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= 032702
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 75.5 bits (184), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 43/95 (45%), Positives = 59/95 (62%), Gaps = 5/95 (5%)
Query: 23 SSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFG 82
S S P R Q PS LFV GLS+ TT+ETL+++F V A+IV RE+G SKGFG
Sbjct: 3 SGSSGPNARSQ--PSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57
Query: 83 FVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPR 117
FV + + E A A E M+ +DG + +++AKP+
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
>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 = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 45/118 (38%), Positives = 61/118 (51%), Gaps = 11/118 (9%)
Query: 10 PRGLRRLFSTSPFSSSLNPPQR---PQAEPST------NLFVSGLSKRTTDETLRDTFSA 60
P R T F P R Q +PS N+F+ L K ++ L DTFSA
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSA 121
Query: 61 FGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQ 118
FG ++ K+V E+G SKG+GFV + T EAA +AIE M+G L+ +FV K R+
Sbjct: 122 FGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 177
>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 = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 45/118 (38%), Positives = 61/118 (51%), Gaps = 11/118 (9%)
Query: 10 PRGLRRLFSTSPFSSSLNPPQR---PQAEPST------NLFVSGLSKRTTDETLRDTFSA 60
P R T F P R Q +PS N+F+ L K ++ L DTFSA
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSA 126
Query: 61 FGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQ 118
FG ++ K+V E+G SKG+GFV + T EAA +AIE M+G L+ +FV K R+
Sbjct: 127 FGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 182
>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 = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 37/82 (45%), Positives = 52/82 (63%), Gaps = 2/82 (2%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
S N+F+ L K ++ L DTFSAFG ++ K+V E+G SKG+GFV + T EAA +AI
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAI 62
Query: 97 EGMDGKFLDGWVIFVEYAKPRQ 118
E M+G L+ +FV K R+
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRK 84
>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 = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 49/79 (62%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
TNL V+ L + T + LR FS+ GEV AK+++ + +G+S G+GFV Y T + A +AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 98 GMDGKFLDGWVIFVEYAKP 116
++G L I V YA+P
Sbjct: 65 TLNGLRLQSKTIKVSYARP 83
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 66.2 bits (160), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 49/79 (62%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
TNL V+ L + T + LR FS+ GEV AK+++ + +G+S G+GFV Y T + A +AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 98 GMDGKFLDGWVIFVEYAKP 116
++G L I V YA+P
Sbjct: 63 TLNGLRLQSKTIKVSYARP 81
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 31 RPQAE--PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
RP +E NL++SGL + T + + D FS FG +++++++ + +G S+G F+++
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 89 LEAAGKAIEGMDG 101
A +AI +G
Sbjct: 140 RSEAEEAITSFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 49/79 (62%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
TNL V+ L + T + LR FS+ GEV AK+++ + +G+S G+GFV Y T + A +AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 98 GMDGKFLDGWVIFVEYAKP 116
++G L I V YA+P
Sbjct: 63 TLNGLRLQSKTIKVSYARP 81
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 31 RPQAE--PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
RP +E NL++SGL + T + + D FS FG +++++++ + +G S+G F+++
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 89 LEAAGKAIEGMDG 101
A +AI +G
Sbjct: 140 RSEAEEAITSFNG 152
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 65.9 bits (159), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 36/81 (44%), Positives = 51/81 (62%), Gaps = 2/81 (2%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
N+F+ L K ++ L DTFSAFG ++ K+V E+G SKG+GFV + T EAA +AIE
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEK 70
Query: 99 MDGKFLDGWVIFVEYAKPRQP 119
M+G L+ +FV K R+
Sbjct: 71 MNGMLLNDRKVFVGRFKSRKE 91
>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 = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 49/79 (62%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
TNL V+ L + T + LR FS+ GEV AK+++ + +G+S G+GFV Y T + A +AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 98 GMDGKFLDGWVIFVEYAKP 116
++G L I V YA+P
Sbjct: 80 TLNGLRLQSKTIKVSYARP 98
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 63.9 bits (154), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 48/81 (59%)
Query: 34 AEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAG 93
A LFV GLS T +++L FS +G++ +VK RE+ S+GFGFV + ++ A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 94 KAIEGMDGKFLDGWVIFVEYA 114
A+ M+GK +DG I V+ A
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQA 89
>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 = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 50/81 (61%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGKFLDGWVIFVEYAKPRQPP 120
+G+ L G I V++ R PP
Sbjct: 70 NGQDLMGQPISVDWCFVRGPP 90
>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 = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 50/81 (61%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 100 DGKFLDGWVIFVEYAKPRQPP 120
+G+ L G I V++ R PP
Sbjct: 86 NGQDLMGQPISVDWCFVRGPP 106
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHA-KIVKHRESGYSKGFGFVKYATLEAAGKA 95
S+ +F+ L ++ L DTFSAFG ++ KI++ ++G SKG+ F+ +A+ +A+ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 96 IEGMDGKFLDGWVIFVEYA 114
IE M+G++L I V YA
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
>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 = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/93 (37%), Positives = 51/93 (54%), Gaps = 2/93 (2%)
Query: 28 PPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYA 87
PP P E T+L V L+ RT+ +TLR F +G V I + R + S+GF FV++
Sbjct: 40 PP--PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97
Query: 88 TLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPP 120
A A++ MDG LDG + V+ A+ +PP
