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= psy13227
(247 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/88 (54%), Positives = 67/88 (76%), Gaps = 1/88 (1%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
RR DD IR++NLS +T E DL++L + FG S++YL++DKT G KGFA+I F + D
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 220 AAKAIQYLNGYGYDHLILSVDWSK-STN 246
AA+AI ++G+GYDHLIL+V+W+K STN
Sbjct: 70 AARAIAGVSGFGYDHLILNVEWAKPSTN 97
>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 = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + + NLS T+E + +L + G K+ + DK C GF ++ + ++ADA A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAM 76
Query: 225 QYLNGYGYDHLILSVDW 241
+Y+NG D I+ DW
Sbjct: 77 RYINGTRLDDRIIRTDW 93
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 50/95 (52%), Gaps = 6/95 (6%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
GP G R D + + LS+ T+E DL ++ ++GP + + + D+ + +
Sbjct: 1 GPLGSRAN------PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 54
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
GFA+++F+N DA +A + NG D + VD+S
Sbjct: 55 GFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + + LS+ T+E DL ++ ++GP + + + D+ + +GFA+++F+N DA +
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 223 AIQYLNGYGYDHLILSVDWS 242
A + NG D + VD+S
Sbjct: 104 AKERANGMELDGRRIRVDFS 123
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + + LS+ T+E DL ++ ++GP + + + D+ + +GFA+++F+N DA +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 223 AIQYLNGYGYDHLILSVDWS 242
A + NG D + VD+S
Sbjct: 73 AKERANGMELDGRRIRVDFS 92
>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 = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T++++ NL+ TS + L + +++G +Y+ RD+ +GFA++ F +K DA A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 226 YLNGYGYDHLILSVDWSK 243
++G D L V ++
Sbjct: 108 AMDGAVLDGRELRVQMAR 125
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + + NLS T+E + +L + G K+ + DK GF ++ + ++ADA A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 225 QYLNGYGYDHLILSVDW 241
+Y+NG D I+ DW
Sbjct: 99 RYINGTRLDDRIIRTDW 115
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T++++ NL+ TS + L + +++G +Y+ RD+ +GFA++ F +K DA A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 226 YLNGYGYDHLILSVDWSK 243
++G D L V ++
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
D + + LS +T+E LE + ++G S++ + +D+ +GF ++ F+N DA A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 224 IQYLNGYGYDHLILSVDWS 242
+ +NG D + VD +
Sbjct: 71 MMAMNGKSVDGRQIRVDQA 89
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
IS L ++ D+ED+ +FG + D+T GL +G A+I F +++A +AI NG
Sbjct: 93 ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Query: 230 Y 230
+
Sbjct: 153 H 153
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L N ++++L L G L RDK G G+ ++++ DA +AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
LNG + V +++ +++
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE 84
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
IS L ++ D+ED+ +FG + D+T GL +G A+I F +++A +AI NG
Sbjct: 93 ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Query: 230 Y 230
+
Sbjct: 153 H 153
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L N ++++L L G L RDK G G+ ++++ DA +AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
LNG + V +++ +++
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE 84
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 44/82 (53%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + + LS+ T+E DL ++ ++GP + + + D+ + +GFA+++F+N DA +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
A + NG D + V S
Sbjct: 73 AKERANGMELDGRRIRVSGPSS 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NLS +SE DLE L +GP S+++ D KGFA++ F A KA ++G
Sbjct: 13 VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG 72
Query: 230 YGYDHLILSV 239
+ +L V
Sbjct: 73 QVFQGRMLHV 82
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + I L+ T+E L+ + + GP S++ L +D+T+ +GFA+I F+N ADA
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKN 63
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
A + +NG + V+ +K
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAK 84
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SNL S+ D+++L +FG K + D++ G G A +HF+ KADA KA++
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQY 89
Query: 228 NGYGYD 233
NG D
Sbjct: 90 NGVPLD 95
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 41/84 (48%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
N + + + ++ + +E + DL GP + + D G KG+A+I F++ +A
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 222 KAIQYLNGYGYDHLILSVDWSKST 245
