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= 043443
(299 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 72.0 bits (175), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 36/76 (47%), Positives = 48/76 (63%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
SL V N+ P+ LR FE++G V DVY+P+D YT E RGFAFV+F D +A +A
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 123 MNGKRFAGREISVVLA 138
M+G GRE+ V +A
Sbjct: 132 MDGAVLDGRELRVQMA 147
>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 = 71.6 bits (174), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 36/76 (47%), Positives = 48/76 (63%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
SL V N+ P+ LR FE++G V DVY+P+D YT E RGFAFV+F D +A +A
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 123 MNGKRFAGREISVVLA 138
M+G GRE+ V +A
Sbjct: 109 MDGAVLDGRELRVQMA 124
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 51/81 (62%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+ P+ LR FE++G V DVY+P++ +T PRGFAFV+F D +A +A+
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 123 MNGKRFAGREISVVLAAESRK 143
M+G GRE+ V +A R+
Sbjct: 75 MDGAELDGRELRVQVARYGRR 95
>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 = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
NH + V ++ + E+++A F FG + D + KD TG+ +G+ FV F + ++A A
Sbjct: 14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73
Query: 120 QHHMNGKRFAGREI 133
M G+ GR+I
Sbjct: 74 IQQMGGQWLGGRQI 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 42/82 (51%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
+ G L V + D + L F ++G + +V + KD T RGF FV F + +A +A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 120 QHHMNGKRFAGREISVVLAAES 141
MNGK GR+I V A +S
Sbjct: 71 MMAMNGKSVDGRQIRVDQAGKS 92
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
NH + V ++ + E++++ F FG + D + KD TG+ +G+ FV F + +A
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 119 AQHHMNGKRFAGREI 133
A HM G+ GR+I
Sbjct: 73 AIVHMGGQWLGGRQI 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
S+ V NIP + E+L+ F G V L D TG+P+G+ F ++ D A A +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 123 MNGKRFAGREISVVLAAESRKRPEEMR 149
+NG+ F+GR + V AA S K EE++
Sbjct: 70 LNGREFSGRALRVDNAA-SEKNKEELK 95
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYY-TGEPRGFAFVQFVDPYE 115
K+Q +LVRNIP E+R F FG ++ V LPK TG RGF FV F+ +
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 116 AAEA------QHHMNGKR----FAGREISV 135
A +A H+ G+R +A E++V
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWADSEVTV 100
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L VRN+ E+L F +G + +++ P D T +P+GFAFV F+ P A +A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 124 NGKRFAGREISVV 136
+G+ F GR + V+
Sbjct: 71 DGQVFQGRMLHVL 83
>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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L+V +P + EE R+ F G + L +D TG+ G+ FV ++DP +A +A +
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 123 MNGKRFAGREISV 135
+NG R + I V
Sbjct: 64 LNGLRLQTKTIKV 76
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 58 EQNH-GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
E +H G L + + + + L+A F + G + +V L KD T + RGFAF+ F +P +A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 117 AEAQHHMNGKRFAGREISV 135
A MNGK G+ I V
Sbjct: 62 KNAAKDMNGKSLHGKAIKV 80
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L+V IP +LR FER+G + V + D T + RG+ FV+F A +A
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 123 MNGKRFAGREISVVLAAESRKRP 145
+NG + + V LAA +RP
Sbjct: 104 LNGFNILNKRLKVALAASGHQRP 126
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
L A F FG + D+ +P DY T + RGFAFV+F +AA A +MN GR I V L
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 138 A 138
A
Sbjct: 140 A 140
>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 = 50.1 bits (118), Expect = 1e-06, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
L A F FG + D+ +P DY T + RGFAFV+F +AA A +MN GR I V L
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 138 A 138
A
Sbjct: 84 A 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 40/75 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + + L A F FG + D+ +P DY T + RGFAFV+F +AA A +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 124 NGKRFAGREISVVLA 138
N GR I V LA
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
L A F FG + D+ +P DY T + RGFAFV+F +AA A +MN GR I V L
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 138 A 138
A
Sbjct: 82 A 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
L A F FG + D+ +P DY T + RGFAFV+F +AA A +MN GR I V L
Sbjct: 19 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 138 A 138
A
Sbjct: 79 A 79
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+ ++ ++ V N+ D R +L+ F FG + +YL KD TG+ +GFAF+ F +A
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 117 AEAQHHMNG 125
A A ++G
Sbjct: 71 ARAIAGVSG 79
>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 = 5e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L+V +P + +E ++ F G + L +D TG+ G+ FV + DP +A +A +
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 123 MNGKRFAGREISV 135
+NG + + I V
Sbjct: 66 LNGLKLQTKTIKV 78
