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= 024012
(274 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 68.2 bits (165), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 50/76 (65%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
KLFV GLSF T+E++L F +G++ EV ++ D+ ++RS+G+ F+ + + A A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 247 MNGKIINGWMIVVDVA 262
MNGK ++G I VD A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 39/88 (44%), Positives = 53/88 (60%), Gaps = 1/88 (1%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
KLF+ GL+ T+EK L+A F G + EV +I D+ SK S+G+AFI + A A K+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK-SRGFAFITFENPADAKNAAKD 67
Query: 247 MNGKIINGWMIVVDVAKTTPKYSRGRPR 274
MNGK ++G I V+ AK S GR R
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQSGGRRR 95
>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 = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 47/78 (60%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
K LFV +++ T+E LR FE +G + + ++ K S + +GYAFIEY E +A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 246 EMNGKIINGWMIVVDVAK 263
+GK I+G ++VDV +
Sbjct: 163 HADGKKIDGRRVLVDVER 180
>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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 47/78 (60%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
K LFV +++ T+E LR FE +G + + ++ K S + +GYAFIEY E +A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 246 EMNGKIINGWMIVVDVAK 263
+GK I+G ++VDV +
Sbjct: 163 HADGKKIDGRRVLVDVER 180
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V GLS YT+E+ LR F +G + +V I+ D+ S+RS+G+AF+ + + A A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++G I VD + T
Sbjct: 75 NGMELDGRRIRVDFSIT 91
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V GLS YT+E+ LR F +G + +V I+ D+ S+RS+G+AF+ + + A A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++G I VD + T
Sbjct: 78 NGMELDGRRIRVDFSIT 94
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V GLS YT+E+ LR F +G + +V I+ D+ S+RS+G+AF+ + + A A +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++G I VD + T
Sbjct: 109 NGMELDGRRIRVDFSIT 125
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 52/88 (59%), Gaps = 6/88 (6%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
K+FV GL ++T++ +LR FEGFG++ E +I D+ + +S+GY F+ AA A K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 247 MNGKIINGWMIVVDVAKTTPKYSRGRPR 274
N II+G V++A Y +PR
Sbjct: 79 PN-PIIDGRKANVNLA-----YLGAKPR 100
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 44/72 (61%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V GLS YT+E+ LR F +G + +V I+ D+ S+RS+G+AF+ + + A A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 248 NGKIINGWMIVV 259
NG ++G I V
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 50/79 (63%), Gaps = 3/79 (3%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+K LFV GLS T+E+TL+ +F+G V +I+ D+ + SKG+ F+++ +EE A AA
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 245 KEMNGKIINGWMIVVDVAK 263
+ M I+G + +D AK
Sbjct: 72 EAMEDGEIDGNKVTLDWAK 90
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 6/81 (7%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y
Sbjct: 4 SPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 236 TEEAASAAL----KEMNGKII 252
T E AA+ +++G+++
Sbjct: 62 TVEEVDAAMNARPHKVDGRVV 82
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 88 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 147
Query: 231 FIEY 234
F+ +
Sbjct: 148 FVTF 151
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 6/81 (7%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y
Sbjct: 6 SPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 236 TEEAASAAL----KEMNGKII 252
T E AA+ +++G+++
Sbjct: 64 TVEEVDAAMNARPHKVDGRVV 84
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 90 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 149
Query: 231 FIEY 234
F+ +
Sbjct: 150 FVTF 153
>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 = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 6/81 (7%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y
Sbjct: 5 SPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 236 TEEAASAAL----KEMNGKII 252
T E AA+ +++G+++
Sbjct: 63 TVEEVDAAMNARPHKVDGRVV 83
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 89 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 148
Query: 231 FIEY 234
F+ +
Sbjct: 149 FVTF 152
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 40/63 (63%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+L+V L F +E LR FE FG + ++++MD + RSKGY FI ++ E A AL++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 247 MNG 249
+NG
Sbjct: 88 LNG 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 6/81 (7%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y
Sbjct: 7 SPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 64
Query: 236 TEEAASAAL----KEMNGKII 252
T E AA+ +++G+++
Sbjct: 65 TVEEVDAAMNARPHKVDGRVV 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 91 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 150
Query: 231 FIEY 234
F+ +
Sbjct: 151 FVTF 154
>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 = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 6/81 (7%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y
Sbjct: 6 SPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 236 TEEAASAAL----KEMNGKII 252
T E AA+ +++G+++
Sbjct: 64 TVEEVDAAMNARPHKVDGRVV 84
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 90 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 149
Query: 231 FIEY 234
F+ +
Sbjct: 150 FVTF 153
>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 = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 51/77 (66%), Gaps = 6/77 (7%)
Query: 180 PTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEA 239
P Q++ KLF+ GLSF T++++LR+ FE +G L + ++ D +KRS+G+ F+ Y T E
Sbjct: 3 PEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 240 ASAAL----KEMNGKII 252
AA+ +++G+++
Sbjct: 61 VDAAMNARPHKVDGRVV 77
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
V + S+ + KK+FV G+ T E LR FE +G++ ++I+ D+ S + +G+A
Sbjct: 83 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 142
Query: 231 FIEY 234
F+ +
Sbjct: 143 FVTF 146
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 54/89 (60%)
Query: 175 SSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
SS +S + L+V GL+ +K L AAF FG++ +++I +D +++ +G+AF+E+
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 235 TTEEAASAALKEMNGKIINGWMIVVDVAK 263
E A+AA+ MN + G I V++AK
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 57.8 bits (138), Expect = 7e-09, Method: Composition-based stats.
Identities = 30/80 (37%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 185 TKK-LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA 243
TK+ L+V GL+ +K L AAF FG++ +++I +D +++ +G+AF+E+ E A+AA
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 244 LKEMNGKIINGWMIVVDVAK 263
+ MN + G I V++AK
Sbjct: 64 IDNMNESELFGRTIRVNLAK 83
>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 = 57.8 bits (138), Expect = 7e-09, Method: Composition-based stats.
