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= psy4080
(403 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 126 bits (316), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 56/91 (61%), Positives = 71/91 (78%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ D
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHT 263
DA AK+ GME+DGR+IRVDFS+T+R HT
Sbjct: 69 DAKEAKERANGMELDGRRIRVDFSITKRPHT 99
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 125 bits (314), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 56/91 (61%), Positives = 71/91 (78%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ D
Sbjct: 6 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHT 263
DA AK+ GME+DGR+IRVDFS+T+R HT
Sbjct: 66 DAKEAKERANGMELDGRRIRVDFSITKRPHT 96
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 124 bits (310), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 70/90 (77%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ D
Sbjct: 40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAH 262
DA AK+ GME+DGR+IRVDFS+T+R H
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSITKRPH 129
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 49/81 (60%), Positives = 62/81 (76%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ D
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 233 DAAAAKDACTGMEIDGRQIRV 253
DA AK+ GME+DGR+IRV
Sbjct: 69 DAKEAKERANGMELDGRRIRV 89
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 47/73 (64%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GLS T EQ + +FSKYG + V VV D +T RSRGF FV FE+ DDA A A
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 242 TGMEIDGRQIRVD 254
G +DGRQIRVD
Sbjct: 75 NGKSVDGRQIRVD 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 37/80 (46%), Positives = 50/80 (62%), Gaps = 3/80 (3%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
QPS+ L V GLS TTE+ + F G V R +V D +TG S+GF FV F S +DA A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 237 AKDACTGMEIDGRQIRVDFS 256
AK+A EIDG ++ +D++
Sbjct: 70 AKEAMEDGEIDGNKVTLDWA 89
>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 = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 45/81 (55%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
+ S L V LS YTTE+QI +FSK G ++++ + +D + GFCFV + SR DA
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 237 AKDACTGMEIDGRQIRVDFSV 257
A G +D R IR D+
Sbjct: 97 AMRYINGTRLDDRIIRTDWDA 117
>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 = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V ++ TTE ++ F YGP++R+ +V ++G+ RG+ F+ +E D +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 240 ACTGMEIDGRQIRVD 254
G +IDGR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V ++ TTE ++ F YGP++R+ +V ++G+ RG+ F+ +E D +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 240 ACTGMEIDGRQIRVD 254
G +IDGR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 40/76 (52%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V L+ T+ + +F KYG V V + D T SRGF FV F + DA A DA
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 241 CTGMEIDGRQIRVDFS 256
G +DGR++RV +
Sbjct: 109 MDGAVLDGRELRVQMA 124
>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 = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 32/74 (43%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS YTTE+QI +FSK G ++++ + +D K + GFCFV + SR DA A
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRYI 79
Query: 242 TGMEIDGRQIRVDF 255
G +D R IR D+
Sbjct: 80 NGTRLDDRIIRTDW 93
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 39/73 (53%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V L+ T+ + +F KYG V V + D T SRGF FV F + DA A DA
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 241 CTGMEIDGRQIRV 253
G +DGR++RV
Sbjct: 132 MDGAVLDGRELRV 144
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 175 NPQPS--RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
NP+P R L V + E Q+ +F +YGP+E V++V D +T +SRG+ FV F+S
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVT 258
A A G I ++++V + +
Sbjct: 96 SAQQAIAGLNGFNILNKRLKVALAAS 121
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL+ T E+ + +F K+GP+ V ++ D +T +SRGF F+ FE+ DA A
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 242 TGMEIDGRQIRVD 254
G + G+ I+V+
Sbjct: 69 NGKSLHGKAIKVE 81
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 39/73 (53%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V L+ T+ + +F KYG V V + + T RGF FV F R DA A+ A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 241 CTGMEIDGRQIRV 253
G E+DGR++RV
Sbjct: 75 MDGAELDGRELRV 87
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 171 DGRENPQPSRCLG---VFGLSIY--TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF 225
D P P R + +F SI+ E +I F YG ++ + + +D +TG S+G+
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
V +E+ A AAK+A G EI G+ I+VD+
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 45/82 (54%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+Q+ IFS+ GPV +V D +TG+ +G+ F ++ ++ A +A G E GR +
Sbjct: 21 TEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRAL 80
Query: 252 RVDFSVTQRAHTPTPGIYMGRP 273
RVD + +++ + G P
Sbjct: 81 RVDNAASEKNKEELKSLGTGAP 102