A++ LNGY L +S ++
Sbjct: 61 SAVRNLNGYQLGSRFLKCGYSSNS 84
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SNL S+ D+++L +FG K + D++ G G A +HF+ KADA KA +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAXKQY 90
Query: 228 NGYGYD 233
NG D
Sbjct: 91 NGVPLD 96
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 41/82 (50%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + + ++ + +E + DL GP + + D G KG+A+I F++ +A A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 225 QYLNGYGYDHLILSVDWSKSTN 246
+ LNGY L +S +++
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSD 83
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 41/82 (50%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ + + ++ + +E + DL GP + + D G KG+A+I F++ +A A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 225 QYLNGYGYDHLILSVDWSKSTN 246
+ LNGY L +S +++
Sbjct: 63 RNLNGYQLGSRFLKCGYSSNSD 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%)
Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
++ + N+ +E L+D+ + GP L D+ G KG+ + ++++ A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 227 LNGYGYDHLILSVDWSKS 244
LNG + L VD + S
Sbjct: 70 LNGREFSGRALRVDNAAS 87
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D +++ NL+ TS + L + +++G +Y+ R+ +GFA++ F ++ DA
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
A ++G D L V ++
Sbjct: 71 AEAAMDGAELDGRELRVQVAR 91
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+SNL S+ D+++L +FG K + D++ G G A +HF+ +ADA KA++ G
Sbjct: 93 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKG 151
Query: 230 YGYDHLILSV 239
D + +
Sbjct: 152 VPLDGRPMDI 161
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
PG +R VEG+ + ++ + +E D+ D ++G ++L+ D+ G K
Sbjct: 1 PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 51
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
G+ + ++ +A A++ LNG +SVDW
Sbjct: 52 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
PG +R VEG+ + ++ + +E D+ D ++G ++L+ D+ G K
Sbjct: 15 PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
G+ + ++ +A A++ LNG +SVDW
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+R+ + + ++ + +E D+ D ++G ++L+ D+ G KG+ + ++ +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
A A++ LNG +SVDW
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDW 83
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
++ + + +L N +E+ L + + FG + L +D G KG+ +I F + A +A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 225 QYLNGY 230
+ LNG+
Sbjct: 65 EQLNGF 70
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+R+ + + ++ + +E D+ D ++G ++L+ D+ G KG+ + ++ +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
A A++ LNG +SVDW
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDW 83
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 171 SNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+NL VN D+ D L + GP + + RD G G+A++ F ++ D+ +AI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 226 YLNGYGYDHLILSVDWSK 243
LNG + L V +++
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 149 PGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
PGG+ ++ N + ++NL +++ L+ + ++G + + RDK G +G
Sbjct: 82 PGGESIKDTN---------LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 132
Query: 209 FAYIHFKNKADAAKAIQYLN 228
A++ + + +A +AI LN
Sbjct: 133 VAFVRYNKREEAQEAISALN 152
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
PG +R VEG+ + ++ + +E D+ D ++G ++L+ D+ G K
Sbjct: 14 PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
G+ + ++ +A A++ LNG +SVDW
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SNL S+ D+++L +FG K + D++ G G A +HF+ +ADA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQY 96
Query: 228 NGYGYD 233
G D
Sbjct: 97 KGVPLD 102
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SNL S+ D+++L +FG K + D++ G G A +HF+ +ADA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQY 96
Query: 228 NGYGYD 233
G D
Sbjct: 97 KGVPLD 102
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
+R+ + + ++ + +E D+ D ++G ++L+ D+ G KG+ + ++ +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
A A++ LNG +SVDW
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDW 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 171 SNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+NL VN D+ D L + GP + + RD G G+A++ F ++ D+ +AI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 226 YLNGYGYDHLILSVDWSK 243
LNG + L V +++
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 156 GYNARRND-DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
G NA +N+ D + LS +TS+ DL+D +FG + D G +GF +I F
Sbjct: 1 GINASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Query: 215 KNKADAAKAIQ 225