Identities = 30/80 (37%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 185 TKK-LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA 243
TK+ L+V GL+ +K L AAF FG++ +++I +D +++ +G+AF+E+ E A+AA
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 244 LKEMNGKIINGWMIVVDVAK 263
+ MN + G I V++AK
Sbjct: 66 IDNMNESELFGRTIRVNLAK 85
>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 = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 46/76 (60%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L++ TS TLR FE +G + +V I D+ +K S+G+AF+ + + A A+ M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 248 NGKIINGWMIVVDVAK 263
+G +++G + V +A+
Sbjct: 110 DGAVLDGRELRVQMAR 125
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+LFV LS+ +SE+ L F +G L E+ +D ++K+ KG+AF+ + E A A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 247 MNGKIINGWMIVV 259
++G++ G M+ V
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 49/77 (63%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+ L+V GL+ +K L AAF FG++ +++I +D +++ +G+AF+E+ E A+AA+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 246 EMNGKIINGWMIVVDVA 262
MN + G I V++A
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 49/86 (56%), Gaps = 6/86 (6%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L++ TS TLR FE +G + +V I D+ +K S+G+AF+ + + A A+ M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 248 NGKIINGWMIVVDVAKTTPKYSRGRP 273
+G +++G + V +A+ GRP
Sbjct: 133 DGAVLDGRELRVQMARY------GRP 152
>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 = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 48/75 (64%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L+V GL+ +K L AAF FG++ +++I +D +++ +G+AF+E+ E A+AA+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 248 NGKIINGWMIVVDVA 262
N + G I V++A
Sbjct: 65 NESELFGRTIRVNLA 79
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+++V + + E T+R AF FG + + + D ++ + KG+AF+EY EAA AL++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 247 MNGKIINGWMIVV 259
MN ++ G I V
Sbjct: 75 MNSVMLGGRNIKV 87
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 8/112 (7%)
Query: 162 GGNNLQNSMVPSDSSEASPT--QIKTK-----KLFVTGLSFYTSEKTLRAAFEGFGELVE 214
GG N++ PS+ +A P Q+ + +++V + S+ +++ FE FG++
Sbjct: 81 GGRNIKVGR-PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 139
Query: 215 VKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ D + + KGY FIEY +++ A+ MN + G + V A T P
Sbjct: 140 CTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 191
>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 = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+++V + + E T+R AF FG + + + D ++ + KG+AF+EY EAA AL++
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 247 MNGKIINGWMIVV 259
MN ++ G I V
Sbjct: 90 MNSVMLGGRNIKV 102
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 8/112 (7%)
Query: 162 GGNNLQNSMVPSDSSEASPT--QIKTK-----KLFVTGLSFYTSEKTLRAAFEGFGELVE 214
GG N++ PS+ +A P Q+ + +++V + S+ +++ FE FG++
Sbjct: 96 GGRNIKVGR-PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 154
Query: 215 VKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ D + + KGY FIEY +++ A+ MN + G + V A T P
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 206
>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 = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 1/91 (1%)
Query: 171 VPSDSSEASPTQ-IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGY 229
V D E P + ++ LFVTG+ +E+ + F +GE+ + + +D+ + KGY
Sbjct: 8 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67
Query: 230 AFIEYTTEEAASAALKEMNGKIINGWMIVVD 260
+EY T + A AA++ +NG+ + G I VD
Sbjct: 68 TLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 47/72 (65%), Gaps = 4/72 (5%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL- 244
+KLF+ GLSF T+E++LR +E +G+L + ++ D SKRS+G+ F+ +++ AA+
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 245 ---KEMNGKIIN 253
++G+++
Sbjct: 88 ARPHSIDGRVVE 99
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 39/65 (60%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+ L+V L F +E LR FE FG++ + ++ D + RSKGY FI ++ E A AL
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 245 KEMNG 249
+++NG
Sbjct: 65 EQLNG 69
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 57/110 (51%), Gaps = 3/110 (2%)
Query: 167 QNSMVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRS 226
++ D+ E K+ L+V LSFYT+E+ + F G++ ++ + +DK+ K +
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80
Query: 227 KGYAFIEYTTEEAASAALKEMNGKIINGWMIVVD---VAKTTPKYSRGRP 273
G+ F+EY + A A++ +NG ++ +I D K +Y RGR
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRS 130
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 1/91 (1%)
Query: 171 VPSDSSEASPTQ-IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGY 229
V D E P + ++ LFVTG+ +E+ + F +GE+ + + +D+ + KGY
Sbjct: 7 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 230 AFIEYTTEEAASAALKEMNGKIINGWMIVVD 260
+EY T + A AA++ +NG+ + G I VD
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDLMGQPISVD 97
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 46/79 (58%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+ +FV + + +E+ L+ F G +V +++ D+ + + KGY F EY +E A +A++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 246 EMNGKIINGWMIVVDVAKT 264
+NG+ +G + VD A +
Sbjct: 69 NLNGREFSGRALRVDNAAS 87
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/107 (30%), Positives = 60/107 (56%), Gaps = 13/107 (12%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
+PSD +E K +F+ LSF + E+ L + FG+L V++++ ++ SKG A
Sbjct: 8 LPSDVTEG-------KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
Query: 231 FIEYTTEEA-----ASAALKEMNGKI-INGWMIVVDVAKTTPKYSRG 271
F ++ T+EA A+A+L+ G + ++G + VD+A T + + G
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107
>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 = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 36/134 (26%), Positives = 63/134 (47%), Gaps = 3/134 (2%)
Query: 130 ELDDECAQELTGVPGVLSVQPDENFGSENKDYGGNNLQNSMVPSDSSEASPTQIKTKK-- 187
E+D++ Q + + + FGS++ + + D E P ++ +
Sbjct: 14 EVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGW 73
Query: 188 -LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
LFVT + E ++ F +GE+ + + +D+ + SKGYA +EY T + A AA +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 247 MNGKIINGWMIVVD 260
+NG I G I VD
Sbjct: 134 LNGAEIMGQTIQVD 147
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 51/91 (56%), Gaps = 2/91 (2%)
Query: 173 SDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFI 232
S SS T+ + L+V L ++ LR AF FG + K++M+ RSKG+ F+
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFV 60
Query: 233 EYTTEEAASAALKEMNGKIINGWMIVVDVAK 263
+++ E A+ A+ EMNG+I+ + V +A+
Sbjct: 61 CFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
>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 = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE- 246
+F+ GLS+ T++K L+ F FGE+V+ + +D I+ RS+G+ F+ + E+ + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 247 ---MNGKIIN 253
+NGK+I+
Sbjct: 62 EHKLNGKVID 71
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
S S K K LFV L+ +E+ L AF FG+L VK + D YAFI +
Sbjct: 2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFD 53
Query: 236 TEEAASAALKEMNGKIINGWMIVVDVAK 263
