMIKLYG--KPIRVNKASS 113
N K G +PI V A++
Sbjct: 148 TSFNGHKPPGSSEPITVKFAAN 169
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 48/207 (23%), Positives = 88/207 (42%), Gaps = 42/207 (20%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + V L +++ + LF G V + + +D+V GYGF+ ++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 93 IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
I +N ++L K I+V+ A + + AN++I L + +K + D FS FG I+ +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRIINS- 118
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
++ D TG S+G AFI +
Sbjct: 119 --------------------------------------RVLVDQTTGLSRGVAFIRFDKR 140
Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
++ +I + +G + PI+V +A
Sbjct: 141 SEAEEAITSFNGHKPPGSSEPITVXFA 167
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA +Y+ GL +++ + ++F + G ++N + D+ T +G FI F +A+ AI
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 94 KIMNMIKLYG--KPIRVNKASS 113
N K G +PI V A++
Sbjct: 148 TSFNGHKPPGSSEPITVXFAAN 169
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 80/190 (42%), Gaps = 40/190 (21%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+ + V L +++ ++ LF GP+ + +D T GY F++F E D+ AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
K++N I + K ++V+ A +++ N+++ NL + + L F +G I+
Sbjct: 63 KVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIV---- 117
Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
QKN I+RD TG +G AF+ Y E
Sbjct: 118 --------------------QKN---------------ILRDKLTGRPRGVAFVRYNKRE 142
Query: 214 ASDASIDAMH 223
+ +I A++
Sbjct: 143 EAQEAISALN 152
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IMRD TG S G+AF+++ S S +I ++G + N+ + VSYA
Sbjct: 34 RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 80
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 39/156 (25%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+ + V L ++ ++ LF GP+ + +D T GY F++F E D+ AI
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
K++N I + K ++V+ A +++ N+++ NL + + L F +G I+Q
Sbjct: 74 KVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 154 IMNMIKLYGKP-----IRVNKASSHQKNLDVGANIF 184
+ + KL G+P +R NK Q+ + N+
Sbjct: 133 LRD--KLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I RD TG S G+AF+++ S S +I ++G + N+ + VSYA
Sbjct: 45 RIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYA 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D +++GGL+ + +E ++ +F + GP+ V + KDR +++ +G+ FI F DA
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKS-RGFAFITFENPADAKN 63
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
A K MN L+GK I+V +A
Sbjct: 64 AAKDMNGKSLHGKAIKVEQA 83
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 51/138 (36%), Gaps = 44/138 (31%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
D +FIG L+ E +EK+L F G I + I +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--------------------- 43
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS-FEASDASIDAMHGQYLCNRPISVSYA 237
T S+GFAFI + + +A +A+ D M+G+ L + I V A
Sbjct: 44 -------------------TSKSRGFAFITFENPADAKNAAKD-MNGKSLHGKAIKVEQA 83
Query: 238 FKKD--SKGDRHGSAAER 253
K S G R A+ R
Sbjct: 84 KKPSFQSGGRRRPPASSR 101
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 47/208 (22%), Positives = 84/208 (40%), Gaps = 42/208 (20%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D + V L +++ LF G + + + +D++T GYGF+ + DAD
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 92 AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
AI +N +KL K I+V+ A ++ AN+++ L + +K + FS +G I+ +
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMSQKEMEQLFSQYGRIITS 120
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
I+ D TG S+G FI +
Sbjct: 121 ---------------------------------------RILLDQATGVSRGVGFIRFDK 141
Query: 212 FEASDASIDAMHGQYLCN--RPISVSYA 237
++ +I ++GQ PI+V +A
Sbjct: 142 RIEAEEAIKGLNGQKPLGAAEPITVKFA 169
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA +YV GL +S+ M +LF Q G ++ + D+ T +G GFI F +A+ AI
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 94 KIMNMIKLYG--KPIRVNKASS 113
K +N K G +PI V A++
Sbjct: 150 KGLNGQKPLGAAEPITVKFANN 171
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 55/94 (58%), Gaps = 5/94 (5%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+++VG + + +E + ++F + GPVV+ + DR T +GYGF E+ +E A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 96 MNMIKLYGKPIRVNKASSHQ-----KNLDVGANI 124
+N + G+ +RV+ A+S + K+L GA +
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 23/121 (19%), Positives = 44/121 (36%), Gaps = 39/121 (32%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
++F+GN+ E E+ L D FS G ++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSF------------------------------- 38
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
++ D +TG KG+ F Y E + +++ ++G+ R + V A + +
Sbjct: 39 --------RLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN 90
Query: 243 K 243
K
Sbjct: 91 K 91
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 45/203 (22%), Positives = 85/203 (41%), Gaps = 42/203 (20%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ V L +++ LF G + + + +D++T GYGF+ ++ +DA+ AI +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
N ++L K I+V+ A ++ AN+++ L + +K L FS +G I+ +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMTQKELEQLFSQYGRIITS----- 118
Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASD 216
I+ D TG S+G FI + ++
Sbjct: 119 ----------------------------------RILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 217 ASIDAMHGQYL--CNRPISVSYA 237
+I ++GQ PI+V +A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA +YV GL +++ + +LF Q G ++ + D+VT +G GFI F +A+ AI
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 94 KIMNMIKLYG--KPIRVNKA 111
K +N K G +PI V A
Sbjct: 148 KGLNGQKPSGATEPITVKFA 167
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 47/84 (55%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+ ++VGGL +E + ++F + G + V + KDR TQ +G+GF+ F +DA A+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 94 KIMNMIKLYGKPIRVNKASSHQKN 117
MN + G+ IRV++A N
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDN 95
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 29/48 (60%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
+++D +T S+GF F+ + + + + ++ AM+G+ + R I V A K
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK 91
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 3/90 (3%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + +YVG L ++E ++ +F G + N+ + KD T +GYGFI F E A A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 93 IKIMNMIKLYGKPIRVNKASSHQKNLDVGA 122
++ +N +L G+P+RV + + LD G+
Sbjct: 64 LEQLNGFELAGRPMRVGHVT---ERLDGGS 90
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 31/49 (63%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+M+D DTG SKG+ FI ++ E + +++ ++G L RP+ V + ++