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V ++ + + LR FE FG + + L D TG +G+ F+ F D A +A +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 124 NGKRFAGREISV 135
NG AGR + V
Sbjct: 89 NGFELAGRPMKV 100
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
S+ V N+ EEL A F G V V + D ++G P+GFA+++F D E+
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 123 MNGKRFAGREISVV 136
++ F GR+I V+
Sbjct: 67 LDESLFRGRQIKVI 80
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
E + S+ V N+ EEL A F G V V + D ++G P+GFA+++F D E+
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESV 60
Query: 118 EAQHHMNGKRFAGREISVV 136
++ F GR+I V+
Sbjct: 61 RTSLALDESLFRGRQIKVI 79
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
+ V IP +C ELR F++FGVV +V + D PRGF F+ F D +A
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 121 -HHMNGKR 127
H + GK+
Sbjct: 73 FHDIMGKK 80
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V + D +LR FE +G ++ +++ +G+PRG+AF+++ + A H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 123 MNGKRFAGREISV 135
+GK+ GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L+V +P + +E ++ F G + L +D TG+ G+ FV + DP +A +A +
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 123 MNGKRFAGREISVVLAAES 141
+NG + + I V A S
Sbjct: 66 LNGLKLQTKTIKVSYARPS 84
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 38/80 (47%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
L V + L +LR F ++G + DV + D + RGFAFV F + +A EA+
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 123 MNGKRFAGREISVVLAAESR 142
NG GR I V + R
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V + D +LR FE +G ++ +++ +G+PRG+AF+++ + A H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 123 MNGKRFAGREISV 135
+GK+ GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V ++ + + LR FE FG + ++ L KD TG +G+ F+ F D A A +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 124 NGKRFAGREISV 135
NG AGR + V
Sbjct: 68 NGFELAGRPMRV 79
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA-- 116
Q L+V +P ++L+ F FG V V + KD TG +GF FV+F + YE
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE-YETQV 71
Query: 117 -AEAQHHMNGKRFA 129
+Q HM R+
Sbjct: 72 KVMSQRHMIDGRWC 85
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 39/82 (47%)
Query: 61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
+ L V + L +LR F ++G + DV + D + RGFAFV F + +A EA+
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 121 HHMNGKRFAGREISVVLAAESR 142
NG GR I V + R
Sbjct: 75 ERANGMELDGRRIRVDFSITKR 96
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 16/82 (19%)
Query: 68 NIPLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+ PLDC+ EL F +G +R V++ ++ P GFAFV+F DP +A
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDA 123
Query: 117 AEAQHHMNGKRFAGREISVVLA 138
A+A ++G+ G + V L+
Sbjct: 124 ADAVRELDGRTLCGCRVRVELS 145
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 16/82 (19%)
Query: 68 NIPLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+ PLDC+ EL F +G +R V++ ++ P GFAFV+F DP +A
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDA 123
Query: 117 AEAQHHMNGKRFAGREISVVLA 138
A+A ++G+ G + V L+
Sbjct: 124 ADAVRDLDGRTLCGCRVRVELS 145
>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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + +P C EEL + G V+D+ L + G+P+G A+V++ + +A++A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 124 NGKRFAGREISVVLA 138
+G I V ++
Sbjct: 79 DGMTIKENIIKVAIS 93
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V+N+ E LR F FG + + + G +GF FV F P EA +A
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 123 MNGKRFAGREISVVLA 138
MNG+ A + + V LA
Sbjct: 75 MNGRIVATKPLYVALA 90
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
E ++ L VR PLD + EL F FG +++V + GFAFV+F + AA
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 79
Query: 118 EAQHHMNGKRFAGREISVVLAAESRKR 144
+A ++GK FA + + VV + KR
Sbjct: 80 KAIEEVHGKSFANQPLEVVYSKLPAKR 106
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 36/73 (49%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
L V + L +LR F ++G + DV + D + RGFAFV F + +A EA+
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 123 MNGKRFAGREISV 135
NG GR I V
Sbjct: 77 ANGMELDGRRIRV 89
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 39/82 (47%)
Query: 61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
+ L V + L +LR F ++G + DV + D + RGFAFV F + +A EA+
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 121 HHMNGKRFAGREISVVLAAESR 142
NG GR I V + R
Sbjct: 72 ERANGMELDGRRIRVDFSITKR 93
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY---EAAEAQ 120
+ + + D + LR F ++G V D+ + KD TG RGF F+ F P E + Q
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 121 HHMNGK 126
H ++GK
Sbjct: 66 HILDGK 71
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
+ G + V I D RP+E F ++G + D L D TG+ RGF FV Y++A
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV----TYDSA 139
Query: 118 EAQHHMNGKRFA 129
+A + +F
Sbjct: 140 DAVDRVCQNKFI 151
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
N + V N+ C +ELR+ FER G V + + KDY AFV +A A
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEADAKAA 59
Query: 120 QHHMNGKRFAGREISVVLAAESRKR 144