+ A A++EMNGK + G I + AK
Sbjct: 54 ERDGAVKAMEEMNGKDLEGENIEIVFAK 81
>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 = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+++V + + E T+R AF FG + + D ++ + KG+AF+EY EAA AL++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 247 MNGKIINGWMIVV 259
N + G I V
Sbjct: 74 XNSVXLGGRNIKV 86
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 54/112 (48%), Gaps = 8/112 (7%)
Query: 162 GGNNLQNSMVPSDSSEASPT--QIKTK-----KLFVTGLSFYTSEKTLRAAFEGFGELVE 214
GG N++ PS+ +A P Q+ + +++V + S+ +++ FE FG++
Sbjct: 80 GGRNIKVGR-PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 138
Query: 215 VKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ D + + KGY FIEY +++ A+ N + G + V A T P
Sbjct: 139 CTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPP 190
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LFVT + E ++ F +GE+ + + +D+ + SKGYA +EY T + A AA + +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 248 NGKIINGWMIVVD 260
NG I G I VD
Sbjct: 89 NGAEIMGQTIQVD 101
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
KLFV GL + T+++TLR+ F +GE+V+ I+ DK + +S+G+ F+++ L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LFVTG+ +E+ + F +GE+ + + +D+ + KGY +EY T + A AA++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 248 NGKIINGWMIVVD 260
NG+ + G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LFVTG+ +E+ + F +GE+ + + +D+ + KGY +EY T + A AA++ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 248 NGKIINGWMIVVD 260
NG+ + G I VD
Sbjct: 72 NGQDLMGQPISVD 84
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+F+ L K L F FG ++ K++ D+ SKGY F+ + T+EAA A+++M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++N + V K+
Sbjct: 164 NGMLLNDRKVFVGRFKS 180
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 42/95 (44%)
Query: 172 PSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAF 231
P S S L+V L +E L F G ++ +++ D I++RS GYA+
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 232 IEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ + A AL MN +I G + + ++ P
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDP 96
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LFVTG+ +E+ + F +GE+ + + +D+ + KGY +EY T + A AA++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 248 NGKIINGWMIVVD 260
NG+ + G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+F+ L K L F FG ++ K++ D+ SKGY F+ + T+EAA A+++M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++N + V K+
Sbjct: 159 NGMLLNDRKVFVGRFKS 175
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L+V L +E L F G ++ +++ D I++RS GYA++ + A AL M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 248 NGKIING 254
N +I G
Sbjct: 73 NFDVIKG 79
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 40/70 (57%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
T LFV L+ ++TLR AF+ F + ++ D + S+GY F+ +T+++ A A+
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146
Query: 245 KEMNGKIING 254
M G+ +NG
Sbjct: 147 DSMQGQDLNG 156
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L+V L +E L+ F+ G + +KI++DK + ++ YAF+EY A+ AL+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 248 NGKIINGWMIVVDVAKTTPKYS 269
NGK I ++ ++ A + + S
Sbjct: 62 NGKQIENNIVKINWAFQSQQSS 83
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LFVTG+ +E+ + F +GE+ + + +D+ + KGY +EY T + A AA++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 248 NGKIINGWMIVVD 260
NG+ + G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 170 MVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGY 229
+VP S + + + K+L V+ + F + LR F FG++++V+II ++ + SKG+
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGF 71
Query: 230 AFIEYTTEEAASAALKEMNGKIINGWMIVVDVA 262
F+ + A A ++++G ++ G I V+ A
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL-- 244
K+F+ GLS+ T+++ LR F FGE+ E ++ D ++KRS+G+ F+ + + L
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 245 --KEMNGKIIN 253
E++ K I+
Sbjct: 87 SRHELDSKTID 97
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 44/79 (55%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+FV LS + + ++AAF FG + + +++ D + +SKGY F+ + + A A+++M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 248 NGKIINGWMIVVDVAKTTP 266
G+ + G I + A P
Sbjct: 78 GGQWLGGRQIRTNWATRKP 96
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+F+ L K L F FG ++ K++ D+ SKGY F+ + T+EAA A+++M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++N + V K+
Sbjct: 72 NGMLLNDRKVFVGRFKS 88
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL-- 244
K+F+ GLS+ T+++ LR F FGE+ E ++ D ++KRS+G+ F+ + + L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 245 --KEMNGKIIN 253
E++ K I+
Sbjct: 62 SRHELDSKTID 72
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+F+ L K L F FG ++ K++ D+ SKGY F+ + T+EAA A+++M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 248 NGKIINGWMIVVDVAKT 264
NG ++N + V K+
Sbjct: 66 NGMLLNDRKVFVGRFKS 82
>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 = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 40/70 (57%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
T LFV L+ ++TLR AF+ F + ++ D + S+GY F+ +T+++ A A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 245 KEMNGKIING 254
M G+ +NG
Sbjct: 61 DSMQGQDLNG 70
>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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%)
Query: 163 GNNLQNSMVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKI 222
G LQ + + S I+ L+V+GL ++K L F +G ++ +I++D++
Sbjct: 66 GLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV 125
Query: 223 SKRSKGYAFIEYTTEEAASAALKEMNGK 250
+ S+G FI + A A+K +NG+
Sbjct: 126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ R+ F GE+ K++ DKI+ +S GY F+ Y + A A+ +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 248 NGKIINGWMIVVDVAK 263
NG + I V A+
Sbjct: 65 NGLRLQTKTIKVSYAR 80
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 181 TQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAA 240
T ++ KLF++GL F +++ L + G + +++++ ++ K KG A++EY E A
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQA 71
Query: 241 SAALKEMNGKIINGWMIVVDVAKTTP 266
S A+ +M+G I +I V ++ + P
Sbjct: 72 SQAVMKMDGMTIKENIIKVAISNSGP 97
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 183 IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASA 242
IK L+VT L ++ L F +G +V+ I+ DK++ R +G AF+ Y E A
Sbjct: 98 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 157
Query: 243 ALKEMNGKIING 254
A+ +N I G
Sbjct: 158 AISALNNVIPEG 169
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ L A F G + +I D + S GYAF+++T+E + A+K +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 248 NGKIINGWMIVVDVAK 263
NG + + V A+
Sbjct: 77 NGITVRNKRLKVSYAR 92
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 53/95 (55%), Gaps = 9/95 (9%)
Query: 177 EASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTT 236
++SP K ++ G++ +++ +R F FG+++E+++ +K GY+F+ ++T
Sbjct: 20 QSSP---KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFST 70
Query: 237 EEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRG 271
E+A+ A+ +NG I G ++ K +P + G
Sbjct: 71 HESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSG 105
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%)
Query: 163 GNNLQNSMVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKI 222