K+ A K +
Sbjct: 61 KDAASVEKVLD 71
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + +LS + D++ FG S + +D G KG+ ++ F NK DA AIQ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 228 NGYGYDHLILSVDWS 242
G + +W+
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + +L N +E+ L + + FG + L D G KG+ +I F + A KA++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 228 NGY 230
NG+
Sbjct: 89 NGF 91
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L + ++ +L L + GP + + RD G G+A++ F ++ D+ +AI+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 226 YLNGYGYDHLILSVDWSK 243
LNG + L V +++
Sbjct: 75 VLNGITVRNKRLKVSYAR 92
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 149 PGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
PGG+ ++ N + ++NL +++ L+ + ++G + + RDK G +G
Sbjct: 93 PGGESIKDTN---------LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 143
Query: 209 FAYIHFKNKADAAKAIQYLN 228
A++ + + +A +AI LN
Sbjct: 144 VAFVRYNKREEAQEAISALN 163
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 39/85 (45%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
+ + + NLS +E DL L +F + G +G A+I F NK A +
Sbjct: 23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 223 AIQYLNGYGYDHLILSVDWSKSTNQ 247
A+ +NGY IL +++ K+ Q
Sbjct: 83 ALHLVNGYKLYGKILVIEFGKNKKQ 107
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 170 ISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+S L S+ ++E L Q+G TS++ L D+ G+ +G +I F + +A +AI+ L
Sbjct: 6 VSGLPKTMSQKEMEQLFSQYGRIITSRILL--DQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 228 NG 229
NG
Sbjct: 64 NG 65
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + +LS + D++ FG S + +D G KG+ ++ F NK DA AI ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 228 NGYGYDHLILSVDWS 242
G + +W+
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 41/84 (48%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D T + ++ L N ++++ + L G L RDK G G+ ++++ + DA K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 223 AIQYLNGYGYDHLILSVDWSKSTN 246
AI LNG + V +++ ++
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSS 85
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 165 TTAIRISNLSVN-----TSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNK 217
+ +IR +NL V+ S+ ++E L Q+G TS++ L D+ G+ +G +I F +
Sbjct: 85 SASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILL--DQATGVSRGVGFIRFDKR 142
Query: 218 ADAAKAIQYLNG 229
+A +AI+ LNG
Sbjct: 143 IEAEEAIKGLNG 154
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++NL + ++ E+LV+ FG + +L + G KG+ + + K AA+A L G
Sbjct: 98 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 157
Query: 230 YGYDHLILSVDWSKS 244
L V W+ +
Sbjct: 158 KPLGPRTLYVHWTDA 172
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++NL + ++ E+LV+ FG + +L + G KG+ + + K AA+A L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 230 YGYDHLILSVDWSKS 244
L V W+ +
Sbjct: 160 KPLGPRTLYVHWTDA 174
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++NL + ++ E+LV+ FG + +L + G KG+ + + K AA+A L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 230 YGYDHLILSVDWSKS 244
L V W+ +
Sbjct: 160 KPLGPRTLYVHWTDA 174
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+S L ++ +LE L Q+G + D+ G+ +G +I F + +A +AI+ LNG
Sbjct: 93 VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L N ++ + L G L RDK G G+ ++++ + DA KAI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 226 YLNGYGYDHLILSVDWSKSTN 246
LNG + V +++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSS 83
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
+ A+ D T + NL E L +L Q GP +K+ + +D+ G K F ++ FK+
Sbjct: 9 FPAQEEADRTVF-VGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKH 66
Query: 217 KADAAKAIQYLNG 229
+ AI LNG
Sbjct: 67 PESVSYAIALLNG 79
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I + NL + D+ED+ ++G + L +++ G FA++ F++ DA A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 228 NGYGYDHLILSVDWSKS 244
+GY YD L V++ +S
Sbjct: 82 DGYDYDGYRLRVEFPRS 98
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + NL N ++ +LE +GP ++++R+ GFA++ F++ DAA A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130
Query: 228 NG 229
+G
Sbjct: 131 DG 132
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G NAR T + + LS +T+E E L + F + + + D+ G KGF ++ F
Sbjct: 7 GPNARSQPSKT-LFVKGLSEDTTE---ETLKESFDGSVRARIVTDRETGSSKGFGFVDFN 62
Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
++ DA A + + D +++DW+K
Sbjct: 63 SEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D T + ++ L N ++++ + L G L RDK G G+ ++++ + DA K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