+NGK G+ I+V L+ + +K+
Sbjct: 60 IAQLNGKEVKGKRINVELSTKGQKK 84
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 85 FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
FG + D + KD TG+ +G+ FV F + ++A A M G+ GR+I
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ- 120
G L V + E LR+ F ++G V D + KD T + RGF FV+F DP
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 121 ---HHMNGKRF 128
H ++G+
Sbjct: 77 SRPHTLDGRNI 87
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
N + V N+P D R +++ F ++G +RD+ L K+ G P FAFV+F DP +A +
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAED 76
Query: 119 AQHHMNGKRFAGREISV 135
A + +G + G + V
Sbjct: 77 AVYGRDGYDYDGYRLRV 93
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V +I + + +E++ F +G +++++L D TG +G+A V++ +A A+ +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 124 NGKRFAGREISV 135
NG G+ I V
Sbjct: 135 NGAEIMGQTIQV 146
>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 = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
KE + S+ V N+ ++L A F G + + + D ++G P+G+A+++F + +
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNS 90
Query: 117 AEAQHHMNGKRFAGREISVV 136
+A M+ F GR I V+
Sbjct: 91 VDAAVAMDETVFRGRTIKVL 110
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L VRN+ E L F +FG + V KDY AF+ F + A +A M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDERDGAVKAMEEM 65
Query: 124 NGKRFAGREISVVLAA-ESRKRPEEMRQRH 152
NGK G I +V A +KR E QR
Sbjct: 66 NGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V +I + + +E++ F +G +++++L D TG +G+A V++ +A A+ +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 124 NGKRFAGREISV 135
NG G+ I V
Sbjct: 89 NGAEIMGQTIQV 100
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
+ +L+V +P D EL A F G + + +DY TG G+AFV F ++ A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 121 HHMNGKRFAGREISV 135
+NG + + V
Sbjct: 63 KVLNGITVRNKRLKV 77
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+P ++L F ++G + + +D TG PRG AFV++ EA EA
Sbjct: 91 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Query: 123 MN 124
+N
Sbjct: 151 LN 152
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L++RN+P EE+ F ++G +R + + T E RG A+V + D ++A A H+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHL 77
Query: 124 NGKRFAGREISVV 136
+G R + V+
Sbjct: 78 SGFNVCNRYLVVL 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 37/76 (48%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
++ V N+P +L F ++G V V + KD T + +G AF+ F+D A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 123 MNGKRFAGREISVVLA 138
+N K+ GR I +A
Sbjct: 78 INNKQLFGRVIKASIA 93
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
E ++ L VR PLD + EL F FG +++V + GFAFV+F + AA
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 52
Query: 118 EAQHHMNGKRFAGREISVVLA 138
+A ++GK FA + + VV +
Sbjct: 53 KAIEEVHGKSFANQPLEVVYS 73
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 15/98 (15%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD----------VYLPKDYYTGEPRGFAF 107
+ ++ ++ V+ + ++L F++ GVV+ +YL K+ TG+P+G A
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE--TGKPKGDAT 69
Query: 108 VQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRP 145
V + DP A A +GK F G ++ V LA RK+P
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA---RKKP 104
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
+ +L+V +P D EL A F G + + +DY TG G+AFV F ++ A
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 121 HHMNGKRFAGREISV 135
+NG + + V
Sbjct: 74 KVLNGITVRNKRLKV 88
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+P ++L F ++G + + +D TG PRG AFV++ EA EA
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 123 MN 124
+N
Sbjct: 162 LN 163
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+P ++L F ++G + + +D TG PRG AFV++ EA EA
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 123 MN 124
+N
Sbjct: 75 LN 76
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 11/94 (11%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L +RN+P EE+ F ++G +R + + T E RG A+V + D ++A A H+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 124 NGKRFAGREISVVL--------AAESRKRPEEMR 149
+G + R + V+ +++K+ E+++
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L +RN+P EE+ F ++G +R + + T E RG A+V + D ++A A H+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHL 77
Query: 124 NGKRFAGREISVV 136
+G R + V+
Sbjct: 78 SGFNVCNRYLVVL 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V ++ ++ E LR F+ F ++ D TG RG+ FV F +A A
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 123 MNGKRFAGREISVVLAAE 140
M G+ GR + + AA+
Sbjct: 149 MQGQDLNGRPLRINWAAK 166
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%)
Query: 66 VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
V +I + + +R F FG ++ + + D T + +GFAFV++ P A A MN
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 126 KRFAGREISV 135
GR I V
Sbjct: 93 VMLGGRNIKV 102
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+ V ++ D +++++ FE FG ++ L +D TG+ +G+ F+++ + +A M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 124 NGKRFAGREISV 135
N G+ + V
Sbjct: 188 NLFDLGGQYLRV 199
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+ VRN+P D + L+ F G V +Y G+ +G V+F P A A M