G LQ + + S I+ L+V+GL S+K + F +G ++ +I++D+
Sbjct: 68 GLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQA 127
Query: 223 SKRSKGYAFIEYTTEEAASAALKEMNGK 250
+ S+G FI + A A+K +NG+
Sbjct: 128 TGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ ++ F G++ K++ DKI+ +S GY F+ Y+ A A+ +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 248 NGKIINGWMIVVDVAK 263
NG + I V A+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
>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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 183 IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASA 242
IK L+VT L ++ L F +G +V+ I+ DK++ R +G AF+ Y E A
Sbjct: 11 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 243 ALKEMNGKIING 254
A+ +N I G
Sbjct: 71 AISALNNVIPEG 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 183 IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASA 242
IK L+VT L ++ L F +G +V+ I+ DK++ R +G AF+ Y E A
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 243 ALKEMNGKIING 254
A+ +N I G
Sbjct: 147 AISALNNVIPEG 158
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ L A F G + +I+ D + S GYAF+++T+E + A+K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 248 NGKIINGWMIVVDVAK 263
NG + + V A+
Sbjct: 66 NGITVRNKRLKVSYAR 81
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 6/89 (6%)
Query: 180 PTQIKT-----KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
PTQ+ + L V + E LR FE +G + VKI+ D+ +++S+GY F+++
Sbjct: 32 PTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91
Query: 235 TTEEAASAALKEMNG-KIINGWMIVVDVA 262
+ +A A+ +NG I+N + V A
Sbjct: 92 QSGSSAQQAIAGLNGFNILNKRLKVALAA 120
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 35/101 (34%), Positives = 48/101 (47%), Gaps = 10/101 (9%)
Query: 173 SDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGF--GELVEVKIIMDKISKRSKGYA 230
S SS T K L+V L TSE+ + F G + VK I D YA
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YA 54
Query: 231 FIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRG 271
F+ ++ E A A+K +NGK+++G I V +AK K S G
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEV-KIIMDKISKRSKGYAFIEYTTEEAASAA 243
+ +F+ L EK L F FG +++ KI+ D + SKGYAFI + + +A+ AA
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 244 LKEMNGKIINGWMIVVDVA 262
++ MNG+ + I V A
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
>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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ LR+ F GE+ K+I DK++ S GY F+ Y T + A A+ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 248 NGKIINGWMIVVDVAKTT 265
NG + I V A+ +
Sbjct: 67 NGLRLQSKTIKVSYARPS 84
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKR---SKGYAFIEYTTEEAASAAL 244
LF+ L+F T+E+TL+ F G + I K S G+ F+EY E A AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 245 KEMNGKIINGWMIVVDVAKTTPKYSRG 271
K++ G ++G + V +++ K + G
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPASG 94
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L++ TS +LR FE +G + +V I + +K +G+AF+ + A A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 248 NGKIINGWMIVVDVAK 263
+G ++G + V VA+
Sbjct: 76 DGAELDGRELRVQVAR 91
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ LR+ F GE+ K+I DK++ S GY F+ Y T + A A+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 248 NGKIINGWMIVVDVAKTTPK-------YSRGRPR 274
NG + I V A+ + + Y G PR
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPR 98
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%)
Query: 163 GNNLQNSMVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKI 222
G LQ+ + + S IK L+++GL ++K + F FG ++ ++++D+
Sbjct: 66 GLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQT 125
Query: 223 SKRSKGYAFIEYTTEEAASAALKEMNG 249
+ S+G AFI + A A+ NG
Sbjct: 126 TGLSRGVAFIRFDKRSEAEEAITSFNG 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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 4/80 (5%)
Query: 178 ASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTE 237
AS + K FV GLS+ TS+K L+ F FGE+V+ I D + RS+G+ FI +
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 238 EAASAALKE----MNGKIIN 253
+ L + ++G++I+
Sbjct: 64 ASVEKVLDQKEHRLDGRVID 83
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ LR+ F GE+ K+I DK++ S GY F+ Y T + A A+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 248 NGKIINGWMIVVDVAKTTPK-------YSRGRPR 274
NG + I V A+ + + Y G PR
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPR 98
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%)
Query: 163 GNNLQNSMVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKI 222
G LQ+ + + S IK L+++GL ++K + F FG ++ ++++D+
Sbjct: 66 GLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQT 125
Query: 223 SKRSKGYAFIEYTTEEAASAALKEMNG 249
+ S+G AFI + A A+ NG
Sbjct: 126 TGLSRGVAFIRFDKRSEAEEAITSFNG 152
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 42/70 (60%), Gaps = 3/70 (4%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
K+F+ GL++ T+E LR F +G + ++KI+ D + RS+G+ F+ + + +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 247 ---MNGKIIN 253
++GK+I+
Sbjct: 65 QHILDGKVID 74
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 49/97 (50%), Gaps = 5/97 (5%)
Query: 174 DSSEASPT--QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAF 231
D A P Q KT K+FV G+ K F +G +++ ++++DK + +S+G+ F
Sbjct: 74 DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133
Query: 232 IEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKY 268
+ Y ++A A + K I+ +++ + P++
Sbjct: 134 VTY---DSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 167
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ LR+ F GE+ K+I DK++ S GY F+ Y T + A A+ +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 248 NGKIINGWMIVVDVAK 263
NG + I V A+
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
KK+FV GLS T E+ +R F GFGE+ +++ MD + + +G+ FI + EE +
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 245 KE 246
++
Sbjct: 61 EK 62
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+FV LS + + +++AF FG++ + +++ D + +SKGY F+ + + A A+ M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 248 NGKIINGWMIVVDVAKTTPKYSRG 271
G+ + G I + A P G
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSG 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 44/75 (58%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
++V+ L F + L F +G++V+V I+ DK +++SKG AFI + +++A + +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 248 NGKIINGWMIVVDVA 262
N K + G +I +A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 178 ASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTE 237
+S + T K+FV +S + + LR+ FE G ++E ++ D YAF+ E
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKE 53
Query: 238 EAASAALKEMNGKIINGWMIVVDVAKTTPKYS 269
A AA+ ++NGK + G I V+++ K S
Sbjct: 54 ADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 49/87 (56%), Gaps = 1/87 (1%)
Query: 174 DSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIE 233
D+ E K+ L+V LSFYT+E+ + F G++ ++ + +DK+ K + G+ F+E
Sbjct: 7 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVE 65
Query: 234 YTTEEAASAALKEMNGKIINGWMIVVD 260
Y + A A++ +NG ++ +I D
Sbjct: 66 YYSRADAENAMRYINGTRLDDRIIRTD 92
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 45/77 (58%), Gaps = 2/77 (2%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