Sbjct: 98 DKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/101 (35%), Positives = 55/101 (54%), Gaps = 6/101 (5%)
Query: 21 PFSSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKG 80
P S NP +P+ L V GLS TT+ LR+ FS +G + IV ++S S+G
Sbjct: 2 PLGSRANP------DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 55
Query: 81 FGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPT 121
F FV + ++ A +A E +G LDG I V+++ ++P T
Sbjct: 56 FAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 96
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/98 (35%), Positives = 55/98 (56%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
SS + R +P+ L V GLS TT+ LR+ FS +G + IV ++S S+GF F
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPT 121
V + ++ A +A E +G LDG I V+++ ++P T
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 99
>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 = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 100 DGKFLDGWVIFVEYAKPRQP 119
+G+ L G I V++ R P
Sbjct: 72 NGQDLMGQPISVDWCFVRGP 91
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 59.7 bits (143), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGKFLDGWVIFVEYAKPRQP 119
+G+ L G I V++ R P
Sbjct: 70 NGQDLMGQPISVDWCFVRGP 89
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 34 AEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAG 93
A+ LFV GL TT ETLR FS +GEVV I+K + + S+GFGFVK+ G
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72
Query: 94 KAI----EGMDGKFLD 105
+ +DG+ +D
Sbjct: 73 TVLASRPHTLDGRNID 88
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 44/79 (55%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
TNL V+ L + T E R F + GE+ K+V+ + +G S G+GFV Y + A KAI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 98 GMDGKFLDGWVIFVEYAKP 116
++G L I V YA+P
Sbjct: 63 TLNGLRLQTKTIKVSYARP 81
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 42/64 (65%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
NL+VSGL K T + L FS +G ++ ++I+ + +G S+G GF+++ A +AI+G
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 99 MDGK 102
++G+
Sbjct: 150 LNGQ 153
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 51/90 (56%)
Query: 30 QRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATL 89
R +P+ L V GLS TT+ LR+ FS +G + IV ++S S+GF FV + +
Sbjct: 39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 90 EAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
+ A +A E +G LDG I V+++ ++P
Sbjct: 99 DDAKEAKERANGMELDGRRIRVDFSITKRP 128
>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 = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 100 DGKFLDGWVIFVEYA 114
+G+ L G I V++
Sbjct: 85 NGQDLMGQPISVDWC 99
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 48/75 (64%), Gaps = 3/75 (4%)
Query: 34 AEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAG 93
+ +++L V GL +TT++ L++ FS FGEV+ ++ K ++G+SKGFGFV++ E
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Query: 94 KAI---EGMDGKFLD 105
K + +DG++ D
Sbjct: 72 KVMSQRHMIDGRWCD 86
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+G+ + T+E + D F+ +GE+ + + R +GY KG+ V+Y T + A A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGKFLDGWVIFVEYA 114
+G+ L G I V++
Sbjct: 70 NGQDLMGQPISVDWC 84
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 36/106 (33%), Positives = 55/106 (51%), Gaps = 1/106 (0%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
SS + Q+ ++FV LS T E ++ F+ FG + A++VK +G SKG+GF
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNTN 129
V + A AI+ M G++L G I +A R+PP S +N
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT-RKPPAPKSTYESN 106
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
NL+V L DE LR FS FG + AK++ E G SKGFGFV +++ E A KA+
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVT 73
Query: 98 GMDGKFLDGWVIFVEYAKPRQ 118
M+G+ + ++V A+ ++
Sbjct: 74 EMNGRIVATKPLYVALAQRKE 94
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 53/94 (56%), Gaps = 1/94 (1%)
Query: 23 SSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFG 82
SS + P R +A+ + + V+ LS+ T + L++ F FG + + K + +G SKGF
Sbjct: 2 SSGSSGPNR-RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 83 FVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKP 116
F+ + E A +AI G+ G D ++ VE+AKP
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWAKP 94
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 48/88 (54%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
E T+L V L+ RT+ +TLR F +G V I + R + S+GF FV++ A
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 93 GKAIEGMDGKFLDGWVIFVEYAKPRQPP 120
A++ MDG LDG + V+ A+ +PP
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYGRPP 153
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 56.2 bits (134), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 45/82 (54%)
Query: 35 EPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGK 94
+ TNL V+ L + T + + F + G++ K+V+ + +G S G+GFV Y+ A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 95 AIEGMDGKFLDGWVIFVEYAKP 116
AI ++G L I V YA+P
Sbjct: 62 AINTLNGLKLQTKTIKVSYARP 83
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 42/64 (65%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
NL+VSGL K + + + FS +G ++ ++I+ + +G S+G GF+++ A +AI+G
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 99 MDGK 102
++G+
Sbjct: 152 LNGQ 155
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 45/82 (54%)
Query: 35 EPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGK 94
+ TNL V+ L + T + + F + G++ K+V+ + +G S G+GFV Y+ A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 95 AIEGMDGKFLDGWVIFVEYAKP 116
AI ++G L I V YA+P
Sbjct: 62 AINTLNGLKLQTKTIKVSYARP 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 34/97 (35%), Positives = 52/97 (53%), Gaps = 1/97 (1%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
SS + Q+ ++FV LS T E ++ F+ FG++ A++VK +G SKG+GF
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGF 61
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPP 120
V + A AI M G++L G I +A R+PP
Sbjct: 62 VSFYNKLDAENAIVHMGGQWLGGRQIRTNWAT-RKPP 97
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 30 QRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATL 89
Q+ ++ + NLFV L+ DETLR+ F F + ++ ++G S+G+GFV + +
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 90 EAAGKAIEGMDGKFLDG 106
+ A A++ M G+ L+G