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 124 NGKRFAGREISV 135
NG + +GREI V
Sbjct: 69 NGMKLSGREIDV 80
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 86 NGQDLMGQPISV 97
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 66 VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
V N+ EL F +G +R V++ ++ P GFAFV+F DP +A +A ++G
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG 59
Query: 126 KRFAGREISVVLAA 139
K G + V L+
Sbjct: 60 KVICGSRVRVELST 73
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+ VRN+P D + L+ F G V +Y G+ +G V+F P A A M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 124 NGKRFAGREISV 135
NG + +GREI V
Sbjct: 66 NGMKLSGREIDV 77
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V NIP R +LR F +FG + DV + + +GF FV F + +A A+ +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 89
Query: 124 NGKRFAGREISV 135
+G GR+I V
Sbjct: 90 HGTVVEGRKIEV 101
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 85 NGQDLMGQPISV 96
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V NIP R +LR F +FG + DV + + +GF FV F + +A A+ +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 75
Query: 124 NGKRFAGREISV 135
+G GR+I V
Sbjct: 76 HGTVVEGRKIEV 87
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+L +N+P E++ F RFG + V LP+ T A V+F++P EA +A H+
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFRHL 66
Query: 124 NGKRF 128
+F
Sbjct: 67 AYSKF 71
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 37/67 (55%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
K+ + L + IP + ++L+ FE FG + ++ + KD +TG +G AF+ + + A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 117 AEAQHHM 123
+AQ +
Sbjct: 69 LKAQSAL 75
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 35/76 (46%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L+V +P D EL A F G + + +DY TG G+AFV F ++ A
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 123 MNGKRFAGREISVVLA 138
+NG + + V A
Sbjct: 65 LNGITVRNKRLKVSYA 80
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 70 NGQDLMGQPISV 81
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 37/78 (47%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V ++ ++ E LR F+ F ++ D TG RG+ FV F +A A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 123 MNGKRFAGREISVVLAAE 140
M G+ GR + + AA+
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
E++ G V + D ++L+ F +FG V D + D TG RGF F+ F D
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 118 ----EAQHHMNGK 126
+ +H ++G+
Sbjct: 68 KVLDQKEHRLDGR 80
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%)
Query: 66 VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
V +I + + +R F FG ++ + + D T + +GFAFV++ P A A MN
Sbjct: 18 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 77
Query: 126 KRFAGREISV 135
GR I V
Sbjct: 78 VMLGGRNIKV 87
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+ V ++ D +++++ FE FG ++ L +D TG+ +G+ F+++ + +A M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 124 NGKRFAGREISV 135
N G+ + V
Sbjct: 173 NLFDLGGQYLRV 184
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V NI C +ELRA FE +G V + + KDY AFV +A EA +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIRGL 64
Query: 124 NGKRFAGREISVVLAAESRKRP 145
+ F G+ + V L+ SR R
Sbjct: 65 DNTEFQGKRMHVQLST-SRLRT 85
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 76 EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS 134
E+LR +FG +R + L + P G A V F DP EA ++G+ F GR+I+
Sbjct: 41 EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V + + E++ F +G +++++L D TG +G+ V++ EA A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 124 NGKRFAGREISV 135
NG+ G+ ISV
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
++ V N+ E+++ F +FG V +V L D T +P+GF FV+ + +EA
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAK 61
Query: 123 MNGKRFAGREISVVLA 138
++ F GR I V A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P D EE+R FE++G +V++ KD +GF F++ A A+ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 124 NGKRFAGREISVVLAAES 141
+ G+++ V A S
Sbjct: 72 DNMPLRGKQLRVRFACHS 89
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P D EE+R FE++G +V++ KD +GF F++ A A+ +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 78
Query: 124 NGKRFAGREISVVLAAES 141
+ G+++ V A S
Sbjct: 79 DNMPLRGKQLRVRFACHS 96
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
KE++ +LL +N+P +EL+ FE +R + KD G+ +G A+++F +A
Sbjct: 89 KERDARTLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADA 143
Query: 117 AEAQHHMNGKRFAGREISV 135
+ G GR IS+
Sbjct: 144 EKTFEEKQGTEIDGRSISL 162
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEA 119
+ + + D ++L+ F +FG V D L D TG RGF FV F + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 120 QHHMNGK 126
+H +NGK
Sbjct: 62 EHKLNGK 68
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF---VDPYEAAEA 119
++ V I + E+R+ F R+G V++V + D TG +G+ FV F VD + E+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 120 QHHMNGKRF 128
Q + +GK+
Sbjct: 70 QINFHGKKL 78
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 65 LVRNIPLDCRPEELRAPFERFGVVRDVYLPKD-YYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L RN+ D + F +G ++ + +P + + +G+A+V+F +P EA +A HM