K+L V+ + F + LR F FG++++V+II ++ + SKG+ F+ + A A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 73
Query: 246 EMNGKIINGWMIVVDVA 262
+++G ++ G I V+ A
Sbjct: 74 KLHGTVVEGRKIEVNNA 90
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 44.3 bits (103), Expect = 7e-05, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+FV GLS T E+ +R F GFGE+ +++ MD + + +G+ FI + EE +++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 3/79 (3%)
Query: 170 MVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGY 229
M P+DS + + ++ +KLF+ +S +E +R F FG++ E +I+ S+G
Sbjct: 94 MKPADSEKNN--AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 150
Query: 230 AFIEYTTEEAASAALKEMN 248
AF+ +TT A A+K M+
Sbjct: 151 AFVTFTTRAMAQTAIKAMH 169
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISK--RSKGYAFIEYTTEEAASAAL 244
K+FV + SEK LR FE +G + E+ ++ D+ +SKG F+ + T +AA A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 245 KEM-NGKIING 254
+ N K++ G
Sbjct: 77 NALHNMKVLPG 87
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L++ GL T+++ L + +G++V K I+DK + + KGY F+++ + AA A+ +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 248 NGKIINGWM 256
+ M
Sbjct: 68 KASGVQAQM 76
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 184 KTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA 243
KT L V GL + T+E+ L+ F FGE++ V++ D + SKG+ F+ +T E
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 244 LKEMNGKIING 254
+ + + +I+G
Sbjct: 74 MSQRH--MIDG 82
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 3/79 (3%)
Query: 170 MVPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGY 229
M P+DS + + ++ +KLF+ +S +E +R F FG++ E +I+ S+G
Sbjct: 82 MKPADSEKNNA--VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 138
Query: 230 AFIEYTTEEAASAALKEMN 248
AF+ +TT A A+K M+
Sbjct: 139 AFVTFTTRAMAQTAIKAMH 157
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISK--RSKGYAFIEYTTEEAASAAL 244
K+FV + SEK LR FE +G + E+ ++ D+ +SKG F+ + T +AA A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 245 KEM-NGKIING 254
+ N K++ G
Sbjct: 65 NALHNMKVLPG 75
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 2/97 (2%)
Query: 171 VPSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYA 230
VP S P KLF+ GL Y ++ ++ FG L ++ D + SKGYA
Sbjct: 102 VPGVVSTVVPD--SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159
Query: 231 FIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPK 267
F EY A+ +NG + ++V A K
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 37/81 (45%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
KLF+ GL Y ++ ++ FG L ++ D + SKGYAF EY A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 247 MNGKIINGWMIVVDVAKTTPK 267
+NG + ++V A K
Sbjct: 63 LNGMQLGDKKLLVQRASVGAK 83
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L+V+GL S+K + F +G ++ +I++D+ + S+G FI + A A+K +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 248 NGK 250
NG+
Sbjct: 64 NGQ 66
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 4/78 (5%)
Query: 184 KTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA 243
++K L ++ LS+ +E+TL+ FE + +K+ ++ K SKGYAFIE+ + E A A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGK-SKGYAFIEFASFEDAKEA 69
Query: 244 LKEMNGKIINGWMIVVDV 261
L N + I G I +++
Sbjct: 70 LNSCNKREIEGRAIRLEL 87
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 173 SDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFI 232
S SS K K LFV L+ +E+ L +F FG+L VK + D YAF+
Sbjct: 3 SGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFV 54
Query: 233 EYTTEEAASAALKEMNGK 250
+ AA A+ EMNGK
Sbjct: 55 HFEDRGAAVKAMDEMNGK 72
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 179 SPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEE 238
SP + + +F L+ + L F G++ +V+II D+ S+RSKG A++E+ +
Sbjct: 19 SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Query: 239 AASAALKEMNGKIINGWMIVVDVAKT 264
+ A+ + G+ + G I+V ++
Sbjct: 79 SVPLAIG-LTGQRLLGVPIIVQASQA 103
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 41/65 (63%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
++ +++ + + +E+ + G ++ +K++ D + RSKGYAFIE+ E++++A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 245 KEMNG 249
+ +NG
Sbjct: 64 RNLNG 68
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+KLFV L+ SE +R FE FG + E I+ SKG AF++Y++ A AA+
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAIN 74
Query: 246 EMNG 249
++G
Sbjct: 75 ALHG 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 190 VTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
VT LS T E L+ F FG + + + DK + +SKG+AFI + E A+ A+ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 250 KIINGWMIVVDVAK 263
+ ++ V+ AK
Sbjct: 80 FGYDHLILNVEWAK 93
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 1/88 (1%)
Query: 172 PSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAF 231
P S +I + ++V + + ++ + L A F G + + I+ DK S KGYA+
Sbjct: 23 PQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAY 82
Query: 232 IEYTTEEAASAALKEMNGKIINGWMIVV 259
IE+ + AA+ M+ + G I V
Sbjct: 83 IEFAERNSVDAAVA-MDETVFRGRTIKV 109
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
KLF+ GL Y ++ ++ FG L ++ D + SKGYAF EY A+
Sbjct: 96 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 245 KEMNGKIINGWMIVVDVA 262
+NG + ++V A
Sbjct: 156 AGLNGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
KLF+ GL Y ++ ++ FG L ++ D + SKGYAF EY A+
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 245 KEMNGKIINGWMIVVDVA 262
+NG + ++V A
Sbjct: 154 AGLNGMQLGDKKLLVQRA 171
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA---- 243
+FV GLS T+ + ++ FE FG++ + ++ DK + R +G+ F+ + +E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 244 LKEMNGKII 252
E+N K++
Sbjct: 62 FHEINNKMV 70
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 41/65 (63%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
++ +++ + + +E+ + G ++ +K++ D + RSKGYAFIE+ E++++A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 245 KEMNG 249
+ +NG
Sbjct: 63 RNLNG 67
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 41/65 (63%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
++ +++ + + +E+ + G ++ +K++ D + RSKGYAFIE+ E++++A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 245 KEMNG 249
+ +NG
Sbjct: 62 RNLNG 66
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 41.6 bits (96), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 182 QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAAS 241
++ +LFV E L F FG + EVKI+ G+AF+E+ E+A+
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 52
Query: 242 AALKEMNGK 250
A++E++GK
Sbjct: 53 KAIEEVHGK 61
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+ ++V + + + + L A F G G + V I+ DK S KG+A+IE++ +E+ +L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 182 QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAAS 241
++ +LFV E L F FG + EVKI+ G+AF+E+ E+A+
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 79
Query: 242 AALKEMNGKIINGWMIVVDVAKTTPKYSR 270
A++E++GK + V +K K R
Sbjct: 80 KAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 46/84 (54%), Gaps = 3/84 (3%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+ ++V L + + + ++ F FG++ VK+I D+ +K+ KG+ F+E EE+ S A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 246 EMNGKIINGWMIVVDVAKTTPKYS 269
+++ G I V + PK S