Sbjct: 37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER 85
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 48/209 (22%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFMGEE---DADY 91
++VG + SE + ELF Q G V +++ +DR Q G F+ F + +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 92 AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
A+ M ++ PI++ A S + N +FIG + + E + FS+FG I +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
I+R PD G S+G AF+ + +
Sbjct: 126 ---------------------------------------RILRGPD-GLSRGCAFVTFTT 145
Query: 212 FEASDASIDAMH-GQYL--CNRPISVSYA 237
+ +I AMH Q + C+ P+ V +A
Sbjct: 146 RAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 48/209 (22%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFMGEE---DADY 91
++VG + SE + ELF Q G V +++ +DR Q G F+ F + +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 92 AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
A+ M ++ PI++ A S + N +FIG + + E + FS+FG I +
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 137
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
I+R PD G S+G AF+ + +
Sbjct: 138 ---------------------------------------RILRGPD-GLSRGCAFVTFTT 157
Query: 212 FEASDASIDAMH-GQYL--CNRPISVSYA 237
+ +I AMH Q + C+ P+ V +A
Sbjct: 158 RAMAQTAIKAMHQAQTMEGCSSPMVVKFA 186
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
T+YVG L +E ++ELF +SG + + M D++ +T G+ F+E+ DA+ A++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 95 IMNMIKLYGKPIRVN 109
+N +L + IR +
Sbjct: 100 YINGTRLDDRIIRTD 114
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 47/112 (41%), Gaps = 41/112 (36%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
NIFI NLD +D K LYDTFSAFG IL +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--------------------------- 39
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
D SKG+ F+++ + EA++ +I+ M+G L +R + V
Sbjct: 40 --------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 9/106 (8%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G I++ LD + +++ F G +++ + D +GYGF+ F +E A+ A
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 61
Query: 93 IKIMNMIKLYGKPIRVNK-ASSHQKNLDVGA------NIFIGNLDP 131
I+ MN + L + + V + S ++ ++GA N++I N P
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGP 107
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T+YVG L V+E L+ +LF Q GP + M + + + Y F+EF DA A+
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAA 74
Query: 96 MNMIKLYGKPIRVNKASS 113
MN K+ GK ++VN A++
Sbjct: 75 MNGRKILGKEVKVNWATT 92
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
IYVG L + + ELF Q G V NV + DR T+ +G+GF+E M EE AI +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 97 NMIKLYGKPIRVNKAS 112
+ G+ IRV +A+
Sbjct: 63 DNTDFMGRTIRVTEAN 78
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 33/113 (29%), Positives = 47/113 (41%), Gaps = 41/113 (36%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
NIFI NLD +D K LYDTFSAFG IL +
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-------------------------- 45
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
D SKG+ F+++ + EA++ +I+ M+G L +R + V
Sbjct: 46 ---------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G I++ LD + +++ F G +++ + D +GYGF+ F +E A+ A
Sbjct: 10 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 67
Query: 93 IKIMNMIKLYGKPIRVNKASSHQK 116
I+ MN + L + + V + S ++
Sbjct: 68 IEKMNGMLLNDRKVFVGRFKSRKE 91
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA +YV GL +S+ M +LF Q G ++ + D+ T +G GFI F +A+ AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 94 KIMNMIKLYG--KPIRVNKASS 113
K +N K G +PI V A++
Sbjct: 61 KGLNGQKPLGAAEPITVKFANN 82
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D +ATI V L + ET + ELF G + +++ KD+ T +G+ FI F EDA
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 92 AI 93
AI
Sbjct: 73 AI 74
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
+ +D TG SKGFAFI++ E + +I + G
Sbjct: 47 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G +YVG L ++E ++ +F G + ++ + D T +GYGFI F E A A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 93 IKIMNMIKLYGKPIRVNKAS 112
++ +N +L G+P++V +
Sbjct: 85 LEQLNGFELAGRPMKVGHVT 104
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 47/92 (51%), Gaps = 10/92 (10%)
Query: 156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP-------EIMRDPDTGNSKGFAFIN 208
N+ K P+R+ S H ++ ++ G +P ++M D +TG SKG+ FI
Sbjct: 18 NLQKGSAGPMRLYVGSLH---FNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
Query: 209 YASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
++ E + +++ ++G L RP+ V + ++
Sbjct: 75 FSDSECAKKALEQLNGFELAGRPMKVGHVTER 106
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 77 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 132
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 133 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 156
Query: 212 FEASD 216
++ D
Sbjct: 157 HDSVD 161
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 43 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Score = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 166
Query: 97 NMIKLYGKPIRVNKASSHQK 116
+ G V KA S Q+
Sbjct: 167 KYHTVNGHNCEVRKALSKQE 186
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 49/208 (23%), Positives = 78/208 (37%), Gaps = 48/208 (23%)
Query: 38 YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG--FIEFMGEEDADYAIKI 95
+VG + SE + ELF Q G V +++ +DR Q G F+ F + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 96 MNMIKLY---GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
++ K+ PI+ A S + N +FIG + + E + FS+FG I +
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEEC- 125
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
I+R PD G S+G AF+ + +
Sbjct: 126 --------------------------------------RILRGPD-GLSRGCAFVTFTTR 146
Query: 213 EASDASIDAMHGQYL---CNRPISVSYA 237
+ +I A H C+ P V +A
Sbjct: 147 AXAQTAIKAXHQAQTXEGCSSPXVVKFA 174
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 75 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 130
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 131 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 154
Query: 212 FEASD 216
++ D
Sbjct: 155 HDSVD 159
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 41 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 164
Query: 97 NMIKLYGKPIRVNKASSHQK 116
+ G V KA S Q+
Sbjct: 165 KYHTVNGHNCEVRKALSKQE 184
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 76 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 131
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 132 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 155
Query: 212 FEASD 216
++ D
Sbjct: 156 HDSVD 160
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 42 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 165