Sbjct: 140 DDAQNAMDSMQGQDLNG 156
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V L K T++ L+ F G + + KI+ + + + + FV+Y A A++ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIALQTL 61
Query: 100 DGKFLDGWVIFVEYAKPRQPPT 121
+GK ++ ++ + +A Q +
Sbjct: 62 NGKQIENNIVKINWAFQSQQSS 83
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 48/88 (54%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
SS + R +P+ L V GLS TT+ LR+ FS +G + IV ++S S+GF F
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFV 111
V + ++ A +A E +G LDG I V
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRRIRV 89
>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 = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S P+ P E LF+ GLS TTDE+LR F +G + +++ + S+GFGF
Sbjct: 2 SKSESPKEP--EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
V YAT+E A+ K +DG V+ + A R+ P + T
Sbjct: 60 VTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLT 103
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 151 VTFDDHDSVDKIV 163
>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 = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S P+ P E LF+ GLS TTDE+LR F +G + +++ + S+GFGF
Sbjct: 1 SKSESPKEP--EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 58
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
V YAT+E A+ K +DG V+ + A R+ P + T
Sbjct: 59 VTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLT 102
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 90 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 149
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 150 VTFDDHDSVDKIV 162
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S P+ P E LF+ GLS TTDE+LR F +G + +++ + S+GFGF
Sbjct: 3 SKSESPKEP--EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
V YAT+E A+ K +DG V+ + A R+ P + T
Sbjct: 61 VTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLT 104
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 92 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 151
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 152 VTFDDHDSVDKIV 164
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S P+ P E LF+ GLS TTDE+LR F +G + +++ + S+GFGF
Sbjct: 2 SKSESPKEP--EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 84 VKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
V YAT+E A+ K +DG V+ + A R+ P + T
Sbjct: 60 VTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLT 103
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 151 VTFDDHDSVDKIV 163
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
++FV + T+E L+D FS G VV ++V RE+G KG+GF +Y E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 99 MDGKFLDGWVIFVEYA 114
++G+ G + V+ A
Sbjct: 70 LNGREFSGRALRVDNA 85
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 5/88 (5%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
T +FV GL TTD +LR F FG++ A ++ R++G S+G+GFV A AA +A +
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 98 G----MDGKFLDGWVIFVEYAKPRQPPT 121
+DG+ + + ++ AKPR T
Sbjct: 78 DPNPIIDGRKANVNLAYLG-AKPRSLQT 104
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 52/100 (52%), Gaps = 3/100 (3%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
P+ P E LF+ GLS TTDE+LR F +G + +++ + S+GFGFV YAT
Sbjct: 5 PKEP--EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 62
Query: 89 LEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
+E A+ K +DG V+ + A R+ P + T
Sbjct: 63 VEEVDAAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLT 101
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 89 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 148
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 149 VTFDDHDSVDKIV 161
>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 = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 44/76 (57%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
NLFV L+ DETLR+ F F + ++ ++G S+G+GFV + + + A A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 99 MDGKFLDGWVIFVEYA 114
M G+ L+G + + +A
Sbjct: 63 MQGQDLNGRPLRINWA 78
>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 = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 1/89 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ GLS TTDE+LR F +G + +++ + S+GFGFV YAT+E A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 100 DGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
K +DG V+ + A R+ P + T
Sbjct: 69 PHK-VDGRVVEPKRAVSREDSQRPGAHLT 96
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 25 SLNPPQRPQAEPSTN-LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGF 83
S QRP A + +FV G+ + T + LRD F +G++ +I+ R SG +GF F
Sbjct: 84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 143
Query: 84 VKYATLEAAGKAI 96
V + ++ K +
Sbjct: 144 VTFDDHDSVDKIV 156
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 42/64 (65%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
NL+VSGL K + + + FS +G ++ ++I+ + +G S+G GF+++ A +AI+G
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 99 MDGK 102
++G+
Sbjct: 63 LNGQ 66
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
NLF+ L + TD L TF FG V+ AK+ +++ SK FGFV + ++A AI+
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 98 GMDG 101
M+G
Sbjct: 101 AMNG 104
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 28 PPQRPQAEPST--NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVK 85
PP + EP NL V+ + + LR F +G + KIV RE+ S+G+GFVK
Sbjct: 31 PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 86 YATLEAAGKAIEGMDG 101
+ + +A +AI G++G
Sbjct: 91 FQSGSSAQQAIAGLNG 106
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 1/91 (1%)
Query: 27 NPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
N Q+ A P L+V L T++ LR F FG + +++ E+G SKG+GF+ +
Sbjct: 17 NNLQKGSAGP-MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 87 ATLEAAGKAIEGMDGKFLDGWVIFVEYAKPR 117
+ E A KA+E ++G L G + V + R
Sbjct: 76 SDSECAKKALEQLNGFELAGRPMKVGHVTER 106
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
+A+ LF+ GL++ T ++ L+ F G + ++K R S S+GF F+ + A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADA 61
Query: 93 GKAIEGMDGKFLDGWVIFVEYAK 115
A + M+GK L G I VE AK
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAK 84
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 49/92 (53%), Gaps = 4/92 (4%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESG---YSKGFGFVKYATLEAAG 93