Sbjct: 61 KLDNTDFMGRTI--RVTEANPKKS 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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAA 243
KLF+ + EK L+ FE FG++ E+ ++ D+ + KG AF+ Y E+A A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LF+ L ++ L + F FG ++ K+ +DK + SK + F+ + ++A A+K M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 248 NG 249
NG
Sbjct: 103 NG 104
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 172 PSDSSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAF 231
P+DS + + ++ +KLF+ +S +E +R F FG++ E +I+ S+G AF
Sbjct: 84 PADSEKNNA--VEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAF 140
Query: 232 IEYTTEEAASAALK 245
+ +TT A A+K
Sbjct: 141 VTFTTRAXAQTAIK 154
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+ ++V + + + + L A F G G + V I+ DK S KG+A+IE++ +E+ +L
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 245 KEMNGKIINGWMIVVDVAKT 264
++ + G I V +T
Sbjct: 65 A-LDESLFRGRQIKVIPKRT 83
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
LF+ L ++ L F FG +V K+ +DK + SK + F+ Y +A AA++ M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 248 NGKIINGWMIVVDVAKT 264
NG I + V + ++
Sbjct: 88 NGFQIGMKRLKVQLKRS 104
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 53/102 (51%), Gaps = 10/102 (9%)
Query: 173 SDSSEASPTQIKTKKLFVTGLSFYTSEKT-LRAAFEGFGELVEVKIIMDKISKRSKGYAF 231
S SS + + ++F+ L+ +K+ + A F +G++V + KG+AF
Sbjct: 3 SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAF 54
Query: 232 IEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRGRP 273
++Y E A AA+ +G++I G ++ +++A PK +R P
Sbjct: 55 VQYVNERNARAAVAGEDGRMIAGQVLDINLA-AEPKVNRSGP 95
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 42/84 (50%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
++V GL SE L F G +V + D+++ + +GY F+E+ +EE A A+K M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 248 NGKIINGWMIVVDVAKTTPKYSRG 271
+ + G I V+ A K G
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
K++V L + L AF +G L V I ++ G+AF+E+ A A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 247 MNGKIINGWMIVVDVAKTTPKYSR 270
++GK+I G + V+++ P+ SR
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSR 80
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEA---ASAA 243
KLFV + E+ L+ FE FG + E+ ++ D+++ KG AF+ Y ++ A +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 244 LKEMNGKIINGWMIVVDVAKTTPKYSRGR 272
L E K + G + V P S GR
Sbjct: 77 LHEQ--KTLPGMNRPIQV---KPAASEGR 100
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L ++ ++ F G++ K++ DKI+ +S GY F+ Y+ A A+ +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 248 NGKIINGWMIVVDVAK 263
NG + I V A+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
K L++ LS +E+ L + F F E I ++ R +G AFI + +E A AL
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 245 KEMNGKIINGWMIVVDVAKTTPKYSRG 271
+NG + G ++V++ K + S G
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSSG 111
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISK--RSKGYAFIEYTTEEAASAAL 244
K+FV + SEK LR FE +G + E+ ++ D+ +SKG F+ + T +AA A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 245 KEM-NGKIING 254
+ N K++ G
Sbjct: 65 NALHNMKVLPG 75
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 32/58 (55%)
Query: 209 FGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
FG + + +++ D + +SKGY F+ + + A A+++M G+ + G I + A P
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 39/76 (51%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ L A F G + +I+ D + S GYAF+++T+E + A+K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 248 NGKIINGWMIVVDVAK 263
NG + + V A+
Sbjct: 66 NGITVRNKRLKVSYAR 81
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELV-EVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
L++ L Y E + AF GE V VKII ++++ GY F+E+ A L +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 247 MNGKIING 254
+NGK + G
Sbjct: 72 INGKPLPG 79
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFG--ELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
++V S++T+++ L G ++VE+K ++ + +SKGYA + +E + L+
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 246 EMNGKIINGWMIVVDVA 262
+ GK++NG + V A
Sbjct: 118 LLPGKVLNGEKVDVRPA 134
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 175 SSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
SS +S L+V GL +E LR F FGE+ + ++ + + AFI++
Sbjct: 2 SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQF 55
Query: 235 TTEEAAS-AALKEMNGKIING 254
T +AA AA K N I+NG
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNG 76
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 182 QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
+I +FV G+ E +R+ F +G + EVKII D+ + SKGY F+ +
Sbjct: 7 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 182 QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
+I +FV G+ E +R+ F +G + EVKII D+ + SKGY F+ +
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 227 KGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRGRP 273
KGYAF++Y+ E A AA+ NG+++ G + +++A PK R P
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA-GEPKPDRSGP 107
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 11/100 (11%)
Query: 170 MVPSDSSEASPTQIKTKK---LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRS 226
M P S++ P + +K L+V G + LR AF FG ++++ MD
Sbjct: 21 MGPFRRSDSFPERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLS--MDP----P 72
Query: 227 KGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ AF+ Y E+A A+ E+NG + + V++A+ P
Sbjct: 73 RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 112
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
T +L+V GL TS L F+ FG + + + + +A+I+Y + +AA AA
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAAC 70
Query: 245 KEMNGKIING--WMIVVDVAKTTP 266
+M G + G + VD AK+ P
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSGP 94
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 202 LRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDV 261
LR AF FG ++++ MD + AF+ Y E+A A+ E+NG + + V++
Sbjct: 30 LRGAFSPFGNIIDLS--MDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 262 AKTTPKYSRG 271
A+ P G
Sbjct: 84 ARKQPMLDSG 93
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 183 IKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKR-SKGYAFIEYTTEEAAS 241
+K K+ + L+ ++ + F +G++ + + ++++ SKGYA++E+ + A
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 242 AALKEMNGKIINGWMI 257
ALK M+G I+G I
Sbjct: 62 KALKHMDGGQIDGQEI 77
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
KL V+ L F S+ ++ F FG L + + D+ S RS G A + + + A A+K+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 247 MNGKIING 254
NG ++G
Sbjct: 89 YNGVPLDG 96
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+ L LSF +E L+ FE + +E++++ +SKG A+IE+ +E A L
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNL 70
Query: 245 KEMNGKIINGWMI 257
+E G I+G +
Sbjct: 71 EEKQGAEIDGRSV 83
>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 = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 182 QIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
+I +FV G+ E +R+ F +G + EVKII D+ + SKGY F+ +
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
++FV L F + K L+ F G ++ I M+ + +SKG +++ + E A A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67
Query: 247 MNGKIINGWMIVVDVAKTTPKYSRG 271