Query: 97 NMIKLYGKPIRVNKASSHQK 116
+ G V KA S Q+
Sbjct: 166 KYHTVNGHNCEVRKALSKQE 185
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+G ++ V L + S + +F + G V +V++P+DR T+ +G+ F+ F + DA+
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
A+ M+ L G+ +RV A
Sbjct: 105 AMDAMDGAVLDGRELRVQMA 124
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I RD T S+GFAF+ + ++ ++DAM G L R + V A
Sbjct: 79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 56/125 (44%), Gaps = 13/125 (10%)
Query: 24 LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
L+ G ++ ++VG L ++E LF + G V + +DR G+GFI
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRL 65
Query: 84 MGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFS 143
A+ A ++ L +P+R+ A+ GA + + NL P V +LL FS
Sbjct: 66 ESRTLAEIAKAELDGTILKSRPLRIRFATH-------GAALTVKNLSPVVSNELLEQAFS 118
Query: 144 AFGVI 148
FG +
Sbjct: 119 QFGPV 123
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 69 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 124
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 125 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 148
Query: 212 FEASDASI 219
++ D +
Sbjct: 149 HDSVDKIV 156
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 35 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 158
Query: 97 NMIKLYGKPIRVNKASSHQK 116
+ G V KA S Q+
Sbjct: 159 KYHTVNGHNCEVRKALSKQE 178
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+G ++ V L + S + +F + G V +V++P+DR T+ +G+ F+ F + DA+
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
A+ M+ L G+ +RV A
Sbjct: 128 AMDAMDGAVLDGRELRVQMA 147
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D I RD T S+GFAF+ + ++ ++DAM G L R + V A
Sbjct: 99 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 76 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 131
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 132 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 155
Query: 212 FEASDASI 219
++ D +
Sbjct: 156 HDSVDKIV 163
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 42 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 165
Query: 97 NMIKLYGKPIRVNKASSHQ 115
+ G V KA S Q
Sbjct: 166 KYHTVNGHNCEVRKALSKQ 184
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+ D A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
K+ G+ + +A S + + GA+ IF+G + + +E L D F +G I
Sbjct: 74 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 129
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
+I EIM D +G +GFAF+ +
Sbjct: 130 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 153
Query: 212 FEASDASI 219
++ D +
Sbjct: 154 HDSVDKIV 161
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP+T S+GF F+ YA+ E DA+++A
Sbjct: 40 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ + E + + F Q G + + + DR + +G+ F+ F + D I I
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 163
Query: 97 NMIKLYGKPIRVNKASSHQ 115
+ G V KA S Q
Sbjct: 164 KYHTVNGHNCEVRKALSKQ 182
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 44/81 (54%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + +++ + EL GP+ ++ KD T +GY F E++ D AI +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 97 NMIKLYGKPIRVNKASSHQKN 117
N ++L K + V +AS KN
Sbjct: 64 NGMQLGDKKLLVQRASVGAKN 84
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+++D TG SKG+AF Y +D +I ++G L ++ + V A
Sbjct: 33 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 78
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%)
Query: 31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
G G + V L +++ + LF G V + + +D+V GYGF+ ++ +DA+
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 91 YAIKIMNMIKLYGKPIRVNKA 111
AI +N ++L K I+V+ A
Sbjct: 61 RAINTLNGLRLQSKTIKVSYA 81
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 32/47 (68%)
Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+++RD G+S G+ F+NY + + ++ +I+ ++G L ++ I VSYA
Sbjct: 35 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 81
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ V + V E + +LF + GP+ +V + DR T+ +GYGF++F A AI +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 97 NMIKLYGKPIRVNKASS-HQKNLDVGA 122
N + K ++V A+S HQ+ GA
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGA 131
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 45/86 (52%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D +++GGL + +++ + EL GP+ ++ KD T +GY F E++ D
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 92 AIKIMNMIKLYGKPIRVNKASSHQKN 117
AI +N ++L K + V +AS KN
Sbjct: 172 AIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 40/218 (18%), Positives = 84/218 (38%), Gaps = 50/218 (22%)
Query: 37 IYVGGLDDKVSETLMWELF-----------VQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
+YVG + ++E M + F PV+ V + +D+ + F+EF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRS 60
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQ------KNLDVGANIFIGNLDPEVDEKLLY 139
++ A+ +I G+ +++ + +Q +N V + + P+ KL
Sbjct: 61 VDETTQAMAFDGII-FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 140 DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG 199
+ L ++ ++ +G P++ +++D TG
Sbjct: 120 GGLPNY---LNDDQVKELLTSFG-PLKAFN----------------------LVKDSATG 153
Query: 200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
SKG+AF Y +D +I ++G L ++ + V A
Sbjct: 154 LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG L +++ + F G + + + KD T +GYGF+ F + DA+ AI+ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 97 NMIKLYGKPIRVNKAS 112
L G+ IR N A+
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 39/130 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S +K+ ++F+G+L PE+ + + F+ FG I
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRIS--------------------- 43
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
D +++D TG SKG+ F+++ + ++ +I M GQ+L R
Sbjct: 44 ------------------DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR 85
Query: 231 PISVSYAFKK 240
I ++A +K
Sbjct: 86 QIRTNWATRK 95
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++VGG+D ++ ET + F + G V V + DR T +GYGF+ F D D +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY--NDVDVQKIV 68
Query: 96 MNMIKLYGKPIRVNKASSHQ 115
+ I +GK +++ A Q
Sbjct: 69 ESQINFHGKKLKLGPAIRKQ 88
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T+YVG L +E ++ELF +SG + + M D++ +T G+ F+E+ DA+ A++
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMRY 78
Query: 96 MNMIKLYGKPIRVN 109
+N +L + IR +
Sbjct: 79 INGTRLDDRIIRTD 92
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++VGG+D ++ ET + F + G V V + DR T +GYGF+ F D D +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY--NDVDVQKIV 67
Query: 96 MNMIKLYGKPIRVNKASSHQ 115
+ I +GK +++ A Q
Sbjct: 68 ESQINFHGKKLKLGPAIRKQ 87