AI LNG + V +++
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR 82
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 148 GPGGKRVEGYNAR----RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN 203
G G + G A+ + D T + ISNL ++ E +LE+++K FG + RD ++
Sbjct: 4 GSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SS 62
Query: 204 GLCKGFAYIHFKNKADAAKAIQYLNG 229
G +G + ++ I + NG
Sbjct: 63 GTSRGVGFARMESTEKCEAVIGHFNG 88
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + + ++ E++L ++ FGP K + GFA++ F+ AAKAI+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPM--------KEVKILNGFAFVEFEEAESAAKAIE 83
Query: 226 YLNGYGYDHLILSVDWSK 243
++G + + L V +SK
Sbjct: 84 EVHGKSFANQPLEVVYSK 101
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L N ++++L L G L RDK G G+ ++++ DA +AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 226 YLNGYGYDHLILSVDWSK 243
LNG + V +++
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + NL N ++ +LE +GP ++++R+ GFA++ F++ DAA A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRDL 130
Query: 228 NG 229
+G
Sbjct: 131 DG 132
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
PG +R VEG+ + ++++ E+++++ +G ++L+ D+ G K
Sbjct: 18 PGPQRSVEGW---------ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
G+A + ++ A A + LNG + VDW
Sbjct: 69 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
G + ++ D + I + N E DL+ L ++FG ++ + +D+ G+ KG A++ +
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 216 NKADAAKAIQYLN 228
+ A KA L+
Sbjct: 64 ERESALKAQSALH 76
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
IS L + ++ +LE++ K G + L ++ G KG AY+ ++N++ A++A+ ++G
Sbjct: 22 ISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKMDG 80
Query: 230 YGYDHLILSVDWSKS 244
I+ V S S
Sbjct: 81 MTIKENIIKVAISNS 95
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAI 224
T + I L+ N +++ + ++ +G + + ++ + L KG+AY+ F+N +A KA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 225 QYLNG 229
++++G
Sbjct: 65 KHMDG 69
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + ++ L N ++++L L G L RDK G G+ ++++ DA +AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 226 YLNGYGYDHLILSVDWSK 243
LNG + V +++
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
PG +R VEG+ + ++++ E+++++ +G ++L+ D+ G K
Sbjct: 64 PGPQRSVEGW---------ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
G+A + ++ A A + LNG + VDW
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + NL + +LE +GP ++++R+ GFA++ F++ DA A++ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGL 57
Query: 228 NG 229
+G
Sbjct: 58 DG 59
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 39/80 (48%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
DDT + + +L+VN + L + K F ++ D G +G+ ++ F ++ DA
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 223 AIQYLNGYGYDHLILSVDWS 242
A+ + G + L ++W+
Sbjct: 145 AMDSMQGQDLNGRPLRINWA 164
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 183 EDLVKQF----GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS 238
ED++KQ+ GP + + + DK N +A++ + DA A+Q LNG ++ I+
Sbjct: 14 EDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQTLNGKQIENNIVK 72
Query: 239 VDWSKSTNQ 247
++W+ + Q
Sbjct: 73 INWAFQSQQ 81
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNG---LCKGFAYIHFKNKA 218
+ ++ + I NL+ +T+E L+ + + G +S+ K L GF ++ +K
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 219 DAAKAIQYLNGYGYDHLILSVDWSK 243
A KA++ L G+ D L V S+
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISE 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 170 ISNLSVN-----TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+ NL VN E L L +++GP + + D+ +G+ ++ F++ + A +AI
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 225 QYLNGYGYDHLILSVDWSKSTNQ 247
LNG+ + L V + S +Q
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQ 124
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
++ + I L T++ DL L + +G DKT CKG+ ++ F + + A KA+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 225 QYLNGYG 231
L G
Sbjct: 65 TALKASG 71
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 149 PGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
PGG+ ++ N + ++NL +++ L+ + ++G + + RDK G +G
Sbjct: 6 PGGESIKDTN---------LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 56
Query: 209 FAYIHFKNKADAAKAIQYLN 228
A++ + + +A +AI LN
Sbjct: 57 VAFVRYNKREEAQEAISALN 76
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 41/71 (57%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ ++ +T+E+ L + +GP ++++ K +G +G+A+I ++++ D A ++ +G
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG 166
Query: 230 YGYDHLILSVD 240
D + VD
Sbjct: 167 KKIDGRRVLVD 177