S+ LF+ L+ TT+ETL+ FS G + I K + S GFGFV+Y E A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 94 KAIEGMDGKFLDGWVIFVEYA-KPRQPPTLPS 124
KA++ + G +DG + V + + +P + PS
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKPASGPS 96
>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 = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY---ATLEAAG 93
S +F+ GL+ TT++ LR+ F +G V KI+K +G S+GFGF+ + ++++
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 94 KAIEGMDGKFLD 105
K +DGK +D
Sbjct: 63 KTQHILDGKVID 74
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 31 RPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLE 90
R + + + +FV G+ + + FS +G ++ A+++ +++G S+GFGFV Y + +
Sbjct: 81 RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140
Query: 91 AAGKAIEGMDGKFLD--GWVIFVEYAKPRQ 118
A + + KF+D I ++ A+PR
Sbjct: 141 AVDRVCQ---NKFIDFKDRKIEIKRAEPRH 167
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
N++V L T E +++ FS FG+V + K++ RE+ KGFGFV+ E+ +AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 99 MDGKFLDGWVIFVEYAKPRQ 118
+D G I V A P++
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 31 RPQAEP--STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
RP E TNL+V+ L + TD+ L F +G +V I++ + +G +G FV+Y
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 89 LEAAGKAIEGMDGKFLDG 106
E A +AI ++ +G
Sbjct: 141 REEAQEAISALNNVIPEG 158
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+TNL V+ L + TD L F A G + +I++ ++GYS G+ FV + + + +AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 97 EGMDGKFLDGWVIFVEYAKP 116
+ ++G + + V YA+P
Sbjct: 63 KVLNGITVRNKRLKVSYARP 82
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 48/84 (57%), Gaps = 7/84 (8%)
Query: 33 QAEP-STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
Q+ P + ++ G++ TD+ +R TFS FG+++ ++ KG+ FV+++T E+
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHES 73
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAK 115
A AI ++G ++G V+ + K
Sbjct: 74 AAHAIVSVNGTTIEGHVVKCYWGK 97
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 31 RPQAE--PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
RP E TNL+V+ L + TD+ L F +G +V I++ + +G +G FV+Y
Sbjct: 92 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 151
Query: 89 LEAAGKAIEGMDGKFLDG 106
E A +AI ++ +G
Sbjct: 152 REEAQEAISALNNVIPEG 169
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 44/80 (55%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+TNL V+ L + TD L F A G + +I + ++GYS G+ FV + + + +AI
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 97 EGMDGKFLDGWVIFVEYAKP 116
+ ++G + + V YA+P
Sbjct: 74 KVLNGITVRNKRLKVSYARP 93
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE-- 97
+F+ GLS TT + L+D FS FGEVV + +G S+GFGFV + E+ K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 98 --GMDGKFLD 105
++GK +D
Sbjct: 62 EHKLNGKVID 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 = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 31 RPQAE--PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYAT 88
RP E TNL+V+ L + TD+ L F +G +V I++ + +G +G FV+Y
Sbjct: 5 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 64
Query: 89 LEAAGKAIEGMDGKFLDG 106
E A +AI ++ +G
Sbjct: 65 REEAQEAISALNNVIPEG 82
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 48.9 bits (115), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 47/81 (58%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
S+ L+V L T++ LR F FG++ + ++K ++G SKG+GF+ ++ E A +A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 97 EGMDGKFLDGWVIFVEYAKPR 117
E ++G L G + V + R
Sbjct: 65 EQLNGFELAGRPMRVGHVTER 85
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 26 LNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVK 85
L P +F+ GLS +TT E LR+ F FGEV +++ + S+GFGFV
Sbjct: 14 LVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
Query: 86 YATLEAAGKAI----EGMDGKFLDGWVIFVEYAKPR 117
+ K + +D K +D V F A+P+
Sbjct: 74 FMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>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 = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ GL D+ +++ ++FG + +VK +G SKG+ F +Y + +AI G+
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 100 DGKFLDGWVIFVEYA 114
+G L + V+ A
Sbjct: 177 NGMQLGDKKLLVQRA 191
>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 = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ GL D+ +++ ++FG + +VK +G SKG+ F +Y + +AI G+
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 100 DGKFLDGWVIFVEYA 114
+G L + V+ A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V GL++ D+ L F FG++ +I E+ +GF FV++ E A AI+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 100 DGKFLDGWVIFVEYAKP 116
+ L G I V AKP
Sbjct: 75 NESELFGRTIRVNLAKP 91
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ GL D+ +++ ++FG + +VK +G SKG+ F +Y + +AI G+
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 100 DGKFLDGWVIFVEYA 114
+G L + V+ A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 35 EPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGK 94
E + FV GLS T+ + L+D F+ FGEVV I +G S+GFGF+ + + K
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 95 AIEGMDGKFLDGWVI 109
++ + + LDG VI
Sbjct: 69 VLDQKEHR-LDGRVI 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+TNL V+ L + TD L F A G + +I++ ++GYS G+ FV + + + +AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 97 EGMDGKFLDGWVIFVEYAKP 116
+ ++G + + V YA+P
Sbjct: 63 KVLNGITVRNKRLKVSYARP 82
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 35/63 (55%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
NLF+ L + D+ L F FG VV AK+ +++ SK FGFV Y +A AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 99 MDG 101
M+G
Sbjct: 87 MNG 89
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 32 PQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
P+ + +F L+ R L D FSA G+V +I+ R S SKG +V++ +++
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAK 115
AI G+ G+ L G I V+ ++
Sbjct: 80 VPLAI-GLTGQRLLGVPIIVQASQ 102
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
Q + LFV+ ++ TT+ LR F +G + +V + SG +G+ F++Y
Sbjct: 98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157
Query: 93 GKAIEGMDGKFLDGWVIFVEYAKPR 117
A + DGK +DG + V+ + R
Sbjct: 158 HSAYKHADGKKIDGRRVLVDVERGR 182