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 171 DGRENPQPSRCLG---VFGLSIY--TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF 225
D P P R + +F SI+ E +I F YG ++ + + +D +TG S+G+
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
V +E+ A AAK+A G EI G+ I+VD+
Sbjct: 119 VEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 30/87 (34%), Positives = 47/87 (54%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 240 ACTGMEIDGRQIRVDFSVTQRAHTPTP 266
E+ GR IRV+ + R P
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIKESGP 99
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 240 ACTGMEIDGRQIRVDFS 256
E+ GR IRV+ +
Sbjct: 66 NMNESELFGRTIRVNLA 82
>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 = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 240 ACTGMEIDGRQIRVDFS 256
E+ GR IRV+ +
Sbjct: 63 NMNESELFGRTIRVNLA 79
>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 = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 240 ACTGMEIDGRQIRVDFS 256
E+ GR IRV+ +
Sbjct: 68 NMNESELFGRTIRVNLA 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L TE + IF +G +E +++++D++TGRS+G+ F+ F + A A +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 242 TGMEIDGRQIRVDFSVTQRA 261
G E+ GR ++V VT+R
Sbjct: 89 NGFELAGRPMKVG-HVTERT 107
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL+ ++ ++ F +G + +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 240 ACTGMEIDGRQIRVDFS 256
E+ GR IRV+ +
Sbjct: 124 NMNESELFGRTIRVNLA 140
>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 = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 50/90 (55%), Gaps = 6/90 (6%)
Query: 171 DGRENPQPSRC-----LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF 225
DG E P P R L V G+ TE+ I+ F++YG ++ + + +D +TG +G+
Sbjct: 10 DGDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
V +E+ +A AA + G ++ G+ I VD+
Sbjct: 69 VEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S+ L + LS TE+ + +F K ++ V + G+S+G+ F+ F S +DA A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 239 DACTGMEIDGRQIRVDF 255
++C EI+GR IR++
Sbjct: 71 NSCNKREIEGRAIRLEL 87
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 50/90 (55%), Gaps = 6/90 (6%)
Query: 171 DGRENPQPSRC-----LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF 225
DG E P P R L V G+ TE+ I+ F++YG ++ + + +D +TG +G+
Sbjct: 11 DGDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 226 VYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
V +E+ +A AA + G ++ G+ I VD+
Sbjct: 70 VEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 175 NPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
NP PSR + + + TE+QI + S GPV ++++ D +TGRS+G+ F+ F + +
Sbjct: 1 NP-PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESS 59
Query: 235 AAAKDACTGMEIDGRQIRVDFS 256
A+A G ++ R ++ +S
Sbjct: 60 ASAVRNLNGYQLGSRFLKCGYS 81
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 42/84 (50%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V LS T E + +F +G + R+ + D TG+S+GF F+ F R+DAA A +G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 244 MEIDGRQIRVDFSVTQRAHTPTPG 267
D + V+++ P+ G
Sbjct: 80 FGYDHLILNVEWAKPSTNSGPSSG 103
>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 = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L++ ++ + + F + V+ D +TG SRG+ FV F S+DDA A D+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 242 TGMEIDGRQIRVDFS 256
G +++GR +R++++
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S L V L TE + IF +G ++ + ++ D+ TGRS+G+ F+ F + A A
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 239 DACTGMEIDGRQIRVDFSVTQR 260
+ G E+ GR +RV VT+R
Sbjct: 65 EQLNGFELAGRPMRVG-HVTER 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L++ ++ + + F + V+ D +TG SRG+ FV F S+DDA A D+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 242 TGMEIDGRQIRVDFS 256
G +++GR +R++++
Sbjct: 150 QGQDLNGRPLRINWA 164
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 7/117 (5%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V L TE + F GP+ ++++ID K ++ + FV + DA A
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59
Query: 240 ACTGMEIDGRQIRVD--FSVTQRAHTPTPGIYMGRPTY----EQLNNTQSELGSLLS 290
G +I+ ++++ F Q + T +++G E L N + S LS
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLS 116
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS+ TT + + H F ++G V+ ++ D T R RGF FV FES D
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 45/79 (56%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
PSR + + + TE+QI + S GPV ++++ D +TGRS+G+ F+ F + +A+A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 238 KDACTGMEIDGRQIRVDFS 256
G ++ R ++ +S
Sbjct: 62 VRNLNGYQLGSRFLKCGYS 80
>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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 5/85 (5%)
Query: 176 PQPSRC-----LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
P P R L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 231 RDDAAAAKDACTGMEIDGRQIRVDF 255
+A AA + G ++ G+ I VD+
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 45/79 (56%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
PSR + + + TE+QI + S GPV ++++ D +TGRS+G+ F+ F + +A+A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 238 KDACTGMEIDGRQIRVDFS 256
G ++ R ++ +S
Sbjct: 61 VRNLNGYQLGSRFLKCGYS 79