>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 = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 34/61 (55%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I ++++ + S++D++ + + FG L+RD T G KG+ +I ++ + A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 228 N 228
N
Sbjct: 188 N 188
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDL-EDLVKQ----FGPTSKMYLSRDKTNG 204
GG+++ +A + AI +S + V + +L ED ++Q FGP + +S D
Sbjct: 9 GGQQMGRGSAAQRQGALAI-MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTM 67
Query: 205 LCKGFAYIHFKNKADAAKAIQYLN 228
KGFA++ ++ A A++ +N
Sbjct: 68 KHKGFAFVEYEVPEAAQLALEQMN 91
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL ++TSE +E K+F + R K + +A++HF N+ DA +A++ LNG
Sbjct: 20 VRNLMLSTSEEMIE---KEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNG 73
Query: 230 YGYDHLILSVDWSKSTNQ 247
D + V +K ++
Sbjct: 74 KVLDGSPIEVTLAKPVDK 91
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 34/61 (55%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I ++++ + S++D++ + + FG L+RD T G KG+ +I ++ + A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 228 N 228
N
Sbjct: 173 N 173
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 183 EDLVKQ----FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
ED ++Q FGP + +S D KGFA++ ++ A A++ +N
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMN 76
>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 = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 41/71 (57%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ ++ +T+E+ L + +GP ++++ K +G +G+A+I ++++ D A ++ +G
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG 166
Query: 230 YGYDHLILSVD 240
D + VD
Sbjct: 167 KKIDGRRVLVD 177
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.2 bits (82), Expect = 0.017, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 8/78 (10%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
T + + ++ E++L ++ FGP ++ + GFA++ F+ AAKAI+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEV--------KILNGFAFVEFEEAESAAKAIE 56
Query: 226 YLNGYGYDHLILSVDWSK 243
++G + + L V +SK
Sbjct: 57 EVHGKSFANQPLEVVYSK 74
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.2 bits (82), Expect = 0.017, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
I + LSVNT+ D++ +QFG L DKT +GF ++ F+++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>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 = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF--KNK 217
++ D ++ + N+ ++ DLE G +++ + DK +G KG+AYI F +N
Sbjct: 31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS 90
Query: 218 ADAAKAI 224
DAA A+
Sbjct: 91 VDAAVAM 97
>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 = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
D + I L +++ +++L+ FGP L +D GL KG+A+ + + +
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 223 AIQYLNG 229
AI LNG
Sbjct: 172 AIAGLNG 178
>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 = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 33/75 (44%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ + +LS + + FG S + +D G KG+ ++ F NK DA AIQ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 228 NGYGYDHLILSVDWS 242
G + +W+
Sbjct: 69 GGQWLGGRQIRTNWA 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL+ +E LE QFG ++ +D +A+IHF + A KA++ +NG
Sbjct: 16 VRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNG 67
Query: 230 YGYDHLILSVDWSKSTNQ 247
+ + + ++K +Q
Sbjct: 68 KDLEGENIEIVFAKPPDQ 85
>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 = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I ++++ + S++D++ + + FG L+RD T G KG+ +I ++ + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 228 N 228
N
Sbjct: 172 N 172
Score = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 183 EDLVKQ----FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
ED ++Q FGP + S D KGFA++ ++ A A++ N
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXN 75
>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 = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 183 EDLVKQFGP-----TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL 237
+DL++ F P ++K+++ DK L K F ++ + N A AIQ +NG+ L
Sbjct: 40 QDLLQMFMPFGNVVSAKVFI--DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL 97
Query: 238 SVDWSKSTN 246
V +S N
Sbjct: 98 KVQLKRSKN 106
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 7/88 (7%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYL-SRDKTNGLCKGFAYIHF 214
G ++++ D + NL ++++L+++ F +++ L S+D G KG AYI F
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEV---FEDAAEIRLVSKD---GKSKGIAYIEF 137