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ ET + E F + G V V M D Q +G+GFI F E+ D A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 97 NMIKLYGKPIRVNKA 111
+ + GK + V +A
Sbjct: 72 HFHDIMGKKVEVKRA 86
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D + V L +++ LF G + + + +D++T GYGF+ + DAD
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
AI +N +KL K I+V+ A
Sbjct: 62 AINTLNGLKLQTKTIKVSYA 81
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IG+++ +++RD TG S G+ F+NY+ +D +I+ ++G L + I VSYA
Sbjct: 28 IGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++VGG+D ++ ET + F + G V V + DR T +GYGF+ F + D ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE- 68
Query: 96 MNMIKLYGKPIRVNKASSHQ 115
+ I +GK +++ A Q
Sbjct: 69 -SQINFHGKKLKLGPAIRKQ 87
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG L+ V + + F ++ H+ D T + +GYGF+ F ++DA A+ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 97 NMIKLYGKPIRVNKAS 112
L G+P+R+N A+
Sbjct: 64 QGQDLNGRPLRINWAA 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%)
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
F L +M D TG+S+G+ F+++ S + + ++D+M GQ L RP+ +++A K
Sbjct: 25 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 3/94 (3%)
Query: 28 GESG---DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G SG DG T+ V L + S + +F + G V +V++P++ T+ +G+ F+ F
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNL 118
DA A M+ +L G+ +RV A +++L
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL 97
Score = 27.7 bits (60), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 22/46 (47%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I R+P T +GFAF+ + + + AM G L R + V A
Sbjct: 45 IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+ ++VG L ++E M +LF + G V + KD+ G+GFI A+ A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 95 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
++ + L GK +RV A A++ + NL V +LL + FS FG Q +
Sbjct: 77 ELDNMPLRGKQLRVRFACH-------SASLTVRNLPQYVSNELLEEAFSVFG---QVERA 126
Query: 155 MNMIKLYGKP 164
+ ++ G+P
Sbjct: 127 VVIVDDRGRP 136
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 32/160 (20%), Positives = 62/160 (38%), Gaps = 40/160 (25%)
Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG---------------VILQTPKIMNMIK 159
+K + +F+GNL P++ E+ + F +G + L+T + + K
Sbjct: 16 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAK 75
Query: 160 -------LYGKPIRVNKASSHQKNLDVG-------------ANIFIGNLDPEIMRDPDTG 199
L GK +RV + + H +L V A G ++ ++ D G
Sbjct: 76 VELDNMPLRGKQLRV-RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRG 134
Query: 200 NSKGFAFINYASFEASDASID-AMHGQYLCN---RPISVS 235
G + ++ A+ ++D G +L RP++V
Sbjct: 135 RPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVE 174
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.3 bits (103), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 44/77 (57%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+T+YV L ++ ++ +F + G VV V + KD+ T+ +G FI F+ ++ A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 95 IMNMIKLYGKPIRVNKA 111
+N +L+G+ I+ + A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 31.2 bits (69), Expect = 0.83, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IM+D DT SKG AFI + +++ A++ + L R I S A
Sbjct: 48 IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 70 NGQDLMGQPISVD 82
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 85
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 70 NGQDLMGQPISVD 82
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 85
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 72 NGQDLMGQPISVD 84
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F
Sbjct: 44 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 87
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G +++GGL + +++ + EL GP+ ++ KD T +GY F E++ D A
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 93 IKIMNMIKLYGKPIRVNKAS 112
I +N ++L K + V +AS
Sbjct: 155 IAGLNGMQLGDKKLLVQRAS 174
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 42/212 (19%), Positives = 82/212 (38%), Gaps = 58/212 (27%)
Query: 37 IYVGGLDDKVSETLMWELF-----------VQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
+YVG + ++E M + F PV+ V + +D+ + F+EF
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRS 62
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAF 145
++ A+ +I G+ +++ + +Q L +FIG L +++ + + ++F
Sbjct: 63 VDETTQAMAFDGII-FQGQSLKIRRPHDYQP-LPGAHKLFIGGLPNYLNDDQVKELLTSF 120
Query: 146 GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA 205
G + K N++K D TG SKG+A
Sbjct: 121 GPL----KAFNLVK-----------------------------------DSATGLSKGYA 141
Query: 206 FINYASFEASDASIDAMHGQYLCNRPISVSYA 237
F Y +D +I ++G L ++ + V A
Sbjct: 142 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G +++GGL + +++ + EL GP+ ++ KD T +GY F E++ D A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 93 IKIMNMIKLYGKPIRVNKAS 112
I +N ++L K + V +AS
Sbjct: 153 IAGLNGMQLGDKKLLVQRAS 172
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 42/212 (19%), Positives = 82/212 (38%), Gaps = 58/212 (27%)
Query: 37 IYVGGLDDKVSETLMWELF-----------VQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
+YVG + ++E M + F PV+ V + +D+ + F+EF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRS 60
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAF 145
++ A+ +I G+ +++ + +Q L +FIG L +++ + + ++F
Sbjct: 61 VDETTQAMAFDGII-FQGQSLKIRRPHDYQP-LPGAHKLFIGGLPNYLNDDQVKELLTSF 118
Query: 146 GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA 205
G + K N++K D TG SKG+A
Sbjct: 119 GPL----KAFNLVK-----------------------------------DSATGLSKGYA 139
Query: 206 FINYASFEASDASIDAMHGQYLCNRPISVSYA 237
F Y +D +I ++G L ++ + V A
Sbjct: 140 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG L +++ + F G + + + KD T +GYGF+ F + DA+ AI M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 97 NMIKLYGKPIRVNKAS 112
L G+ IR N A+
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 39/130 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S +K+ ++F+G+L PE+ + + F+ FG I
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKIS--------------------- 43
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
D +++D TG SKG+ F+++ + ++ +I M GQ+L R
Sbjct: 44 ------------------DARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGR 85
Query: 231 PISVSYAFKK 240
I ++A +K
Sbjct: 86 QIRTNWATRK 95
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++V GL + +E + E F S V + DR T + +G+GF++F EEDA A +
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 96 MNMIKLYGKPIRVNKA 111
M ++ G + ++ A
Sbjct: 74 MEDGEIDGNKVTLDWA 89
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 33/54 (61%)
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
F G++ I+ D +TG+SKGF F+++ S E + A+ +AM + +++ +A
Sbjct: 36 FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+ + V L +++ ++ LF GP+ + +D T GY F++F E D+ AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 94 KIMNMIKLYGKPIRVNKA 111