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV L+ T+E L FS FG++ K +K + F+ + + A KA+E M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 100 DGKFLDGWVIFVEYAKP 116
+GK L+G I + +AKP
Sbjct: 66 NGKDLEGENIEIVFAKP 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 45/80 (56%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+ + + ++ +++ F +GE+ + + R +G+SKG+ V+Y T + A A E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 100 DGKFLDGWVIFVEYAKPRQP 119
+G + G I V++ + P
Sbjct: 89 NGAEIMGQTIQVDWCFVKGP 108
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ GL D+ +++ ++FG + +VK +G SKG+ F +Y + +AI G+
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 100 DGKFLDGWVIFVEYA 114
+G L + V+ A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>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 = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
Q + LFV+ ++ TT+ LR F +G + +V + SG +G+ F++Y
Sbjct: 98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157
Query: 93 GKAIEGMDGKFLDGWVIFVEYAKPR 117
A + DGK +DG + V+ + R
Sbjct: 158 HSAYKHADGKKIDGRRVLVDVERGR 182
>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 = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 46/84 (54%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV+ + + ++ +++ F +GE+ + + R +G+SKG+ V+Y T + A A E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 100 DGKFLDGWVIFVEYAKPRQPPTLP 123
+G + G I V++ + P +
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVK 158
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 12 GLRRLFSTSPFSSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVK 71
G+ + T P ++ + E LF+ GLS TT+E+LR+ + +G++ +++
Sbjct: 7 GMEKTLETVPLER-----KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 61
Query: 72 HRESGYSKGFGFVKYATLEAAGKAI----EGMDGKFLD 105
S S+GFGFV ++++ A+ +DG+ ++
Sbjct: 62 DPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVE 99
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 31 RPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLE 90
+ Q + TNL++S L ++ L + FG+V+ +I++ SG S+G GF + + E
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTE 77
Query: 91 AAGKAIEGMDGKFL 104
I +GKF+
Sbjct: 78 KCEAVIGHFNGKFI 91
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V GL++ D+ L F FG++ +I E+ +GF FV++ E A AI+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 100 DGKFLDGWVIFVEYAK 115
+ L G I V AK
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V GL++ D+ L F FG++ +I E+ +GF FV++ E A AI+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 100 DGKFLDGWVIFVEYAK 115
+ L G I V AK
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 40/84 (47%)
Query: 32 PQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
P + L V L+ RT+ ++LR F +G V I + + +GF FV++
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAK 115
A A MDG LDG + V+ A+
Sbjct: 68 AQDAEAAMDGAELDGRELRVQVAR 91
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI- 96
+F+ GLS +TT E LR+ F FGEV +++ + S+GFGFV + K +
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 97 ---EGMDGKFLDGWVIF 110
+D K +D V F
Sbjct: 61 QSRHELDSKTIDPKVAF 77
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ +SK+ T+ +R FS+FG++ +I++ + G S+G FV + T A AI+ M
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAM 168
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 22 FSSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESG--YSK 79
+ +L+ P +P + + +FV + + +++ LR+ F +G V +++ R SK
Sbjct: 1 MNGTLDHPDQPDLD-AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSK 59
Query: 80 GFGFVKYATLEAAGKA 95
G FV + T +AA +A
Sbjct: 60 GCCFVTFYTRKAALEA 75
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 30 QRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATL 89
++ A LF+ +SK+ T+ +R FS+FG++ +I++ + G S+G FV + T
Sbjct: 88 EKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTR 146
Query: 90 EAAGKAIEGM 99
A AI+ M
Sbjct: 147 AMAQTAIKAM 156
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESG--YSKGFGFVKYATLEAAGK 94
+ +FV + + +++ LR+ F +G V +++ R SKG FV + T +AA +
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 95 A 95
A
Sbjct: 63 A 63
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 47/97 (48%), Gaps = 5/97 (5%)
Query: 21 PFSSSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKG 80
P S +N + Q + L VS + R D LR F FG+++ +I+ E G SKG
Sbjct: 16 PRGSHMNTENKSQPK---RLHVSNIPFRFRDPDLRQMFGQFGKILDVEII-FNERG-SKG 70
Query: 81 FGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPR 117
FGFV + A +A E + G ++G I V A R
Sbjct: 71 FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
S+ +FV L T + L+D F+ G V++A I E+G SKG G VK+ + E A +A
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERAC 62
Query: 97 EGMDGKFLDGWVIFVEYAKPRQPPT 121
M+G L G I V + P+
Sbjct: 63 RMMNGMKLSGREIDVRIDRNASGPS 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 38/75 (50%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V GL++ D+ L F FG++ +I E+ +GF FV++ E A AI+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 100 DGKFLDGWVIFVEYA 114
+ L G I V A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
S+ L++ GL TTD+ L +G++V K + + + KG+GFV + + AA KA+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 97 EGM 99
+
Sbjct: 65 TAL 67
>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 = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 39/66 (59%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
PS +++ + T+E + D S G V++ K++ ++G SKG+ F+++ LE++ A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 96 IEGMDG 101
+ ++G
Sbjct: 63 VRNLNG 68
>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 = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 38/75 (50%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V GL++ D+ L F FG++ +I E+ +GF FV++ E A AI+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 100 DGKFLDGWVIFVEYA 114
+ L G I V A
Sbjct: 65 NESELFGRTIRVNLA 79
>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 = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
++V+ + + +D+ ++ F AFG++ A + + +G KG+GF++Y +++ A+ M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 100 DGKFLDGWVIFVEYAKPRQPP 120
+ L G ++ K PP
Sbjct: 188 NLFDLGGQ--YLRVGKAVTPP 206
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 36/74 (48%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+ ++V + ++T+R F+ FG + + + KGF FV+Y EAA A+E