>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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+ +A AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 242 TGMEIDGRQIRVDF 255
G ++ G+ I VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 9/97 (9%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T + I F+ +G + VV D TG+S+G+ FV F ++ DA A G +
Sbjct: 23 LSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 82
Query: 247 DGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQS 283
GRQIR +++ + P P + TYE N QS
Sbjct: 83 GGRQIRTNWATRK---PPAP-----KSTYES-NTKQS 110
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 48.1 bits (113), Expect = 9e-06, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+ +A AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 242 TGMEIDGRQIRVDF 255
G ++ G+ I VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V G+ TE+ I+ F++YG ++ + + +D +TG +G+ V +E+ +A AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 242 TGMEIDGRQIRVDF 255
G ++ G+ I VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 38/71 (53%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T + I F+ +G + VV D TG+S+G+ FV F ++ DA A G +
Sbjct: 23 LSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWL 82
Query: 247 DGRQIRVDFSV 257
GRQIR +++
Sbjct: 83 GGRQIRTNWAT 93
>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 = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS T E++I F +G VE +E+ +D KT + RGFCF+ F+ +
Sbjct: 6 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS T E++I F +G VE +E+ +D KT + RGFCF+ F+ +
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL +TT+ + F +G +E V+ D +TG+SRG+ FV R AAA+ AC
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR---AAAERACKD 78
Query: 244 ME--IDGRQIRVDFS 256
IDGR+ V+ +
Sbjct: 79 PNPIIDGRKANVNLA 93
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
Q + L V GL TTEQ + FS +G V V+V D KTG S+GF FV F +
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE--TQ 70
Query: 237 AKDACTGMEIDGR 249
K IDGR
Sbjct: 71 VKVMSQRHMIDGR 83
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 2/97 (2%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 9 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYM 270
AA +A ++DGR + +V+ R + PG ++
Sbjct: 69 VDAAMNA-RPHKVDGRVVEPKRAVS-REDSQRPGAHL 103
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 110 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 158
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 2/97 (2%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYM 270
AA +A ++DGR + +V+ R + PG ++
Sbjct: 68 VDAAMNA-RPHKVDGRVVEPKRAVS-REDSQRPGAHL 102
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 2/97 (2%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 7 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 66
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPGIYM 270
AA +A ++DGR + +V+ R + PG ++
Sbjct: 67 VDAAMNA-RPHKVDGRVVEPKRAVS-REDSQRPGAHL 101
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 108 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 156
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R P+ +R L + L T +++ IF KYGP+ ++ V T +RG +V +E
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIF 58
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRA 261
DA A D +G + R + V + RA
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYYNANRA 87
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 54/104 (51%), Gaps = 7/104 (6%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQR------AHTPTPGIYMG 271
AA +A ++DGR + +V++ AH I++G
Sbjct: 68 VDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 110
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 54/104 (51%), Gaps = 7/104 (6%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 6 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQR------AHTPTPGIYMG 271
AA +A ++DGR + +V++ AH I++G
Sbjct: 66 VDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 108
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 107 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 155
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 54/104 (51%), Gaps = 7/104 (6%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+ P+ R L + GLS TT++ + F ++G + V+ D T RSRGF FV + + ++
Sbjct: 1 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQR------AHTPTPGIYMG 271
AA +A ++DGR + +V++ AH I++G
Sbjct: 61 VDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 103
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 102 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 150
>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 = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 8/89 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE---SRDDAAAAKDACT 242
GL+ TTE + F KYG V ++++ D TGRSRGF F+ FE S D+ +
Sbjct: 10 GLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILD 69
Query: 243 GMEIDGRQIRVDFSVTQRAHTPTPGIYMG 271
G ID ++ ++ + T I++G
Sbjct: 70 GKVIDPKR-----AIPRDEQDKTGKIFVG 93
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
++ FS++G + ++++D TG+SRGF FV ++S D A C ID + ++
Sbjct: 102 KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD---AVDRVCQNKFIDFKDRKI 158
Query: 254 DFSVTQRAH 262
+ + H
Sbjct: 159 EIKRAEPRH 167
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 8/89 (8%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT---- 242