K++N I + K ++V+ A
Sbjct: 63 KVLNGITVRNKRLKVSYA 80
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IMRD TG S G+AF+++ S S +I ++G + N+ + VSYA
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 80
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F +DA
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 92 AIKIMNMIKLYGKPIRVN 109
A + N ++L G+ IRV+
Sbjct: 104 AKERANGMELDGRRIRVD 121
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
D I+ D + S+GFAF+ + + + + + + +G L R I V ++ K
Sbjct: 75 DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 51 MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK 110
+ LF G V + + +D+V GYGF+ ++ +DA+ AI +N ++L K I+V+
Sbjct: 36 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 95
Query: 111 A 111
A
Sbjct: 96 A 96
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 185 IGNLD-PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IG ++ +++RD G+S G+ F+NY + + ++ +I+ ++G L ++ I VSYA
Sbjct: 43 IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 172 SHQKNLDVGANIF-IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
+ ++ LD+ +N+ + NL ++M DP TG SKG+AFI + E+S +++ ++G L +R
Sbjct: 15 TEEQILDLCSNVGPVINL--KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 72
Query: 231 PISVSYAFKKDSKG 244
+ Y+ D G
Sbjct: 73 FLKCGYSSNSDISG 86
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+Y+G + +E + +L GPV+N+ M D T +GY FIEF E + A++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 96 MNMIKLYGKPIRVNKAS 112
+N +L + ++ +S
Sbjct: 64 LNGYQLGSRFLKCGYSS 80
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 85 NGQDLMGQPISVD 97
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F
Sbjct: 57 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 48/88 (54%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G + D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
+DA A + N ++L G+ IRV+ SS
Sbjct: 67 VDDAKEAKERANGMELDGRRIRVSGPSS 94
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 86 NGQDLMGQPISVD 98
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 29/46 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F +
Sbjct: 58 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 172 SHQKNLDVGANIF-IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
+ ++ LD+ +N+ + NL ++M DP TG SKG+AFI + E+S +++ ++G L +R
Sbjct: 16 TEEQILDLCSNVGPVINL--KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 73
Query: 231 PISVSYAFKKDSKG 244
+ Y+ D G
Sbjct: 74 FLKCGYSSNSDISG 87
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+Y+G + +E + +L GPV+N+ M D T +GY FIEF E + A++
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 96 MNMIKLYGKPIRVNKAS 112
+N +L + ++ +S
Sbjct: 65 LNGYQLGSRFLKCGYSS 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/121 (21%), Positives = 49/121 (40%), Gaps = 41/121 (33%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
N+++ NLD +D++ L FS FG I +M
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--------------------------- 49
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
+ G SKGF F+ ++S E + ++ M+G+ + +P+ V+ A +K+
Sbjct: 50 --------------EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Query: 243 K 243
+
Sbjct: 96 R 96
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVN--VHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+YV LDD + + + + F G + + V M R +G+GF+ F E+A A+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR----SKGFGFVCFSSPEEATKAVT 73
Query: 95 IMNMIKLYGKPIRVNKASSHQKN 117
MN + KP+ V A ++
Sbjct: 74 EMNGRIVATKPLYVALAQRKEER 96
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V G+ ++ +E + + F + G + N+H+ DR T +GY +E+ ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97 NMIKLYGKPIRVN 109
N L G+PI V+
Sbjct: 70 NGQDLMGQPISVD 82
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D TG KG+ + Y +++ + A+++ ++GQ L +PISV + F
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 85
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+Y+G + +E + +L GPV+N+ M D T +GY FIEF E + A++
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 96 MNMIKLYGKPIRVNKASS 113
+N +L + ++ +S+
Sbjct: 66 LNGYQLGSRFLKCGYSSN 83
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 172 SHQKNLDVGANIF-IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
+ ++ LD+ +N+ + NL ++M DP TG SKG+AFI + E+S +++ ++G L +R
Sbjct: 17 TEEQILDLCSNVGPVINL--KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 74
Query: 231 PISVSYA 237
+ Y+
Sbjct: 75 FLKCGYS 81
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G + D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F
Sbjct: 4 GSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 86 EEDADYAIKIMNMIKLYGKPIRVN 109
+DA A + N ++L G+ IRV+
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVD 87
Score = 28.1 bits (61), Expect = 6.2, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
D I+ D + S+GFAF+ + + + + + + +G L R I V ++ K
Sbjct: 41 DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 92
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 8/94 (8%)
Query: 62 VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI--RVNKASSHQKNLD 119
+++ +P R T + + +I+ +EDA Y ++ +N +K+ G + +V+ K D
Sbjct: 146 LSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTD 204
Query: 120 V----GANIFIGNLDPEV-DEKLLYDTFSAFGVI 148
G I I NL E+ DE LL ++F FG I
Sbjct: 205 SATLEGREIXIRNLSTELLDENLLRESFEGFGSI 238
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G + D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 86 EEDADYAIKIMNMIKLYGKPIRVN 109
+DA A + N ++L G+ IRV+
Sbjct: 67 VDDAKEAKERANGMELDGRRIRVD 90
Score = 27.7 bits (60), Expect = 7.4, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
D I+ D + S+GFAF+ + + + + + + +G L R I V ++ K
Sbjct: 44 DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 95
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 20/79 (25%)
Query: 182 NIFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASIDA 221
++F+G+L PE +++D TG SKG+ F+++ + ++ +I
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 222 MHGQYLCNRPISVSYAFKK 240
M GQ+L R I ++A +K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 59 GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
G + + + KD T +GYGF+ F + DA+ AI+ M L G+ IR N A+
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT 84
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
++VGGLD ++ + F Q G VV+ + KD+ T +G+GF++F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
GN++ I+R PD GNSKG AF+ Y+S + A+I+A+HG
Sbjct: 39 FGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINALHG 78
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%)
Query: 30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
GD T++V ++ +E+ + F GP+ +HM + + +GY FIE+ E D
Sbjct: 98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157