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 98 GMDGKFLDGWVIFV 111
M+ L G I V
Sbjct: 89 QMNSVMLGGRNIKV 102
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 37/61 (60%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
++V GL ++ ++ L + F G VV+ + K R +G +G+GFV++ + E A AI+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 100 D 100
D
Sbjct: 78 D 78
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+ +FV L T + L+D F+ G V++A I E+G SKG G VK+ + E A +A
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERAC 65
Query: 97 EGMDGKFLDGWVIFVEYAKPRQPPT 121
M+G L G I V + P+
Sbjct: 66 RMMNGMKLSGREIDVRIDRNASGPS 90
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV L+K+ +++ +R F AFG + I++ + G SKG FVKY++ A AI +
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINAL 76
Query: 100 DG 101
G
Sbjct: 77 HG 78
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L VS + R D LR F FG+++ +I+ E G SKGFGFV + A +A E +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII-FNERG-SKGFGFVTFENSADADRAREKL 75
Query: 100 DGKFLDGWVIFVEYAKPR 117
G ++G I V A R
Sbjct: 76 HGTVVEGRKIEVNNATAR 93
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 39/66 (59%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
PS +++ + T+E + D S G V++ K++ ++G SKG+ F+++ LE++ A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 96 IEGMDG 101
+ ++G
Sbjct: 61 VRNLNG 66
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI-- 96
+F+ LS + +E L + FG++ + ++V H ++ +SKG F ++ T EAA K +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 97 -----EGMDGKFLDGWVIFVEYAKPR 117
EG G LDG + V+ A R
Sbjct: 77 ASLEAEG-GGLKLDGRQLKVDLAVTR 101
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
+A ++V+ + + +D+ ++ F AFG++ + + +G KG+GF++Y +++
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 93 GKAIEGMDGKFLDGWVIFVEYAKPRQPP 120
A+ M+ L G ++ K PP
Sbjct: 166 QDAVSSMNLFDLGGQ--YLRVGKAVTPP 191
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
++V + ++T+R F+ FG + + + KGF FV+Y EAA A+E
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 98 GMDGKFLDGWVIFV 111
M+ L G I V
Sbjct: 74 QMNSVMLGGRNIKV 87
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
++FV LS T + F+ FG + A++VK +G SKG+GFV + A AI+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 99 MDGKFLDGWVIFVEYAKPRQP 119
M G++L G I +A R+P
Sbjct: 68 MGGQWLGGRQIRTNWAT-RKP 87
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 39/66 (59%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
PS +++ + T+E + D S G V++ K++ ++G SKG+ F+++ LE++ A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 96 IEGMDG 101
+ ++G
Sbjct: 62 VRNLNG 67
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
LF+ +SK+ T+ +R FS+FG++ +I++ + G S+G FV + T A AI+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKA 155
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFG--EVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
++V S TTD+ L + G +VV K ++R +G SKG+ V A+ + K +E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 98 GMDGKFLDG 106
+ GK L+G
Sbjct: 118 LLPGKVLNG 126
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+SGL T E L + A G V ++V +R +G KG +V+Y A +A+ M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 100 DGKFLDGWVIFV 111
DG + +I V
Sbjct: 79 DGMTIKENIIKV 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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%)
Query: 34 AEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAG 93
A + ++VS L T+ L FS +G+VV I+K +++ SKG F+ + ++A
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 94 KAIEGMDGKFLDGWVI 109
++ K L G VI
Sbjct: 73 NCTRAINNKQLFGRVI 88
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
Q E +FV L R +E L + F G + I K RE G K FGFV + E+
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESV 70
Query: 93 GKAIEGMDGKFLDGWVIFV 111
AI ++G L G I V
Sbjct: 71 SYAIALLNGIRLYGRPINV 89
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
LFV L K+ TDE +R F FG + +++ + G SKG FVK+ T A AI
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAI 70
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKI-VKHRESGYSKGFGFVKYATLEAAGKAI 96
T + + L++ T + + + FS +G++ + V+ SKG+ +V++ + A KA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 97 EGMDGKFLDG 106
+ MDG +DG
Sbjct: 65 KHMDGGQIDG 74
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGE-VVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
+ +L++ L + + F+ GE V+ KI+++R +G G+ FV++A L A K
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 96 IEGMDGKFLDG 106
+ ++GK L G
Sbjct: 69 LHKINGKPLPG 79
>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 = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
P+T +FV G+ R + +R F+ +G V KI+ R +G SKG+GFV + K
Sbjct: 9 PNT-VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 66
Query: 96 IE 97
+E
Sbjct: 67 VE 68
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 34/57 (59%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
++V+ + + +D+ ++ F AFG++ + + +G KG+GF++Y +++ A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Score = 32.3 bits (72), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
++V + ++T+R F+ FG + + KGF FV+Y EAA A+E
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 98 GMDGKFLDGWVIFV 111
+ L G I V
Sbjct: 73 QXNSVXLGGRNIKV 86
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
P+T +FV G+ R + +R F+ +G V KI+ R +G SKG+GFV + K
Sbjct: 9 PNT-VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 66
Query: 96 IE 97
+E
Sbjct: 67 VE 68
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
P+T +FV G+ R + +R F+ +G V KI+ R +G SKG+GFV + K
Sbjct: 10 PNT-VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 67
Query: 96 IE 97
+E
Sbjct: 68 VE 69
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 47/93 (50%), Gaps = 2/93 (2%)
Query: 24 SSLNPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRE-SGYSKGFG 82
SS + Q P+ + ++ + V + + +R+ FS FGE+ ++ K +G +GFG
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 83 FVKYATLEAAGKAIEGM-DGKFLDGWVIFVEYA 114
FV + T + A KA + L G + +E+A
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA 94
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+FV GLS TT E ++ F FG+V A ++ + + +GFGFV + + + K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV LS +++E L FSA+G + + KGF FV + E A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 100 DGKFLDGWVIFV 111