LS + E+ + + ++G ++ V VV+ T S+G F F +++ A A +
Sbjct: 23 LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE 82
Query: 243 --GMEIDGRQIRVDFSVT--QRAHTPTPG 267
G+++DGRQ++VD +VT + A P+ G
Sbjct: 83 GGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 3/92 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
A+ R P+ +R L + L T +++ IF KYGP+ ++ V T +RG +V +E
Sbjct: 9 ANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYE 65
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRA 261
DA A D +G + R + V + RA
Sbjct: 66 DIFDAKNACDHLSGFNVCNRYLVVLYYNANRA 97
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 36/74 (48%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T + IFSKYG V +V ++ D T +S+G F+ F +D A A
Sbjct: 21 VSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN 80
Query: 244 MEIDGRQIRVDFSV 257
++ GR I+ ++
Sbjct: 81 KQLFGRVIKASIAI 94
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 3/92 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
A+ R P+ +R L + L T +++ IF KYGP+ ++ V T +RG +V +E
Sbjct: 9 ANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYE 65
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVDFSVTQRA 261
DA A D +G + R + V + RA
Sbjct: 66 DIFDAKNACDHLSGFNVCNRYLVVLYYNANRA 97
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L ++ I +F+++G +++ V D ++GRS G V+FE R DA A
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQY 149
Query: 242 TGMEIDGRQIRVDFSVTQ 259
G+ +DGR + + +Q
Sbjct: 150 KGVPLDGRPMDIQLVASQ 167
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 36/72 (50%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS ++E+ + +FS YGP+ + ID+ T + +GF FV F + A A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 242 TGMEIDGRQIRV 253
G GR + V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L + GLS TTE+ + + + ++G + V+ D + RSRGF FV F S + AA
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM- 86
Query: 240 ACTGMEIDGRQI 251
A IDGR +
Sbjct: 87 AARPHSIDGRVV 98
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
A+ R P+ +R L + L T +++ IF KYGP+ ++ V T +RG +V +E
Sbjct: 3 ANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYE 59
Query: 230 SRDDAAAAKDACTGMEIDGRQIRV 253
DA A D +G + R + V
Sbjct: 60 DIFDAKNACDHLSGFNVCNRYLVV 83
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L T+ Q++ IF KYG + + ++ D TGR RG FV + R++A A A
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 242 TGM 244
+
Sbjct: 163 NNV 165
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +F GP+ + D KTG S G+ FV F S D+ A G+ + +++
Sbjct: 27 TDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRL 86
Query: 252 RVDFS 256
+V ++
Sbjct: 87 KVSYA 91
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 5/101 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+ + +F G +E ++V D TG+S G+ FV + +DA A + G+++ + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 252 RVDFSVTQRAHTPTPGIYM-GRPTYEQLNNTQSELGSLLSE 291
+V ++ A +Y+ G P +Q E+ L S+
Sbjct: 77 KVSYARPSSASIRDANLYVSGLPK----TMSQKEMEQLFSQ 113
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL +++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 242 TG 243
G
Sbjct: 153 NG 154
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L T+ Q++ IF KYG + + ++ D TGR RG FV + R++A A A
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 242 TGMEIDG 248
+ +G
Sbjct: 152 NNVIPEG 158
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +F GP+ ++ D KTG S G+ FV F S D+ A G+ + +++
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 252 RVDFS 256
+V ++
Sbjct: 76 KVSYA 80
>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 = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 242 TGMEIDG 248
G + G
Sbjct: 151 NGQKPSG 157
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 3/91 (3%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L T+QQ + +G +ER +V +TG+S+G+ F + +D AA AK
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 242 TGMEIDGRQIRVDFSVTQRAHTPTPGIYMGR 272
G + R + V ++ A TP + R
Sbjct: 156 LGKPLGPRTLYVHWT---DAGQLTPALLHSR 183
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L T+QQ + +G +ER +V +TG+S+G+ F + +D AA AK
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 242 TGMEIDGRQIRVDFS 256
G + R + V ++
Sbjct: 158 LGKPLGPRTLYVHWT 172
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L T+QQ + +G +ER +V +TG+S+G+ F + +D AA AK
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 242 TGMEIDGRQIRVDFS 256
G + R + V ++
Sbjct: 158 LGKPLGPRTLYVHWT 172
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
QP R L V + + + +F ++G + VE++ + + S+GF FV FE+ DA
Sbjct: 28 QPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADR 84
Query: 237 AKDACTGMEIDGRQIRVD 254
A++ G ++GR+I V+
Sbjct: 85 AREKLHGTVVEGRKIEVN 102
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL T++ + +FS++G + V++D TG SRG F+ F+ R +A A +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 242 TG 243
G
Sbjct: 151 NG 152
>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 = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL T++ + +FS++G + V++D TG SRG F+ F+ R +A A +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 242 TG 243
G
Sbjct: 151 NG 152
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GLS T+++ + F+K+G V + D TGRSRGF F+ F+ DAA+ +