MNG ++G I V + + S G
Sbjct: 68 MNGMKLSGREIDVRIDRNASGPSSG 92
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
+E P QI LF+T L T+E L F F EV+++ ++ AF+E+T
Sbjct: 3 TEQPPNQI----LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFT 53
Query: 236 TEEAASAALKEMNG 249
TE ++AA + + G
Sbjct: 54 TELQSNAAKEALQG 67
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L+++ L E+ L + FG+++ +I+ D S S+G F + E A +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 248 NGKII 252
NGK I
Sbjct: 87 NGKFI 91
>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 = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 185 TKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
+ L LSF +E L+ FE + +E++++ +SKG A+IE+ +E A L
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNL 153
Query: 245 KEMNGKIINGWMI 257
+E G I+G +
Sbjct: 154 EEKQGAEIDGRSV 166
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 2/84 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
+FV L F + K L+ F G ++ I M+ + +SKG +++ + E A A + M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 248 NGKIINGWMIVVDVAKTTPKYSRG 271
NG ++G I V + + S G
Sbjct: 66 NGMKLSGREIDVRIDRNASGPSSG 89
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ FG L ++ + + +SKGY F EY +++A+ A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 248 NGKIINGWMIVV---DVAKTTPKYSRGR 272
GK + + V D + TP R
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSR 185
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ FG L ++ + + +SKGY F EY +++A+ A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 248 NGKIINGWMIVV---DVAKTTPKYSRGR 272
GK + + V D + TP R
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSR 185
>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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEM 247
L V L +++ FG L ++ + + +SKGY F EY +++A+ A ++
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 248 NGKIINGWMIVV---DVAKTTPKYSRGR 272
GK + + V D + TP R
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSR 183
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
+LFV L +E+ + FE +GE EV I R +G+ FI + A A E
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 247 MNGKIINGWMIVVDVA 262
++G I+ + + A
Sbjct: 78 LDGTILKSRPLRIRFA 93
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+KLFV L+ SE+ + F+ FG + E ++ SKG AF+++++ A AA+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
Query: 246 EMNG 249
++G
Sbjct: 75 ALHG 78
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 34.3 bits (77), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+KLFV L +++ +R FE FG + E ++ SKG AF+++ T A AA+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAIN 71
Query: 246 EMN 248
++
Sbjct: 72 TLH 74
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.9 bits (76), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
K++V L ++ L AF +G L V + ++ G+AF+E+ A+ A++E
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 129
Query: 247 MNGKIINGWMIVVDVA 262
++G+ + G + V+++
Sbjct: 130 LDGRTLCGCRVRVELS 145
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 215 VKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRG 271
+ I +DK + + KG A + Y A AA++ +GK G + V +A+ P + G
Sbjct: 53 IHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFG--ELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
L++ L+++T+++ L A G +++E+K ++ + +SKG+A + +E ++ +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 246 EMNGKIINGWMIVV 259
+ + ++G VV
Sbjct: 131 LLPKRELHGQNPVV 144
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
K++V L ++ L AF +G L V + ++ G+AF+E+ A+ A+++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRD 129
Query: 247 MNGKIINGWMIVVDVA 262
++G+ + G + V+++
Sbjct: 130 LDGRTLCGCRVRVELS 145
>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 = 0.38, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGK 250
+K L + F G++V ++ +D+ + ++KG+ F+E + A +K +GK
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 13/96 (13%)
Query: 179 SPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEE 238
S + + L L + ++ L+ FE + E++++ +SKG A+IE+ TE
Sbjct: 87 SKKERDARTLLAKNLPYKVTQDELKEVFE---DAAEIRLVSK--DGKSKGIAYIEFKTEA 141
Query: 239 AASAALKEMNGKIINGWMIVVDVAKTTPKYSRGRPR 274
A +E G I+G I + Y G P+
Sbjct: 142 DAEKTFEEKQGTEIDGRSISL--------YYTGEPK 169
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 216 KIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSRGRP 273
K+++D+ + SKGY F+++T E AL E G + G V ++ PK SR +P
Sbjct: 41 KVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK-PVRLSVAIPKASRVKP 96
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 32.0 bits (71), Expect = 0.43, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFG--ELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
L++ L+++T+++ L A G +++E+K ++ + +SKG+A + +E ++ +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 246 EMNGKIINGWMIVV 259
+ + ++G VV
Sbjct: 64 LLPKRELHGQNPVV 77
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKR---SKGYAFIEYTTEEAASA 242
+K+FV GL E + A+F FG LV V SK KGYAF+ + E + A
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQA 67
Query: 243 ---ALKEMNGKI 251
A E +GK+
Sbjct: 68 LIDACLEEDGKL 79
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 189 FVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMN 248
+V L F T + + A F+ + V+++ DK + + KG+ ++E+ ++ AL +
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YD 76
Query: 249 GKIINGWMIVVDVAK 263
G ++ + VD+A+
Sbjct: 77 GALLGDRSLRVDIAE 91
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 215 VKIIMDKISKRSKGYAFIEYTTEEAAS--AALKEMNGKI-INGWMIVVDVAKTTPK 267
V++I DK ++ ++G+AFI+ +T EAA L+ ++ + I+G I V+ AK + +
Sbjct: 55 VRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAKGSKR 110
>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 = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 176 SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYT 235
SE P I LF+T L T+E L F F EV+++ + AF+E+
Sbjct: 202 SENPPNHI----LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFD 252
Query: 236 TEEAASAALKEMNG-KIINGWMIVVDVAK 263
E A AA + G KI + + AK
Sbjct: 253 NEVQAGAARDALQGFKITQNNAMKISFAK 281
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIV 258
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G +
Sbjct: 27 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR 83
Query: 259 VDVAKT 264
+ AKT
Sbjct: 84 IQYAKT 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 = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 26 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 73
>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 = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 27 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
>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 = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 26 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 73
>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 = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 27 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
>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 = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 26 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 73
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 186 KKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+ L+V LS +E + F G K+I + S Y F+E+ A+AAL