Sbjct: 12 LTRNVTKD----HIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67
Query: 124 NGKRFAGREI--SVVLA 138
+G + G+EI + VLA
Sbjct: 68 DGGQIDGQEITATAVLA 84
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGV-VRDVYLPKDYYTGEPRGFAFVQFV---DPYEAAEA 119
+++R +P +++R + GV R+V L ++ +G+ RGFAFV+F D EA
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 120 -QHHMNGKRFAGREISV 135
QH +N G+++S+
Sbjct: 64 NQHSLN---ILGQKVSM 77
>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 = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + +P ++++ FG ++ L KD TG +G+AF ++VD +A +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 124 NGKRFAGREISV 135
NG + +++ V
Sbjct: 159 NGMQLGDKKLLV 170
>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 = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + +P ++++ FG ++ L KD TG +G+AF ++VD +A +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 124 NGKRFAGREISV 135
NG + +++ V
Sbjct: 177 NGMQLGDKKLLV 188
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L +RN+P EE+ F ++G +R + + T E RG A+V + D ++A A H+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHL 71
Query: 124 NGKRFAGREISVV 136
+G R + V+
Sbjct: 72 SGFNVCNRYLVVL 84
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 77 PHKVDGR 83
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + +P ++++ FG ++ L KD TG +G+AF ++VD +A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 124 NGKRFAGREISV 135
NG + +++ V
Sbjct: 157 NGMQLGDKKLLV 168
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V+ + D E L+ F+ G VR + D TG +GF FV F +A A+
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 123 MNGKRFAGREISVVLA 138
M G ++++ A
Sbjct: 74 MEDGEIDGNKVTLDWA 89
>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 = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 75 PHKVDGR 81
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 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 = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 76 PHKVDGR 82
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+E+ ++ V N+ R E L F + G + V + KD G+P+ F FV F P
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESV 70
Query: 117 AEAQHHMNGKRFAGREISV 135
+ A +NG R GR I+V
Sbjct: 71 SYAIALLNGIRLYGRPINV 89
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L++ N+ E L+ FE+ ++ +P++ G+ +G+AF++F +A EA +
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIK---VPQNQ-NGKSKGYAFIEFASFEDAKEALNS 72
Query: 123 MNGKRFAGREISVVL 137
N + GR I + L
Sbjct: 73 CNKREIEGRAIRLEL 87
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 76 PHKVDGR 82
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 69 PHKVDGR 75
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
K+ + L V IP ++L+ FE FG + ++ + KD TG +G AF+ + A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 117 AEAQHHM 123
+AQ +
Sbjct: 71 LKAQSAL 77
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
L + + + E LR+ FE++G + D + +D T RGF FV + E A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 121 -HHMNGK 126
H ++G+
Sbjct: 74 PHKVDGR 80
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
+ V I D LR FE++G + + + D +G+ RGFAFV F D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P D E+ + FER+G +V++ +D RGF F++ A A+ +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 124 NGKRFAGREISVVLAA 139
+G R + + A
Sbjct: 79 DGTILKSRPLRIRFAT 94
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 8/88 (9%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRD--------VYLPKDYYTGEPRGFAFVQFV 111
++ ++ V+ + + E + F++ G+++ + L D TG+ +G A V F
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 112 DPYEAAEAQHHMNGKRFAGREISVVLAA 139
DP A A +GK F+G I V A
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPIKVSFAT 93
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 32/71 (45%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+ E++ F + G ++ + + D GF FV++ +A A +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 123 MNGKRFAGREI 133
+NG R R I
Sbjct: 101 INGTRLDDRII 111
>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 = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
+L + +P +++ F RFG + + + D TG RG AF++F EA EA
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 122 HMNG 125
NG
Sbjct: 149 SFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
+L + +P +++ F RFG + + + D TG RG AF++F EA EA
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 122 HMNG 125
NG
Sbjct: 149 SFNG 152
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
K+ + V +P LR FE FG + + + D TG+ RG+ FV D A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 117 AEAQHHMNGKRFAGREISVVLA 138
A N GR+ +V LA
Sbjct: 73 ERACKDPN-PIIDGRKANVNLA 93
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEA 119
+ + + E LR F +FG V++ + +D T RGF FV F+D A++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 120 QHHMNGK 126
+H ++ K
Sbjct: 88 RHELDSK 94
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.040, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 76 EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEAQHHMNGK 126
E LR F +FG V++ + +D T RGF FV F+D A+++H ++ K
Sbjct: 15 EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSK 69