Sbjct: 16 VGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK---DAASVEKVLDQ 72
Query: 244 ME--IDGRQI 251
E +DGR I
Sbjct: 73 KEHRLDGRVI 82
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 30/54 (55%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
GLS TT++ + FSK+G V + +D TGRSRGF FV F+ + D
Sbjct: 6 GLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G E + L V L ++ I +F+++G +++ V D ++GRS G V+FE R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 86
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQ 259
DA A G+ +DGR + + +Q
Sbjct: 87 ADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +F GP+ ++ D KTG S G+ FV F S D+ A G+ + +++
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 252 RVDFS 256
+V ++
Sbjct: 76 KVSYA 80
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 172 GRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESR 231
G E + L V L ++ I +F+++G +++ V D ++GRS G V+FE R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 86
Query: 232 DDAAAAKDACTGMEIDGRQIRVDFSVTQ 259
DA A G+ +DGR + + +Q
Sbjct: 87 ADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTT--EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
V+ SIY E I F+ +GP++ +++ D+ T + +GF FV +E + A A +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 242 TGMEIDGRQIRV 253
+ + GR I+V
Sbjct: 91 NSVMLGGRNIKV 102
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
++ I +F +G ++ + D TG+ +G+ F+ +E A +++DA + M ++ G
Sbjct: 138 SDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK---AQSSQDAVSSMNLFDLGG 194
Query: 249 RQIRVDFSVTQRAHTPTPG 267
+ +RV +VT TP
Sbjct: 195 QYLRVGKAVTPPMPLLTPA 213
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
P + L + GL Y + Q+ + + +GP++ +V D+ TG S+G+ F + +
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 236 AAKDACTGMEIDGRQIRV 253
A GM++ +++ V
Sbjct: 171 QAIAGLNGMQLGDKKLLV 188
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 203 YGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSV 257
+G + VV D TG+S+G+ FV F ++ DA A G + GRQIR +++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT 84
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
+ +R L LS TE ++ +F + +E+ + ++ G+S+G ++ F+S DA
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 237 AKDACTGMEIDGRQIRVDFS 256
+ G EIDGR + + ++
Sbjct: 152 NLEEKQGAEIDGRSVSLYYT 171
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 212 VIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
V+D +TG +R F +V FES +D A + TG+++ G +I+++
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE 86
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+++ +F KYG V + D +GF F+ E+R A AK M + G+Q+
Sbjct: 28 TEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81
Query: 252 RVDFSVTQRAHTPTP 266
RV F+ + T P
Sbjct: 82 RVRFACHSASLTSGP 96
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 3/96 (3%)
Query: 175 NP-QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
NP +P++ L + LS TE+ + +F+++ + + TGR RG F+ F +++
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79
Query: 234 AAAAKDACTGMEIDGRQIRVDF--SVTQRAHTPTPG 267
A A G ++ G+ + ++F + QR+ P+ G
Sbjct: 80 AWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSSG 115
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 179 SRC-LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
RC L V L TE+ +F +YG E EV I+ R RGF F+ ESR A A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFIN----RDRGFGFIRLESRTLAEIA 74
Query: 238 KDACTGMEIDGRQIRVDFSV 257
K G + R +R+ F+
Sbjct: 75 KAELDGTILKSRPLRIRFAT 94
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V LS + + + FS++GPVE+ VV+D + GR+ G FV F ++ A A +
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR-GRATGKGFVEFAAKPPARKALER 156
Query: 241 C 241
C
Sbjct: 157 C 157
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDG 248
T+ Q++ IF KYG + + ++ D TGR RG FV + R++A A A + +G
Sbjct: 26 TDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL +++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 242 TG 243
G
Sbjct: 64 NG 65
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTT--EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
V+ SIY E I F+ +GP++ +++ D+ T + +GF FV +E + A A +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 242 TGMEIDGRQIRV 253
+ + GR I+V
Sbjct: 76 NSVMLGGRNIKV 87
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
++ I +F +G ++ + D TG+ +G+ F+ +E A +++DA + M ++ G
Sbjct: 123 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEK---AQSSQDAVSSMNLFDLGG 179
Query: 249 RQIRVDFSVTQRAHTPTPG 267
+ +RV +VT TP
Sbjct: 180 QYLRVGKAVTPPMPLLTPA 198
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTT--EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
V+ SIY E I F+ +GP++ ++ D+ T + +GF FV +E + A A +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 242 TGMEIDGRQIRV 253
+ + GR I+V
Sbjct: 75 NSVXLGGRNIKV 86
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 36/76 (47%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
++ I +F +G ++ + D TG+ +G+ F+ +E + A + ++ G+ +
Sbjct: 122 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Query: 252 RVDFSVTQRAHTPTPG 267
RV +VT TP
Sbjct: 182 RVGKAVTPPXPLLTPA 197
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 6/75 (8%)
Query: 196 INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