DG+ G ++ V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+FV GLS T +E +R+ F FGEV ++ ++ +GF F+ + E K +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LF+ L + T++ +R F +G+V+ I+K+ +GFV AA AI +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 100 DGKFLDGWVIFVEYAKPRQPPT 121
L G I VE +K + +
Sbjct: 63 HHYKLHGVNINVEASKNKSKAS 84
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+T LFV + L + F FG + KI+ GF FV++ E+A KAI
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 82
Query: 97 EGMDGKFLDGWVIFVEYAK 115
E + GK + V Y+K
Sbjct: 83 EEVHGKSFANQPLEVVYSK 101
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+FV GLS T +E +R+ F FGEV ++ ++ +GF F+ + E K +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
+ LF+ + + ++ L+ F FG++ ++K R +G KG F+ Y E+A KA
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 42/87 (48%)
Query: 27 NPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
N Q + S L+V LS TT+E + + FS G++ + + + GF FV+Y
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 87 ATLEAAGKAIEGMDGKFLDGWVIFVEY 113
+ A A+ ++G LD +I ++
Sbjct: 89 YSRADAENAMRYINGTRLDDRIIRTDW 115
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 33 QAEPSTNLF-VSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
Q +P+ L V+ L T + + FG + +V +G SKG+GF +Y ++
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAKPRQ 118
A +A + GK L ++V + Q
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQ 176
Score = 29.6 bits (65), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 74 ESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
+ G KGF ++Y T E A +A + DG L G + V + P P
Sbjct: 221 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266
>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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 33 QAEPSTNLF-VSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
Q +P+ L V+ L T + + FG + +V +G SKG+GF +Y ++
Sbjct: 88 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 147
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAKPRQ 118
A +A + GK L ++V + Q
Sbjct: 148 AARAKSDLLGKPLGPRTLYVHWTDAGQ 174
Score = 29.6 bits (65), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 74 ESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
+ G KGF ++Y T E A +A + DG L G + V + P P
Sbjct: 219 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 264
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 33 QAEPSTNLF-VSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
Q +P+ L V+ L T + + FG + +V +G SKG+GF +Y ++
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAKPRQ 118
A +A + GK L ++V + Q
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQ 176
Score = 29.6 bits (65), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 74 ESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
+ G KGF ++Y T E A +A + DG L G + V + P P
Sbjct: 221 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L V LS ++E L FS FG V A +V + G + G GFV++A A KA+E
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157
Query: 100 -DGKFL 104
DG FL
Sbjct: 158 GDGAFL 163
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
LFV L T+E + F +GE I + R GFGF++ + A A
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKA 76
Query: 98 GMDGKFLDGWVIFVEYA 114
+DG L + + +A
Sbjct: 77 ELDGTILKSRPLRIRFA 93
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
+T LFV + L + F FG + KI+ GF FV++ E+A KAI
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 55
Query: 97 EGMDGKFLDGWVIFVEYAK 115
E + GK + V Y+K
Sbjct: 56 EEVHGKSFANQPLEVVYSK 74
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
+ LFV + + ++ L+ F FG + ++K R +G KG F+ Y ++A KA
Sbjct: 15 AIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 27 NPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
N Q + S L+V LS TT+E + + FS G++ I+ + + GF FV+Y
Sbjct: 8 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI-IMGLDKMKTACGFCFVEY 66
Query: 87 ATLEAAGKAIEGMDGKFLDGWVI 109
+ A A+ ++G LD +I
Sbjct: 67 YSRADAENAMRYINGTRLDDRII 89
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L+V L T++E + F+ ++ K R+ + FV ++ E A +A++ +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD------YAFVHFSNREDAVEAMKAL 71
Query: 100 DGKFLDGWVIFVEYAKP 116
+GK LDG I V AKP
Sbjct: 72 NGKVLDGSPIEVTLAKP 88
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.4 bits (80), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
+FV G+ + LR+ F FG V ++ E +GFGF+ + ++ +A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 100 DGKFLDGWVIFVEYAKPR 117
+ G + V+ A+PR
Sbjct: 72 HFHDIMGKKVEVKRAEPR 89
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV L+ T+E L +FS FG++ K +K + FV + AA KA++ M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 100 DGK 102
+GK
Sbjct: 70 NGK 72
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
T L+V GL T+ LR+ F FGE+ +V+ ++ F+++AT +AA A E
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 10/90 (11%)
Query: 37 STNLFVSGLSKRTTDET-LRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
++ +F+ L+ ++ + FS +G++V + KGF FV+Y A A
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAA 66
Query: 96 IEGMDGKFLDGWVIFVEY-AKPRQPPTLPS 124
+ G DG+ + G V+ + A+P+ + PS
Sbjct: 67 VAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
+FV +S T + LR F G V+ +VK + FV A AI +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 100 DGKFLDGWVIFVEYAKPRQPPTLPS 124
+GK + G I VE + Q + PS
Sbjct: 64 NGKEVKGKRINVELSTKGQKKSGPS 88
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 33 QAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA 92
+A P+T L+V GL T+ L F FG + VK F +++Y +L+AA
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK------GDSFAYIQYESLDAA 66
Query: 93 GKAIEGMDGKFLDG 106
A M G L G
Sbjct: 67 QAACAKMRGFPLGG 80
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 35 EPSTN--LFVSGLSKRTTDETLRDTFSAFGEVVHAK--------IVKHRESGYSKGFGFV 84
E S N ++V GL+ T + L D F G V K I +E+G KG V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 85 KYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
Y A A+E DGK G + V A+ + P
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 34/53 (64%), Gaps = 3/53 (5%)
Query: 66 HAKIVKHRESGYSKGFGFVKYATLEAAG--KAIEGMDGKF-LDGWVIFVEYAK 115
+ +++K +++ ++GF F++ +T+EAA + ++ + +DG I VE+AK