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
L F + G V + ++PKD TG+ +G+ FV+F+ +A A M+ + G+ I V
Sbjct: 32 LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV 89
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 72 DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
D +ELR F ++G V DV++PK + R FAFV F D
Sbjct: 16 DMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFAD 51
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 35.0 bits (79), Expect = 0.046, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF---VDPYEAAEA 119
++ V I + E+R+ F R+G V++V + D TG +G+ FV F VD + E+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 120 QHHMNGKRF 128
Q + +GK+
Sbjct: 71 QINFHGKKL 79
>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 = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%)
Query: 66 VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
V +I + + +R F FG ++ + D T + +GFAFV++ P A A N
Sbjct: 17 VGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNS 76
Query: 126 KRFAGREISV 135
GR I V
Sbjct: 77 VXLGGRNIKV 86
Score = 34.7 bits (78), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 37/72 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
+ V ++ D +++++ FE FG ++ L +D TG+ +G+ F+++ + +A
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 124 NGKRFAGREISV 135
N G+ + V
Sbjct: 172 NLFDLGGQYLRV 183
>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 = 35.0 bits (79), Expect = 0.049, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF---VDPYEAAEA 119
++ V I + E+R+ F R+G V++V + D TG +G+ FV F VD + E+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 120 QHHMNGKRF 128
Q + +GK+
Sbjct: 70 QINFHGKKL 78
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.0 bits (79), Expect = 0.055, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 68 NIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR 127
+IP D E++ G V ++ + D TG +G+AF++F D +A A ++NG +
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 128 FAGR 131
R
Sbjct: 69 LGSR 72
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.0 bits (79), Expect = 0.055, Method: Composition-based stats.
Identities = 31/81 (38%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L VRN+ E L F FG + V KDY AFV F D A +A M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY--------AFVHFEDRGAAVKAMDEM 69
Query: 124 NGKRFAGREISVVLAAESRKR 144
NGK G EI +VLA K+
Sbjct: 70 NGKEIEGEEIEIVLAKPPDKK 90
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 35.0 bits (79), Expect = 0.056, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 72 DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
D EEL+ F ++G V DV++PK + R FAFV F D
Sbjct: 22 DMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFAD 57
>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 = 34.7 bits (78), Expect = 0.062, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 68 NIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR 127
+IP D E++ G V ++ + D TG +G+AF++F D +A A ++NG +
Sbjct: 10 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 128 FAGR 131
R
Sbjct: 70 LGSR 73
>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 = 34.3 bits (77), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 34/75 (45%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L + ++P + ++L F FG V + D T + F FV + +P A A
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 123 MNGKRFAGREISVVL 137
MNG + + + V L
Sbjct: 87 MNGFQIGMKRLKVQL 101
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 34.3 bits (77), Expect = 0.095, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 39/80 (48%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + +P ++++ FG ++ L KD TG +G+AF ++VD +A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 124 NGKRFAGREISVVLAAESRK 143
NG + +++ V A+ K
Sbjct: 64 NGMQLGDKKLLVQRASVGAK 83
>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 = 33.9 bits (76), Expect = 0.099, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 68 NIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR 127
+IP D E++ G V ++ + D TG +G+AF++F D +A A ++NG +
Sbjct: 11 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 128 FAGR 131
R
Sbjct: 71 LGSR 74
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.9 bits (76), Expect = 0.10, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRD--------VYLPKDYYTGEPRGFAFVQFV 111
++ ++ V+ + + E + F++ G+++ + L D TG+ +G A V F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 112 DPYEAAEAQHHMNGKRFAGREISVVLA 138
DP A A +GK F+G I V A
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF 110
+ V + ++ E+++ FE+FG V D L D T RGF FV F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+EQ+ +L + N+PL +EL + FG V + +D +G RG F + +
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKC 79
Query: 117 AEAQHHMNGK 126
H NGK
Sbjct: 80 EAVIGHFNGK 89
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+ D + F + G + + ++ + +P + FV+F + +AA A
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 123 MNGKRFAGREISVVLAA 139
MNG++ G+E+ V A
Sbjct: 75 MNGRKILGKEVKVNWAT 91
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 2/87 (2%)
Query: 57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
+E++ ++ + RP +L F G VRDV + D + +G A+V+F + ++