+ +F ++G + VE++ + + S+GF FV FE+ DA A++ G ++GR+I V+
Sbjct: 32 LRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN- 88
Query: 256 SVTQRAHT---PTPG 267
+ T R T P+ G
Sbjct: 89 NATARVMTNSGPSSG 103
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+ + +F G +E ++V D TG+S G+ FV + +DA A + G+++ + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 252 RVDFS 256
+V ++
Sbjct: 77 KVSYA 81
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 50/94 (53%), Gaps = 3/94 (3%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
++ QP R L V LS TE I +FS+ GP + +++ + + +CFV F
Sbjct: 10 EDDGQP-RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHR 66
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTP 266
DAAAA A G +I G++++V+++ T + P
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 176 PQP-SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
P P + L + GL Y + Q+ + + +GP++ +V D+ TG S+G+ F + +
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 235 AAAKDACTGMEIDGRQIRV 253
A GM++ +++ V
Sbjct: 152 DQAIAGLNGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 176 PQP-SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
P P + L + GL Y + Q+ + + +GP++ +V D+ TG S+G+ F + +
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 235 AAAKDACTGMEIDGRQIRV 253
A GM++ +++ V
Sbjct: 150 DQAIAGLNGMQLGDKKLLV 168
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L ++ I +F+++G +++ V D ++GRS G V+FE + DA A
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 89
Query: 242 TGMEIDGRQIRVDF 255
G+ +DGR + +
Sbjct: 90 NGVPLDGRPMNIQL 103
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF--ESRDDAAAA 237
R + V L T +Q+ +FS++G V V+++ D +T + +GF FV ES +A A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 238 KDACTGMEIDGRQIRV 253
D M GR IRV
Sbjct: 62 LDNTDFM---GRTIRV 74
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V L+ TE+ + FS++G +ERV+ + D + F++F+ RD A A +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 63
Query: 240 ACTGMEIDGRQIRVDFS 256
G +++G I + F+
Sbjct: 64 EMNGKDLEGENIEIVFA 80
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD-ACTGM 244
GLS TT++ + F ++G V+ V+ D T RSRGF FV F D A K A +
Sbjct: 32 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF--MDQAGVDKVLAQSRH 89
Query: 245 EIDGRQIRVDFSVTQRAH 262
E+D + I + +RA
Sbjct: 90 ELDSKTIDPKVAFPRRAQ 107
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+++ +F KYG V + D +GF F+ E+R A AK M + G+Q+
Sbjct: 35 TEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL 88
Query: 252 RVDFS 256
RV F+
Sbjct: 89 RVRFA 93
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S L V L Y + + + FS +G VER V++D + GR G V F + A A
Sbjct: 96 SASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDR-GRPSGKGIVEFSGKPAARKAL 154
Query: 239 DACT 242
D C+
Sbjct: 155 DRCS 158
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 51/103 (49%), Gaps = 13/103 (12%)
Query: 170 ADGRENPQPS-RCLGVFGLSIYTTEQQINHIFS--KYGPVERVEVVIDAKTGRSRGFCFV 226
+ G E+ S + L V L + T+E+ I F+ K G VERV+ + R + FV
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFV 56
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIRVDFS--VTQRAHTPTPG 267
+F +R+DA A A G +DG I V + V + + P+ G
Sbjct: 57 HFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGR-SRGFCFVYFESRDDAAAAKDACTGME 245
L+ T+ I IFS YG ++ +++ ++ S+G+ +V FE+ D+A A G +
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ 71
Query: 246 IDGRQI 251
IDG++I
Sbjct: 72 IDGQEI 77
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL TT++ + FS+YG V ++ D T +SRGF FV F+ + A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-AS 77
Query: 242 TGMEIDGRQI 251
+DGR I
Sbjct: 78 RPHTLDGRNI 87
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S L + GL TT+Q + + YG + + ++D T + +G+ FV F D +AA+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF---DSPSAAQ 61
Query: 239 DACTGMEIDGRQIRV 253
A T ++ G Q ++
Sbjct: 62 KAVTALKASGVQAQM 76
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
+ +R L LS TE ++ +F + +E+ + ++ G+S+G ++ F+S DA
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIAYIEFKSEADAEK 68
Query: 237 AKDACTGMEIDGRQIRVDFS 256
+ G EIDGR + + ++
Sbjct: 69 NLEEKQGAEIDGRSVSLYYT 88
>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 = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L ++ I +F+++G +++ V D ++GRS G V+FE + DA A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQY 90
Query: 242 TGMEIDGR 249
G+ +DGR
Sbjct: 91 NGVPLDGR 98
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 9/94 (9%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGR-----SRGFCFVYFESRDD 233
S L + L+ TTE+ + +FSK G ++ I K + S GF FV ++ +
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIK--SCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 234 AAAAKDACTGMEIDGRQIRVDFSVTQRAHTPTPG 267
A A G +DG ++ V +++RA P G
Sbjct: 63 AQKALKQLQGHTVDGHKLEVR--ISERATKPASG 94
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL Y + Q+ + + +GP++ +V D+ TG S+G+ F + + A
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 242 TGMEIDGRQIRVDFSVTQRA 261
GM++ +++ V QRA
Sbjct: 64 NGMQLGDKKLLV-----QRA 78
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL +E + +F + GPV + D TG+ +G+ FV F S +DA A
Sbjct: 20 VGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM 79