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALA 73
Query: 246 EMNGKIINGWMIVVDVAKTTPKYSRGRP 273
MNG+ I G + V+ A TTP + P
Sbjct: 74 AMNGRKILGKEVKVNWA-TTPSSQKSGP 100
>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 = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 24 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 71
>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 = 30.8 bits (68), Expect = 0.76, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 21 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 68
>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 = 30.8 bits (68), Expect = 0.76, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 22 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 69
>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 = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 226 SKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVAKTTPKYSR 270
S+ +A+I+ T++E A ++++NG I G+ +V V+ K R
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR 202
>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 = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 23 KKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 70
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 30.8 bits (68), Expect = 0.91, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 41/96 (42%), Gaps = 11/96 (11%)
Query: 170 MVPSDS-SEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKG 228
M P+ SE P I LF+T L T+E L F F EV+++ +
Sbjct: 1 MAPAQPLSENPPNHI----LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HD 51
Query: 229 YAFIEYTTEEAASAALKEMNG-KIINGWMIVVDVAK 263
AF+E+ E A AA + G KI + + AK
Sbjct: 52 IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 87
>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 = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 32/55 (58%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIIN 253
+K L + F G++V ++ +D+ + ++KG+ F+E + A +K +GK ++
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELV--EVKIIMDKISKRSKGYAFIEYTTEEAASAALK 245
+ + ++ +T ++ A + L +++I DK +++++G+AF++ ++ AS L+
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 246 EMNGKI----INGWMIVVDVAKT 264
+ I+G I VD AK+
Sbjct: 72 ILQSLHPPLKIDGKTIGVDFAKS 94
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 27 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 188 LFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAAL 244
L V L Y S + L AF FG++ +I+D R G +E++ + AA AL
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDD-RGRPSGKGIVEFSGKPAARKAL 154
>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 = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 198 SEKTLRAAFEGFG-ELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWM 256
+E +R + G + EV+++ +K S +S+G+AF+E++ + A+ + E N +N
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM-EANQHSLN--- 69
Query: 257 IVVDVAKTTPKYSRGRPR 274
+ K + YS +P+
Sbjct: 70 --ILGQKVSMHYSDPKPK 85
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 25/37 (67%)
Query: 226 SKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVA 262
S+ +A+I+ T++E A ++++NG I G+ +V V+
Sbjct: 44 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 80
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 25/37 (67%)
Query: 226 SKGYAFIEYTTEEAASAALKEMNGKIINGWMIVVDVA 262
S+ +A+I+ T++E A ++++NG I G+ +V V+
Sbjct: 121 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 157
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNG 249
+K+L A F FG++++ I+ S + +G AF+ + +A+ AL+ M G
Sbjct: 26 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 73
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 187 KLFVTGL-SFYTSEKTLR---AAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASA 242
+LF+ G+ E+ L EG +++ DK+ R G+AF+EY + AA+
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNR--GFAFVEYESHRAAAM 67
Query: 243 ALKE-MNGKI-INGWMIVVDVAK 263
A ++ M G+I + G I VD A+
Sbjct: 68 ARRKLMPGRIQLWGHQIAVDWAE 90
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 177 EASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTT 236
++P ++ T ++ + + +E L F+ FG I+D KG FI+Y T
Sbjct: 21 RSAPPRVTTA--YIGNIPHFATEADLIPLFQNFG------FILDFKHYPEKGCCFIKYDT 72
Query: 237 EEAASAALKEM 247
E A+ + +
Sbjct: 73 HEQAAVCIVAL 83
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 190 VTGLSFYTSEKTLRAAFEGFGELVEVKIIMD-KISKRSKGYAFIEYTTEEAASAALKEMN 248
+ GL F S++ + F G E+V + + RS G AF+++ ++E A ALK+
Sbjct: 20 LRGLPFGCSKEEIVQFFSGL-EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHK 78
Query: 249 GKIINGWMIVVDVAKTTPKYS 269
+I + ++ + ++ + S
Sbjct: 79 ERIGHRYIEIFKSSRAEVRTS 99
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 28.1 bits (61), Expect = 5.1, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 175 SSEASPTQIKTKKLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEY 234
SS +S T T KL G F +EK + F + V ++I+ + ++ GY F+++
Sbjct: 2 SSGSSGTTCHTVKL--RGAPFNVTEKNV-MEFLAPLKPVAIRIVRNAHGNKT-GYIFVDF 57
Query: 235 TTEEAASAALKEMNGKIINGWMIVVDVAKTTP 266
+ EE ALK N + + G I V K+ P
Sbjct: 58 SNEEEVKQALK-CNREYMGGRYIEVFREKSGP 88
>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 = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 199 EKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKEMNGKIINGWMIV 258
+++L A F FG +V++ + + + +G AF+ + +++ AL+++ G G +
Sbjct: 24 KRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTNALRQLQGFPFYGKPMR 80
Query: 259 VDVAKT 264
+ AKT
Sbjct: 81 IQYAKT 86
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 27.7 bits (60), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELV-EVKIIMDKI----SKRSKGYAFIEYTTEEAAS 241
+++V L+ + EK L+ F + + E + IM I R KG AFI E+AA+
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 242 AALKEMNGKIINGWMIVVDVAKTT 265
ALKE NG ++ G +VV A++
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSA 130
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 187 KLFVTGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFIEYTTEEAASAALKE 246
KL++ LS + LR F + ++++ GYAF++Y + A A++
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIET 63
Query: 247 MNGKI-INGWMIVVDVAKTTPKYSRG 271
++GK+ ++G ++ VD + + S G
Sbjct: 64 LSGKVELHGKIMEVDYSVSKKLRSSG 89
>pdb|3V6B|R Chain R, Vegfr-2VEGF-E Complex Structure
Length = 424
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 6/90 (6%)
Query: 78 LVRMDKPGVGVVTKAQMVDRYAQILTKVLGNEKDAQMCIYHVSWQSNFGFCCELDDECAQ 137
LV P +G + VD Y T+ L A +H+ W +L++ECA
Sbjct: 285 LVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWY------WQLEEECAN 338
Query: 138 ELTGVPGVLSVQPDENFGSENKDYGGNNLQ 167
E + V + P E + S GGN ++
Sbjct: 339 EPSQAVSVTNPYPCEEWRSVEDFQGGNKIE 368
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 0.133 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,426,775
Number of Sequences: 62578
Number of extensions: 345998
Number of successful extensions: 1150
Number of sequences better than 100.0: 191
Number of HSP's better than 100.0 without gapping: 144
Number of HSP's successfully gapped in prelim test: 47
Number of HSP's that attempted gapping in prelim test: 954
Number of HSP's gapped (non-prelim): 219
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
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: 51 (24.3 bits)