Query: 215 KNKADAAKAIQYLNGYGYDHLILSVDWS 242
K +ADA K + G D +S+ ++
Sbjct: 138 KTEADAEKTFEEKQGTEIDGRSISLYYT 165
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
NLS N +E++L+++ + +S+D G KG AYI FK++ADA K ++ G
Sbjct: 106 NLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 232 YDHLILSVDWS 242
D +S+ ++
Sbjct: 161 IDGRSVSLYYT 171
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
NLS N +E++L+++ + +S+D G KG AYI FK++ADA K ++ G
Sbjct: 23 NLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 232 YDHLILSVDWS 242
D +S+ ++
Sbjct: 78 IDGRSVSLYYT 88
>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 = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L +++ +++L+ FGP L +D GL KG+A+ + + +AI LNG
Sbjct: 101 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 160
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I L +++ +++L+ FGP L +D GL KG+A+ + + +AI LNG
Sbjct: 99 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 158
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+ + +SNL + + NDL + ++G K+ + +DK KG A+I F +K A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 226 YLN 228
+N
Sbjct: 77 AIN 79
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SN+ + DL + QFG + + ++ KGF ++ F+N ADA +A + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 228 NG 229
+G
Sbjct: 90 HG 91
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ +SN+ + DL + QFG + + ++ KGF ++ F+N ADA +A + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 228 NG 229
+G
Sbjct: 76 HG 77
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%)
Query: 161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADA 220
++ D + + + E DL+ L ++FG ++ + +D+ GL KG A++ + + A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 221 AKAIQYLN 228
KA L+
Sbjct: 71 LKAQSALH 78
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 6/60 (10%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL + +E D + L +++G S+++++RD +GF +I +++ A A L+G
Sbjct: 27 VGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDG 80
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
A+ + NLS S LE QFGP K + D G G ++ F K A KA++
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I LS T++ L + QFG + + RD +GF ++ F ++A K +
Sbjct: 30 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 34.7 bits (78), Expect = 0.054, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I LS +T++ DL+D +FG L D G +GF ++ FK K +
Sbjct: 4 IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ I L +++ +++L+ FGP L +D GL KG+A+ + + +AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 228 NG 229
NG
Sbjct: 64 NG 65
>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 = 34.3 bits (77), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
++ + +L + +E L + GP + + RD G+AY++F+ ADA +A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 226 YLN 228
+N
Sbjct: 76 TMN 78
Score = 30.4 bits (67), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I I NL + L D FG + D+ NG KG+ ++HF+ + A +AI+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NG-SKGYGFVHFETQEAAERAIEKM 163
Query: 228 NG 229
NG
Sbjct: 164 NG 165
>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 = 34.3 bits (77), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
T + + +L+VN + L + K F ++ D G +G+ ++ F ++ DA A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 225 QYLNGYGYDHLILSVDWS 242
+ G + L ++W+
Sbjct: 61 DSMQGQDLNGRPLRINWA 78
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.9 bits (76), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL+ +E LE +FG ++ +D +A++HF+++ A KA+ +NG
Sbjct: 20 VRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEMNG 71
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.9 bits (76), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA- 218
R + + I LS T+E L + +Q+G + + RD + +GF ++ F + A
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Query: 219 -DAAKAIQ 225
DAA A +
Sbjct: 82 VDAAMAAR 89
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
++ + +L + +E L + GP + + RD G+AY++F+ ADA +A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 226 YLN 228
+N
Sbjct: 71 TMN 73
Score = 30.4 bits (67), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I I NL + L D FG + D+ NG KG+ ++HF+ + A +AI+ +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NG-SKGYGFVHFETQEAAERAIEKM 158
Query: 228 NG 229
NG
Sbjct: 159 NG 160
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
D +I + N+ + +LE G +++ + DK +G KGFAYI F +K
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK 58
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
GK++EG + + I +L ++ DL FG + DK L K F
Sbjct: 32 GKQIEG------PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFG 85