Query: 244 MEIDGRQIRVD 254
+++ G+ IRV+
Sbjct: 80 IKLYGKPIRVN 90
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
+R L L T+ ++ +F + E+ + +K G+S+G ++ F++ DA
Sbjct: 93 ARTLLAKNLPYKVTQDELKEVFE-----DAAEIRLVSKDGKSKGIAYIEFKTEADAEKTF 147
Query: 239 DACTGMEIDGRQIRVDFS 256
+ G EIDGR I + ++
Sbjct: 148 EEKQGTEIDGRSISLYYT 165
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 211 VVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
V+D + G +R F +V FES +D A + TG+++ G +I+++
Sbjct: 38 AVVDVRIGMTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 193 EQQINHIFSKYGPVERV-EVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E+ + FS +G + + +++ D TG S+G+ F+ F S D + AA +A G + R I
Sbjct: 19 EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI 78
Query: 252 RVDFSVTQRAHTPTP 266
V ++ + + P
Sbjct: 79 TVSYAFKKDSKGSGP 93
>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 = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTG--RSRGFCFVYFESRDDAAAAKDACTGMEI 246
+E+ + +F +YG V + V+ D +S+G CFV F +R A A++A M++
Sbjct: 16 SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV 72
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 7/98 (7%)
Query: 172 GRENP-QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
G+E P +P V L T + I+ IF + V +V D T + +GFC+V F
Sbjct: 7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEF-- 63
Query: 231 RDDAAAAKDACT--GMEIDGRQIRVDFSVTQRAHTPTP 266
D+ + K+A T G + R +RVD + ++ P
Sbjct: 64 -DEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSGP 100
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V +S T Q++ F +YGPV ++V D + FV+ E +DA A
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 242 TGMEIDGRQIRVDFSVTQ 259
E G+++ V S ++
Sbjct: 65 DNTEFQGKRMHVQLSTSR 82
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTG--RSRGFCFVYFESRDDAAAAKDACTGMEI 246
+E+ + +F +YG V + V+ D +S+G CFV F +R A A++A M++
Sbjct: 28 SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV 84
>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 = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEID 247
++ + +FSK G V +E ID TG+++GF FV S +DA + G +D
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 36.6 bits (83), Expect = 0.023, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEID 247
++ + +FSK G V +E ID TG+++GF FV S +DA + G +D
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTG--RSRGFCFVYFESRDDAAAAKDACTGMEI 246
+E+ + +F +YG V + V+ D +S+G CFV F +R A A++A M++
Sbjct: 16 SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV 72
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E ++N IF +GP++ V+++ GF FV FE + AA A + G + +
Sbjct: 18 ESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE 69
Query: 253 VDFS 256
V +S
Sbjct: 70 VVYS 73
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD-ACTGM 244
GLS TT++ + F ++G V+ V+ D T RSRGF FV F D A K A +
Sbjct: 7 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF--MDQAGVDKVLAQSRH 64
Query: 245 EIDGRQI 251
E+D + I
Sbjct: 65 ELDSKTI 71
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.4 bits (80), Expect = 0.053, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E ++N IF +GP++ V+++ GF FV FE + AA A + G + +
Sbjct: 45 ESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE 96
Query: 253 VDFS 256
V +S
Sbjct: 97 VVYS 100
>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 = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T Q + +F YG V+RV+++ + K V + A A G ++ G+
Sbjct: 47 VTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSHLNGHKLHGKP 101
Query: 251 IRVDFSVTQRAHTPTPG 267
IR+ S Q P G
Sbjct: 102 IRITLSKHQNVQLPREG 118
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E ++ F K+G V V ++ DA+ R RGF F+ FE A + +I G+++
Sbjct: 24 ETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF-HDIMGKKVE 82
Query: 253 V 253
V
Sbjct: 83 V 83
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T Q + +F YG V+RV+++ + K V + A A G ++ G+
Sbjct: 16 VTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSHLNGHKLHGKP 70
Query: 251 IRVDFSVTQRAHTPTPG 267
IR+ S Q P G
Sbjct: 71 IRITLSKHQNVQLPREG 87
>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 = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTG--RSRGFCFVYFESRDDAAAAKDACTGMEI 246
+E+ + +F +YG V + V+ D +S+G CFV F +R A A++A ++
Sbjct: 16 SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKV 72
>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 = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 180 RCLGVFGLSIYTTEQQINH-----IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
R GV + I ++ I++ FS +G + +VV D S+G+ FV+FE+++ A
Sbjct: 99 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAA 156
Query: 235 AAAKDACTGMEIDGRQIRV 253
A + GM ++ R++ V
Sbjct: 157 ERAIEKMNGMLLNDRKVFV 175
>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 = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 183 GVFGLSIYTTEQQINH-----IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
GV + I ++ I++ FS +G + +VV D S+G+ FV+FE+++ A A
Sbjct: 97 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 154
Query: 238 KDACTGMEIDGRQIRV 253
+ GM ++ R++ V
Sbjct: 155 IEKMNGMLLNDRKVFV 170
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
FS +G + +VV D S+G+ FV+FE+++ A A + GM ++ R++ V