Query: 90 DYAIKIMNMIKLYGKPIRVN 109
A K + K+ G+ + V+
Sbjct: 158 HSAYKHADGKKIDGRRVLVD 177
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V + ++ E + E F G + N+H+ DR T +GY +E+ + A A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 97 NMIKLYGKPIRVN 109
N ++ G+ I+V+
Sbjct: 135 NGAEIMGQTIQVD 147
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 44/87 (50%)
Query: 23 KLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
+LE G + ++V + ++ E + E F G + N+H+ DR T +GY +E
Sbjct: 15 ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74
Query: 83 FMGEEDADYAIKIMNMIKLYGKPIRVN 109
+ + A A + +N ++ G+ I+V+
Sbjct: 75 YETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 ELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAIK-IMNMIKLYGKPIRVNK 110
ELF G + V +PK T H+G+GF++F+ ++DA A + + LYG+ + +
Sbjct: 34 ELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW 93
Query: 111 ASS 113
A S
Sbjct: 94 ADS 96
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%)
Query: 31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
GD T++V ++ +E+ + F GP+ +HM + + +GY FIE+ E D
Sbjct: 99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMH 158
Query: 91 YAIKIMNMIKLYGKPIRVN 109
A K + K+ G+ + V+
Sbjct: 159 SAYKHADGKKIDGRRVLVD 177
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
++V L SE + +LF GP+ +H P D +T+ +G+ F+ FM E A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 34/67 (50%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G +++GGL + ++ + E F Q G V + +D +T+ +G+GF+ FM +
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 87 EDADYAI 93
D +
Sbjct: 78 AGVDKVL 84
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+S + T+Y GG+ +++ LM + F G ++ + + ++ GY F+ F E
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHES 73
Query: 89 ADYAIKIMNMIKLYGKPIRV 108
A +AI +N + G ++
Sbjct: 74 AAHAIVSVNGTTIEGHVVKC 93
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVS-ETL---MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ ++DK+ E L ++ LF Q G VV++ K T +G F+ F +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTN 64
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ + YGKP+R+ A +
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAKT 86
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAIKI 95
+++G L V++ + E+F G + + MP +R+ +GY ++EF ++A+ A+K
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 96 MNMIKLYGKPI 106
M+ ++ G+ I
Sbjct: 67 MDGGQIDGQEI 77
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 36.6 bits (83), Expect = 0.016, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
I+VGGL E + E F G V ++ +P D T +G+ FI F EE
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
I+VGGL E + E F G V ++ +P D T +G+ FI F EE
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
G SG + +++VG L V + +++E FV+ P T +GYGF++F E
Sbjct: 4 GSSGP-EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 88 DADYAI-KIMNMIKLYGKPIRVNKA 111
+ A+ + + L KP+R++ A
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVA 87
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/122 (22%), Positives = 47/122 (38%), Gaps = 40/122 (32%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
++F+G+L P+VD+ +LY+ F +K+Y R K Q
Sbjct: 11 SLFVGDLTPDVDDGMLYEFF---------------VKVY-PSCRGGKVVLDQ-------- 46
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYA-SFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
TG SKG+ F+ + E A + L ++P+ +S A K
Sbjct: 47 ---------------TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA 91
Query: 242 SK 243
S+
Sbjct: 92 SR 93
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
D +YVG L + ++T + F GP+ +V V + G+ F+EF DA A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVW-----VARNPPGFAFVEFEDPRDAADAV 127
Query: 94 KIMNMIKLYGKPIRVNKASSHQK 116
+ ++ L G +RV ++ ++
Sbjct: 128 RDLDGRTLCGCRVRVELSNGEKR 150
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
D +YVG L + ++T + F GP+ +V V + G+ F+EF DA A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVW-----VARNPPGFAFVEFEDPRDAADAV 127
Query: 94 KIMNMIKLYGKPIRVNKASSHQK 116
+ ++ L G +RV ++ ++
Sbjct: 128 RELDGRTLCGCRVRVELSNGEKR 150
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 35.8 bits (81), Expect = 0.027, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 31/54 (57%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
+++GGL + ++ + E F Q G V + +D +T+ +G+GF+ FM + D
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 56
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%)
Query: 31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
G +++ L + ++T + F+ G V++ + D+ T + +GF+ F + A
Sbjct: 37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96
Query: 91 YAIKIMNMIKLYGKPIRV 108
AIK MN ++ K ++V
Sbjct: 97 VAIKAMNGFQVGTKRLKV 114
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
GFAF+ + E++ +I+ +HG+ N+P+ V Y+
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 35.0 bits (79), Expect = 0.051, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
I+VGGL + + F Q G V + + D+ T H+G+GF+ F E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 32 DGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
D DA ++VG + + E + LF + G + + + KDR+T H+G F+ + + A
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 91 YAIKIMNMIKLY---GKPIRVNKASSHQKN 117
A ++ K +PI+V A+S +
Sbjct: 72 KAQSALHEQKTLPGMNRPIQVKPAASEGRG 101
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC---NRPISVSYA 237
+++D TG KG AF+ Y + +++ + A+H Q NRPI V A
Sbjct: 47 VLKDRLTGLHKGCAFLTYCARDSALKAQSALHEQKTLPGMNRPIQVKPA 95
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 24/33 (72%), Gaps = 1/33 (3%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
++R PD G+SKG AF+ ++S + A+I A+HG
Sbjct: 47 VLRGPD-GSSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 34.7 bits (78), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G ++G +T++V LD KV + E+F +G VV + +D+ ++ +G G + F
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS-RGIGTVTFEQ 65
Query: 86 EEDADYAIKIMNMIKLYGKPIRVN 109
+A AI + N L+ +P+ V
Sbjct: 66 SIEAVQAISMFNGQLLFDRPMHVK 89
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 42/127 (33%)
Query: 120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV 179
+G+ +F+ NLD +V K L + FS GV+++
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRA---------------------------- 45
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYA-SFEASDASIDAMHGQYLCNRPISVSYAF 238
+I+ D D G S+G + + S EA A I +GQ L +RP+ V
Sbjct: 46 -----------DILEDKD-GKSRGIGTVTFEQSIEAVQA-ISMFNGQLLFDRPMHVKMDE 92
Query: 239 KKDSKGD 245
+ KGD
Sbjct: 93 RALPKGD 99
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 34.7 bits (78), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GGGE + A + V LD VS+ + ELF + G + + DR ++ G + F
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL-GTADVHFER 138