Query: 211 YIHFKNKADAAKAIQYLNGY 230
++ F N A AI+ +NG+
Sbjct: 86 FVSFDNPDSAQVAIKAMNGF 105
>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 = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
D +I + N+ + +LE G +++ + DK +G KGFAYI F +K
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK 57
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 11/81 (13%)
Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLED--LVKQFGP-----TSKMYLSRDKTNGLCKG 208
G + D T ++ NL V ++ ++D L K F P ++K+ + G KG
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME----GGRSKG 56
Query: 209 FAYIHFKNKADAAKAIQYLNG 229
F ++ F + +A KA+ +NG
Sbjct: 57 FGFVCFSSPEEATKAVTEMNG 77
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 11/56 (19%), Positives = 31/56 (55%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I L+ +T+E++L + ++G + + + +D G +GF ++ F+ + + ++
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
D T I + + + + E+ Q+G L DK G +GF ++ + + ADA
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAV 142
Query: 222 KAI 224
+
Sbjct: 143 DRV 145
>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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKA 223
++ I I NL E L D FG + + RD G KG+A+I+F + + A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 224 IQYLNG 229
I+ +NG
Sbjct: 65 IEAMNG 70
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
+T I + N+S + +L L ++ G + + +D +A++H + +ADA A
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAA 59
Query: 224 IQYLNG 229
I LNG
Sbjct: 60 IAQLNG 65
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + +T E+ L D +Q+G + + D+ +G +GFA++ F + K +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
+ NL NT + D++ + K S + L RDK KGF Y+ F ++ D+ K +G
Sbjct: 20 VGNLPFNTVQGDIDAIFKDLSIRS-VRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDG 77
Query: 230 YGYDHLILSVDWSKSTNQ 247
L VD ++ Q
Sbjct: 78 ALLGDRSLRVDIAEGRKQ 95
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 32.0 bits (71), Expect = 0.32, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I LS T++ L + QFG + + RD +GF ++ F ++A K +
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 26/54 (48%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
D+ + + L +T++ L Q+G + +DKT +GF ++ FK+
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 28/65 (43%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
R T+ + + L T+E DL++ FG + + +D G KGF ++ F
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 220 AAKAI 224
K +
Sbjct: 70 QVKVM 74
>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 = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 177 TSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
+E+D+ ++ G ++ + L R+K++G +GFA++ F + DA + ++
Sbjct: 13 ATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLS--RDKTNGLCKGFAYIHFKNKADAAKAI 224
A+ I NL+ T++ DL + V G + + ++ NG KGFA + ++A + K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 225 QYL 227
L
Sbjct: 63 DLL 65
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
+T + + N+S + +L +++GP + + +D +A++H + DA +AI
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAI 61
Query: 225 QYLNGYGYDHLILSVDWSKS 244
+ L+ + + V S S
Sbjct: 62 RGLDNTEFQGKRMHVQLSTS 81
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLS--RDKTNGLCKGFAYIHFKNKADAAKAI 224
A+ I NL+ T++ DL + V G + + ++ NG KGFA + ++A + K +
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 225 QYL 227
L
Sbjct: 130 DLL 132
>pdb|3NO0|A Chain A, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|B Chain B, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|C Chain C, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
Length = 276
Score = 30.8 bits (68), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 141 VPPSLREGPGGKRVEGYNARRNDDTTAIRISN 172
VPPS PG + V+G +ND+T+ +RI N
Sbjct: 147 VPPST---PGARGVQGIKLEKNDETSGLRIWN 175
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 29/57 (50%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
I + + N E +L + K+FG +++ + D +GF +I F+++ +A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL + ++ D+ ++GP ++ R +G AY+ +++ DA A+ +L+G
Sbjct: 13 IRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69
Query: 230 YGYDHLILSVDW 241
+ + L V +
Sbjct: 70 FNVSNRYLVVLY 81
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
++ + +SNLS + +E L+++ F + + + +++ NG KG+A+I F + DA +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEV---FEKATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 224 IQYLN 228
+ N
Sbjct: 70 LNSCN 74
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I I NL + L D FG + D+ NG KG+ ++HF+ + A +AI+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NG-SKGYGFVHFETQEAAERAIEKM 65