Sbjct: 32 FSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 212 VIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
V+D +TG +R F +V FES +D A + TG+++ G +I+++
Sbjct: 49 VVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE 90
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 206 VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG----MEIDGRQIRVDFS 256
V + ++ D +T ++RGF FV S DA+ ++IDG+ I VDF+
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 169 FADGRENPQPSRCLGVF--GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV 226
F D P C V+ G++ T+Q + FS +G + + V + +G+ FV
Sbjct: 14 FEDVVNQSSPKNCT-VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFV 66
Query: 227 YFESRDDAAAAKDACTGMEIDGRQIR 252
F + + AA A + G I+G ++
Sbjct: 67 RFSTHESAAHAIVSVNGTTIEGHVVK 92
>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 = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
FS +G + +VV D S+G+ FV+FE+++ A A + GM ++ R++ V
Sbjct: 26 FSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V L+ TE+ + FS++G +ERV+ + D + FV+FE R A A D
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMD 67
Query: 240 ACTG 243
G
Sbjct: 68 EMNG 71
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRS-RGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+ I +F KYG + ID K R F FV FE DA A G + DG ++R
Sbjct: 37 KDIEDVFYKYGAIRD----IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR 92
Query: 253 VDFSVTQRAHTPTP 266
V+F + R P
Sbjct: 93 VEFPRSGRGTGSGP 106
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 32.3 bits (72), Expect = 0.49, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 195 QINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
++ FS YGP+ V + + GF FV FE DA A G I G ++RV+
Sbjct: 16 ELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 70
Query: 255 FS 256
S
Sbjct: 71 LS 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 195 QINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
++ F YGP+ V V + GF FV FE DAA A G + G ++RV+
Sbjct: 89 ELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE 143
Query: 255 FS 256
S
Sbjct: 144 LS 145
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 7/59 (11%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
++++ FS +G + +V+++ GRS+GF FV F S ++A A E++GR +
Sbjct: 29 DERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAV-----TEMNGRIV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 183 GVF--GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
G+F L T + + F++ G V ++ ++ G+S+G V FES + A A
Sbjct: 7 GIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 64
Query: 241 CTGMEIDGRQIRVDFSVTQRAHTPTPG 267
GM++ GR+I D + + A P+ G
Sbjct: 65 MNGMKLSGREI--DVRIDRNASGPSSG 89
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 195 QINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
++ F YGP+ V V + GF FV FE DAA A G + G ++RV+
Sbjct: 89 ELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVE 143
Query: 255 FS 256
S
Sbjct: 144 LS 145
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 31.2 bits (69), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 4/84 (4%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T + + F++ G V ++ ++ G+S+G V FES + A A G
Sbjct: 13 VRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 244 MEIDGRQIRVDFSVTQRAHTPTPG 267
M++ GR+I D + + A P+ G
Sbjct: 71 MKLSGREI--DVRIDRNASGPSSG 92
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+++ +FS G V R +++ D K G+SRG V FE +A A G + R + V
Sbjct: 30 KKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 28.9 bits (63), Expect = 4.9, Method: Composition-based stats.
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 190 YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR 249
+ TE + +F +G ++D K +G CF+ +++ + AA A GR
Sbjct: 38 FATEADLIPLFQNFG------FILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91
Query: 250 QIR 252
+R
Sbjct: 92 NLR 94
>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 = 28.1 bits (61), Expect = 8.1, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 192 TEQQINHIFSKYGPVER-VEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT-GMEIDGR 249
TE I +G R V ++ + +G+SRGF FV F DA +A + I G+
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 250 QIRVDFS 256
++ + +S
Sbjct: 74 KVSMHYS 80
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 28.1 bits (61), Expect = 8.6, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
TEQ+I +F +YG V +++ + + FV+ E D AA+DA + ++ G
Sbjct: 21 TEQEIRSLFEQYGKVLECDII--------KNYGFVHIE---DKTAAEDAIRNLHHYKLHG 69
Query: 249 RQIRVDFSVTQRAHTPTP 266
I V+ S + + P
Sbjct: 70 VNINVEASKNKSKASSGP 87
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
0.318 0.135 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,268,953
Number of Sequences: 62578
Number of extensions: 384153
Number of successful extensions: 831
Number of sequences better than 100.0: 142
Number of HSP's better than 100.0 without gapping: 115
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 682
Number of HSP's gapped (non-prelim): 164
length of query: 403
length of database: 14,973,337
effective HSP length: 101
effective length of query: 302
effective length of database: 8,652,959
effective search space: 2613193618
effective search space used: 2613193618
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)