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSH 114
DA A+K + L G+P+ + +S
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVASQ 167
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.3 bits (77), Expect = 0.081, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
GFAF+ + E++ +I+ +HG+ N+P+ V Y+
Sbjct: 39 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 73
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 31/97 (31%), Positives = 42/97 (43%), Gaps = 15/97 (15%)
Query: 28 GESGDGDA-----TIYVGGLDDKVSETLMWELF--VQSGPVVNVHMPKDRVTQTHQGYGF 80
G SGD D +YV L SE ++ + F ++ G V V +D Y F
Sbjct: 4 GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAF 55
Query: 81 IEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
+ F EDA A+K +N L G PI V A K+
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD 92
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA--FKKDSKGDRHG 248
+ +AF+++++ E + ++ A++G+ L PI V+ A KDS G G
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 8/90 (8%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G +++G L + +E + LF Q G V+ + K+ YGF+ +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDK 52
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
A+ AI+ ++ KL+G I V + + K
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEASKNKSK 82
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 6/90 (6%)
Query: 28 GESG--DGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G SG D DA +++G + + E + LF + G + + + KDR T H+G F+ +
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 85 GEEDADYAIKIMNMIKLY---GKPIRVNKA 111
E A A ++ K +PI+V A
Sbjct: 64 ERESALKAQSALHEQKTLPGMNRPIQVKPA 93
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC---NRPISVSYA 237
+++D TG KG AF+ Y E++ + A+H Q NRPI V A
Sbjct: 45 VLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPA 93
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL ++ + + F + G VV+ + D +T +G+GF+ F E D K+M
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD---KVM 58
Query: 97 NMI--KLYGKPIRVNKA 111
+ KL GK I +A
Sbjct: 59 DQKEHKLNGKVIDPKRA 75
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 188 LDPEIMRDPDTGNSKGFAFINYASFEASDASID 220
+D + DP TG S+GF F+ + E+ D +D
Sbjct: 27 VDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG L ++E M +LF + G V + KD+ G+GFI A+ A +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 71
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVG 121
+ + L GK +RV + + H +L G
Sbjct: 72 DNMPLRGKQLRV-RFACHSASLTSG 95
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
A++++G L+ + E + F G V++V + ++R+T GY F+EF AD A
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF-----ADLAT 64
Query: 94 KIMNMIKLYGKPI 106
+ K+ GKP+
Sbjct: 65 AEKCLHKINGKPL 77
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + ++ +F Q G ++++ + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++ L ++ + + F G V +V + DR ++ +G ++EF + AI +
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86
Query: 96 MNMIKLYGKPIRVNKASSHQKN 117
+L G PI + +AS +KN
Sbjct: 87 TGQ-RLLGVPI-IVQASQAEKN 106
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GGGE + A + V LD VS+ + ELF + G + + DR ++ G + F
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL-GTADVHFER 85
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSH 114
DA A+K + L G+P+ + +S
Sbjct: 86 RADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GGGE + A + V LD VS+ + ELF + G + + DR ++ G + F
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL-GTADVHFER 85
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSH 114
DA A+K + L G+P+ + +S
Sbjct: 86 RADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + ++ +F Q G ++++ + + + +G F+ F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 17/81 (20%)
Query: 46 VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP 105
V + + LF ++G VVN+ P D T +G+ F+E DA IK
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK----------- 72
Query: 106 IRVNKASSHQKNLDVGANIFI 126
S H K LD+ +F+
Sbjct: 73 ------SFHGKRLDLKHRLFL 87
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF--MGEEDADYAIK 94
+++GGL + +E + + Q G + + + +D ++ +G+GF+ F M E DA A +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
D +MRDP + S+GF F+ ++S DA++ A
Sbjct: 56 DCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 31/65 (47%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + +Y+ GL ++ + +L G +V+ D+ T +GYGF++F A A
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 93 IKIMN 97
+ +
Sbjct: 64 VTALK 68
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 28 GESGDGDA--TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G SG+ T+YVGGL D ++ET + F Q G + + V Q Q FI+F
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTI-----TVVQRQQ-CAFIQFAT 57
Query: 86 EEDADYAI-KIMNMIKLYGKPIRV 108
+ A+ A K N + + G+ + V
Sbjct: 58 RQAAEVAAEKSFNKLIVNGRRLNV 81
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 1/95 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGGL ++ + + F G + + DR T +GYGF+ A+ A K
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP 131
N I + G+ VN A K + IG P
Sbjct: 80 NPI-IDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + ++ +F Q G ++++ + + + +G F+ F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 61 VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM----IKLYGKPIRVNKASS 113
V N+ + KD+ TQ ++G+ F++ DA ++I+ +K+ GK I V+ A S
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V + + + + ++F Q G +++V + + + +G+GF+ F DAD A + +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 75
Query: 97 NMIKLYGKPIRVNKASSH 114
+ + G+ I VN A++
Sbjct: 76 HGTVVEGRKIEVNNATAR 93
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.0 bits (71), Expect = 0.43, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 17/73 (23%)
Query: 54 LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
LF ++G VVN+ P D T +G+ F+E DA IK S
Sbjct: 32 LFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK-----------------SF 74
Query: 114 HQKNLDVGANIFI 126
H K LD+ +F+
Sbjct: 75 HGKRLDLKHRLFL 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++V + + + + ++F Q G +++V + + + +G+GF+ F DAD A + +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKL 89
Query: 97 NMIKLYGKPIRVNKASS 113
+ + G+ I VN A++
Sbjct: 90 HGTVVEGRKIEVNNATA 106
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG + + + F + GPV+ + KD Y F+ EDA AI+ +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 97 NMIKLYGKPIRVNKASS 113
+ + GK + V ++S
Sbjct: 65 DNTEFQGKRMHVQLSTS 81
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 31.2 bits (69), Expect = 0.68, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T+ + L +E + E+F ++ + +P+++ ++ +GY FIEF EDA A+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQNGKS-KGYAFIEFASFEDAKEALNS 72
Query: 96 MNMIKLYGKPIRV 108
N ++ G+ IR+
Sbjct: 73 CNKREIEGRAIRL 85
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