Query: 228 NG 229
NG
Sbjct: 66 NG 67
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I I NL + L D FG + D+ NG KG+ ++HF+ + A +AI+ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NG-SKGYGFVHFETQEAAERAIEKM 71
Query: 228 NG 229
NG
Sbjct: 72 NG 73
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 28/58 (48%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
T I + L +T++ L + FG + + D+ G +G+ ++ ++A A +A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 12/80 (15%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFG----------PTSKMYLSRDKTNGLCKGF 209
+ N D I + L N + + D KQ G P +Y R+ G KG
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE--TGKLKGE 59
Query: 210 AYIHFKNKADAAKAIQYLNG 229
A + F + A AI + +G
Sbjct: 60 ATVSFDDPPSAKAAIDWFDG 79
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL + ++ D+ ++GP ++ R +G AY+ +++ DA A +L+G
Sbjct: 17 IRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHLSG 73
Query: 230 Y 230
+
Sbjct: 74 F 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
FG + + + D +GFA++ F+ DAA AI +N
Sbjct: 29 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
FG + + + D +GFA++ F+ DAA AI +N
Sbjct: 36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 75
>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 = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
FG + + + D +GFA++ F+ DAA AI +N
Sbjct: 31 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 70
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 197 LSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG----YGYDHLILSVDWSKS 244
L +DK +GFA++ + DA++ +Q L D + VD++KS
Sbjct: 43 LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
FG + + + D +GFA++ F+ DAA AI +N
Sbjct: 87 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 126
>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 = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
+ I NL + ++ D+ ++GP ++ R +G AY+ +++ DA A +L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 228 NGY 230
+G+
Sbjct: 78 SGF 80
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 10/97 (10%)
Query: 142 PPSLREGPGGKR-------VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFG--PT 192
PP +R+ P K + Y+ RN A+ + + S T++ L +++ G
Sbjct: 26 PPPVRQEPSPKPNNKTPAILYTYSGLRNR-RAAVYVGSFSWWTTDQQLIQVIRSIGVYDV 84
Query: 193 SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
++ + ++ NG KG+A + ++ K ++ L G
Sbjct: 85 VELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG 121
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 20/51 (39%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
D + L+ DLED G + + D+ + KG AY+ F
Sbjct: 24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
I NL + ++ D+ ++GP ++ R +G AY+ +++ DA A +L+G
Sbjct: 23 IRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHLSG 79
Query: 230 Y 230
+
Sbjct: 80 F 80
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 27.7 bits (60), Expect = 5.9, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 25/58 (43%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I + LS +T E + + FG + L D +GF +I FK + K ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 207 KGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST 245
KG++++ F AA AI +NG + ++ W K +
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99
>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 = 27.7 bits (60), Expect = 6.4, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 25/58 (43%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
I + LS +T E + + FG + L D +GF +I FK + K ++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>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 = 27.7 bits (60), Expect = 6.6, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
FG + + + D +GFA++ F+ DAA AI +N
Sbjct: 26 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 65
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
I + NL + + +++L QFG + L D+ KGF ++ + ++ ++AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKL 62
Query: 228 N 228
+
Sbjct: 63 D 63
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 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,452,156
Number of Sequences: 62578
Number of extensions: 219904
Number of successful extensions: 574
Number of sequences better than 100.0: 145
Number of HSP's better than 100.0 without gapping: 119
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 421
Number of HSP's gapped (non-prelim): 167
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
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: 50 (23.9 bits)