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE-IQS 79
Query: 117 AEAQHHMNGKRFAGREISVVLAAESRK 143
+ G+R G I +V A+++ K
Sbjct: 80 VPLAIGLTGQRLLGVPI-IVQASQAEK 105
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 64 LLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
L VRN+ L E + F G V V +DY AFV F + +A EA
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDY--------AFVHFSNREDAVEAMK 69
Query: 122 HMNGKRFAGREISVVLA 138
+NGK G I V LA
Sbjct: 70 ALNGKVLDGSPIEVTLA 86
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 23/43 (53%)
Query: 88 VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG 130
V V + ++ TG P G+ FV+F D A + H +NGK G
Sbjct: 37 VMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.7 bits (73), Expect = 0.23, Method: Composition-based stats.
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGE---PRGFAFVQFVDPYEAAEAQ 120
L ++N+ E L+ F + G ++ + K GF FV++ P +A +A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 121 HHMNGKRFAGREISVVLAAESRK 143
+ G G ++ V ++ + K
Sbjct: 68 KQLQGHTVDGHKLEVRISERATK 90
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 3/86 (3%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
N G + +R +P C EE+ F +V + LP D + G G AFVQF E AE
Sbjct: 14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQ-EIAE 71
Query: 119 AQHHMNGKRFAGREISVVLAAESRKR 144
+ +R R I + ++ + R
Sbjct: 72 KALKKHKERIGHRYIEIFKSSRAEVR 97
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.25, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 103 RGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESR 142
+GFAFVQ+V+ A A +G+ AG+ + + LAAE +
Sbjct: 50 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK 89
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L + ++P + +L + F FG V + D T + F FV F +P A A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 123 MNGKRFAGREISVVL 137
MNG + + + V L
Sbjct: 102 MNGFQVGTKRLKVQL 116
>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 = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF 110
+ V + D E++R F FG V + LP D T + RGF F+ F
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD------PYEA 116
++ +RN+ D E L ++FG ++ V + T +G AF QF+ A
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 117 AEAQHHMNGKRFAGREISVVLAA 139
A + G + GR++ V LA
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAV 99
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.3 bits (72), Expect = 0.33, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF 110
+ V + D E++R F FG V + LP D T + RGF F+ F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
>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 = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+LL +N+ + +EL+ FE +R + +D G+ +G A+++F +A +
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIR--LVSQD---GKSKGIAYIEFKSEADAEKNLEE 155
Query: 123 MNGKRFAGREISV 135
G GR +S+
Sbjct: 156 KQGAEIDGRSVSL 168
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 76 EELRAPFERFGVVRDVYLPK--DYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
E++R ++G+V+ + +P+ D G FV+F ++ +A + G++FA R +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 72 DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR 131
D P LR F FG + D+ + PR AFV + A +A +NG +
Sbjct: 24 DMTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESV 77
Query: 132 EISVVLAAESRKRP 145
++ V +A RK+P
Sbjct: 78 QLKVNIA---RKQP 88
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 76 EELRAPFERFGVVRDVYLPKDYYTGEPRGF--AFVQFVDPYEAAEAQHHMNGKRFAGREI 133
E++R ++G+V+ + +P+ E G FV+F ++ +A + G++FA R +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 31.6 bits (70), Expect = 0.50, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 82 FERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
F FGV+ + + +D TG +G+AF+ F + A MNG+ R I+V A
Sbjct: 26 FSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 83
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 76 EELRAPFERFGVVRDVYLPK--DYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
E++R ++G+V+ + +P+ D G FV+F ++ +A + G++FA R +
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 76 EELRAPFERFGVVRDVYLPK--DYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
E++R ++G+V+ + +P+ D G FV+F ++ +A + G++FA R +
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 37/81 (45%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L ++N+ +L + F RF + + TG RG AF+ F + A +A H +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 124 NGKRFAGREISVVLAAESRKR 144
NG + G+ + + ++R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.2 bits (69), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P ++ FG + +L TG+ +G+ F +++ AA A+ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 124 NGKRFAGREISV 135
GK R + V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.2 bits (69), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P ++ FG + +L TG+ +G+ F +++ AA A+ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 124 NGKRFAGREISV 135
GK R + V
Sbjct: 158 LGKPLGPRTLYV 169
>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 = 31.2 bits (69), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L V N+P ++ FG + +L TG+ +G+ F +++ AA A+ +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 124 NGKRFAGREISV 135