G SKG+AFI +ASFE + ++++ + + + R I +
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRL 85
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 47/108 (43%), Gaps = 15/108 (13%)
Query: 14 PCLQSLSQTKLEGGG------------ESGDGDA-TIYVGGLDDKVSETLMWELFVQSGP 60
PC+Q+ + +K+ G E + D ++YVG +D + + F G
Sbjct: 4 PCMQT-THSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS 62
Query: 61 VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
+ + + D+ + +GY +IEF D A+ M+ G+ I+V
Sbjct: 63 INRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKV 109
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 26/112 (23%), Positives = 54/112 (48%), Gaps = 13/112 (11%)
Query: 37 IYVGGLDDKVS----ETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+++G L+ S + + ELF ++ VV+V T T++ +G+++F ED +
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR------TGTNRKFGYVDFESAEDLEK 69
Query: 92 AIKIMNMIKLYGKPIRVNKASSH-QKNLDVGANIFIGNLDPEVDEKLLYDTF 142
A+++ + K++G I++ K K + + NL + E L + F
Sbjct: 70 ALELTGL-KVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVF 120
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDA-MHGQYLCNRPISVSYA 237
+MR+ +G S+GFAF+ ++ + + ++A H + + +S+ Y+
Sbjct: 34 LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS 80
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.8 bits (68), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+ D +TG KG A +++ ++ A+ID G+ PI VS+A ++
Sbjct: 47 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRR 95
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 15/86 (17%)
Query: 179 VGANIFIGNLDPEIMRDPDT-----------GNS--KGFAFINYASFEASDASIDAMHGQ 225
+ + +FIGNL+ +++ D G S KG+AF+ Y++ + A++ +G+
Sbjct: 26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 226 YLCNRPISVSYAFKKDSKGDRHGSAA 251
L + + ++ A + K DR G ++
Sbjct: 86 VLAGQTLDINMA--GEPKPDRSGPSS 109
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKT 83
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 62
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKT 84
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMH 223
++R PD G SKG AF+ + + + A+I+ +H
Sbjct: 44 VLRGPD-GTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+ D +TG KG A +++ ++ A+ID G+ PI VS+A
Sbjct: 53 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 63
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKT 85
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 28 GESGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G +G G++ + V L+ ++V+ ++ LF G V V ++ + ++
Sbjct: 28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADG 82
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSHQ 115
A A+ +N KL+GKPIR+ S HQ
Sbjct: 83 NQAQLAMSHLNGHKLHGKPIRIT-LSKHQ 110
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ V LD VS+ + ELF + G + + DR ++ G + F + DA A+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAMKQY 89
Query: 97 NMIKLYGKPIRVNKASS 113
N + L G+P+ + +S
Sbjct: 90 NGVPLDGRPMNIQLVTS 106
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 64
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKT 86
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + + +F + G ++++ + + + +G F+ F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMH---GQYL-CNRPIS 233
++ +D TG+SKGF F+ + +E + H G++ C P S
Sbjct: 46 QVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS 92
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 5/82 (6%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG--FIEFMGEE---DADY 91
++VG + SE + ELF Q G V +++ +DR Q G F+ F + +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A+ M ++ PI++ A S
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADS 87
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 38 YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
+VGGL S+ + + F + G VV+ + D T +G+GFI F +DA K+++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
Query: 98 MI--KLYGKPIRVNKA 111
+L G+ I KA
Sbjct: 72 QKEHRLDGRVIDPKKA 87
Score = 27.7 bits (60), Expect = 7.8, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 188 LDPEIMRDPDTGNSKGFAFINYASFEASDASID 220
+D I DP+TG S+GF FI + + + +D
Sbjct: 39 VDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMH 223
I+RD TG +G AF+ Y E + +I A++
Sbjct: 45 ILRDKLTGRPRGVAFVRYNKREEAQEAISALN 76
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 191 EIMRDPDTGNSKGFAFINYASFEASD--ASIDAMHGQYLCNRPISVSYAFKKDSKGDRHG 248
+++D T ++GFAFI ++ EA+ + A+H + +++ F K SK D
Sbjct: 56 RVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGK-TINVEFAKGSKRDMAS 114
Query: 249 SAAERLLAA 257
+ R+ AA
Sbjct: 115 NEGSRISAA 123
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+++V G V + E F+ GPV +V M KD+ + +E MG+ A A+
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVE-MGDVGAREAVLS 63
Query: 96 MNMIKLYGKPIRVN 109
+ L G +RV
Sbjct: 64 QSQHSLGGHRLRVR 77
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 17/99 (17%)
Query: 28 GESGDGD-----ATIYVGGLDDKVSETLMWELFVQSG----------PVVNVHMPKDRVT 72
G SGD D + IYV GL+D V+ + + F Q G P++++++ D+ T
Sbjct: 4 GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKET 61
Query: 73 QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+G + + A A++ + G ++V+ A
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
A+ QK GAN+FI +L E ++ L F FG +
Sbjct: 15 AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNV---------------------- 52
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
V A +FI D T SK F F++Y + ++ A+I +M+G
Sbjct: 53 --------VSAKVFI---------DKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ V LD VS+ + ELF + G + + DR ++ G + F + DA A K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAXKQY 90
Query: 97 NMIKLYGKPIRVNKASS 113
N + L G+P + +S
Sbjct: 91 NGVPLDGRPXNIQLVTS 107
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 28.5 bits (62), Expect = 5.0, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVG L + + F GP+ V + ++ G+ F+EF DA+ A++ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 97 NMIKLYGKPIRV 108
+ + G +RV
Sbjct: 58 DGKVICGSRVRV 69
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
G + ++VG ++E + E F Q G V++V +PK + + F+ F ++ A
Sbjct: 4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIA 55
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,415,066
Number of Sequences: 62578
Number of extensions: 350732
Number of successful extensions: 1070
Number of sequences better than 100.0: 169
Number of HSP's better than 100.0 without gapping: 123
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 707
Number of HSP's gapped (non-prelim): 385
length of query: 305
length of database: 14,973,337
effective HSP length: 98
effective length of query: 207
effective length of database: 8,840,693
effective search space: 1830023451
effective search space used: 1830023451
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)