GK R + V
Sbjct: 156 LGKPLGPRTLYV 167
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 3/86 (3%)
Query: 60 NHGSLLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
N G + +R +P C EE+ F +V + LP D G+ G AFVQF E AE
Sbjct: 41 NDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD-PEGKITGEAFVQFASQ-ELAE 98
Query: 119 AQHHMNGKRFAGREISVVLAAESRKR 144
+ +R R I V +++ R
Sbjct: 99 KALGKHKERIGHRYIEVFKSSQEEVR 124
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 30.8 bits (68), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEP--RGFAFVQFVDPYEAAEAQH 121
+ V +P ++LR FE++G V ++ + +D P +G FV F A EAQ+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 122 HMNGKR 127
++ +
Sbjct: 66 ALHNMK 71
>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 = 30.8 bits (68), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 72 DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR 131
D P LR F FG + D+ + PR AFV + A +A +NG +
Sbjct: 48 DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESV 101
Query: 132 EISVVLAAESRKRP 145
++ V +A RK+P
Sbjct: 102 QLKVNIA---RKQP 112
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEP--RGFAFVQFVDPYEAAEAQH 121
+ V +P ++LR FE++G V ++ + +D P +G FV F A EAQ+
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 122 HMNGKR 127
++ +
Sbjct: 78 ALHNMK 83
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEP--RGFAFVQFVDPYEAAEAQH 121
+ V +P ++LR FE++G V ++ + +D P +G FV F A EAQ+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 122 HMNGKR 127
++ +
Sbjct: 66 ALHNMK 71
>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 = 1.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 76 EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF 128
+ L + F + G V ++ P D TG+ +GF FV+ +A + +GKR
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE-AQ 120
G++ ++N+ + L F FG + + D +G+ FV F + EAAE A
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHF-ETQEAAERAI 62
Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
MNG R++ V ++R E+ R +
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAK 95
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
L + N+P + +E+R+ FE++G V + + K+Y FV D A +A ++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTAAEDAIRNL 62
Query: 124 NGKRFAGREISV 135
+ + G I+V
Sbjct: 63 HHYKLHGVNINV 74
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 65 LVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEP--RGFAFVQFVDPYEAAEAQHH 122
V +P ++LR FE++G V ++ + +D P +G FV F A EAQ+
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 123 MNGKR 127
++ +
Sbjct: 67 LHNXK 71
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE-AQ 120
G++ ++N+ + L F FG + + D +G+ FV F + EAAE A
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHF-ETQEAAERAI 160
Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
MNG R++ V ++R E+ R +
Sbjct: 161 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAK 193
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+LL +N+ + +EL+ FE +R V G+ +G A+++F +A +
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 123 MNGKRFAGREISVVLAAE 140
G GR +S+ E
Sbjct: 73 KQGAEIDGRSVSLYYTGE 90
>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 = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE-AQ 120
G++ ++N+ + L F FG + + D +G+ FV F + EAAE A
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHF-ETQEAAERAI 155
Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
MNG R++ V ++R E+ R +
Sbjct: 156 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAK 188
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 99 TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE---ISVVLAAESRKRPEE 147
TG +G+ FV+F D E A G G + +SV + SR +P E
Sbjct: 47 TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVE 98
>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 = 28.9 bits (63), Expect = 3.3, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF 128
L + F + G V ++ P D TG+ +GF FV+ +A + +GKR
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>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 = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
+L V N+ E++ F + G ++ + + D GF FV++ +A A +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAMRY 78
Query: 123 MNGKRFAGREI 133
+NG R R I
Sbjct: 79 INGTRLDDRII 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 103 RGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE 140
+G+AFVQ+ + A A NG+ AG+ + + +A E
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
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
0.316 0.135 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,775,793
Number of Sequences: 62578
Number of extensions: 254987
Number of successful extensions: 598
Number of sequences better than 100.0: 161
Number of HSP's better than 100.0 without gapping: 122
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 180
length of query: 299
length of database: 14,973,337
effective HSP length: 98
effective length of query: 201
effective length of database: 8,840,693
effective search space: 1776979293
effective search space used: 1776979293
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)