Sbjct: 54 NVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAK 106
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
LFV L+K+ ++E + F FG + +++ + G SKG FVK+++ A AI +
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 100 DG 101
G
Sbjct: 77 HG 78
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAK--------IVKHRESGYSKGFGFVKYATLEA 91
+FV GL + T E++ D F G + K + RE+G KG V + +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAKPR 117
A AI+ DGK G I V +A R
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRR 95
>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 = 33.5 bits (75), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFG-EVVHAKIVKHRESGYSKGFGFVKYATLEAAGKA 95
S + + L + T++ +R + G + ++++++ SG S+GF FV+++ L+ A +
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW 60
Query: 96 IEGMDGKF-LDGWVIFVEYAKPR 117
+E + G + + Y+ P+
Sbjct: 61 MEANQHSLNILGQKVSMHYSDPK 83
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+ LFV L T+E +R F +G+ ++ H++ KGFGF++ T A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKD----KGFGFIRLETRTLAEIAKV 76
Query: 98 GMDGKFLDGWVIFVEYA 114
+D L G + V +A
Sbjct: 77 ELDNMPLRGKQLRVRFA 93
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 28 PPQRPQAEPSTNL-----FVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFG 82
PPQ AE + +V + +T + L FS+ G + I+ + SG+ KG+
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 83 FVKYATLEAAGKAIEGMDGKFLDGWVIFV 111
++++A + A+ MD G I V
Sbjct: 82 YIEFAERNSVDAAV-AMDETVFRGRTIKV 109
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.7 bits (73), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%)
Query: 52 ETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLD 105
+ L FS G+VV+ + +G +KGF FV+ ++ A K I+ GK LD
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 32.7 bits (73), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%)
Query: 52 ETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLD 105
+ L FS G+VV+ + +G +KGF FV+ ++ A K I+ GK LD
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 32.7 bits (73), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAK--------IVKHRESGYSKGFGFVKYATLEA 91
+FV GL + T E++ D F G + K + RE+G KG V + +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 92 AGKAIEGMDGKFLDGWVIFVEYA 114
A AI+ DGK G I V +A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 32 PQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEA 91
P ++V L + + D F +G + + K+R G F FV++
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGG--PPFAFVEFEDPRD 73
Query: 92 AGKAIEGMDGKFLDGWVIFVEYAK 115
A A+ G DG DG+ + VE+ +
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEFPR 97
>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 = 32.0 bits (71), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+ LFV L T+E +R F +G+ ++ H++ KGFGF++ T A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKD----KGFGFIRLETRTLAEIAKV 69
Query: 98 GMDGKFLDGWVIFVEYA 114
+D L G + V +A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 43 SGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGK 102
+ L K++ ET+ FS +G V + KG+ FV+Y+ A A+ G +G+
Sbjct: 37 TALVKKSDVETI---FSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGR 85
Query: 103 FLDGWVIFVEYAKPRQP 119
L G + + A +P
Sbjct: 86 VLAGQTLDINMAGEPKP 102
>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 = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESG--YSKGFGFVKYATLEAAGK 94
+ +FV + + +++ LR+ F +G V +++ R SKG FV + T +AA +
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 95 A 95
A
Sbjct: 63 A 63
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 29.6 bits (65), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
++V L L FS +G + I ++ GF FV++ A A+ G+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 100 DGKFLDGWVIFVEYA 114
DGK + G + VE +
Sbjct: 58 DGKVICGSRVRVELS 72
>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 = 0.63, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%)
Query: 36 PSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
P +LFV L+ D L + F V ++G SKG+GFVK+
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKF 58
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 29.3 bits (64), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAI 96
S+ +FV + T++ LR+ FS +G+V+ I K + F FV +A + A +++
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIA-QSL 58
Query: 97 EGMDGKFLDGWVIFVEYAKPRQ 118
G D + G + + A+P+
Sbjct: 59 CGED-LIIKGISVHISNAEPKH 79
>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 = 29.3 bits (64), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 11/89 (12%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
+++V + T E L F G V I+ + SG+ KGF +++++ E+ ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 99 MDGKFLDGWVIFVEYAKPRQPPTLPSQNN 127
+D G RQ +P + N
Sbjct: 66 LDESLFRG----------RQIKVIPKRTN 84
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.3 bits (64), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 5/87 (5%)
Query: 27 NPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
+P + + L LS T++ L++ F + + ++V + G SKG ++++
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKEVFE---DALEIRLVS--QDGKSKGIAYIEF 60
Query: 87 ATLEAAGKAIEGMDGKFLDGWVIFVEY 113
+ A K +E G +DG + + Y
Sbjct: 61 KSEADAEKNLEEKQGAEIDGRSVSLYY 87
>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 = 28.9 bits (63), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 11/89 (12%)
Query: 39 NLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEG 98
+++V + T E L F G V I+ + SG+ KGF +++++ E+ ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 99 MDGKFLDGWVIFVEYAKPRQPPTLPSQNN 127
+D G RQ +P + N
Sbjct: 67 LDESLFRG----------RQIKVIPKRTN 85
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 53 TLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLD 105
+ FS FG++ + E G +KG+ F++YA+ A A++ DG LD
Sbjct: 23 VIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 53 TLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLD 105
+ FS FG++ + E G +KG+ F++YA+ A A++ DG LD
Sbjct: 37 VIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/82 (18%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGE--VVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+ + ++ T +++ S + V + +++K +++ ++GF FV+ ++ A + ++
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 98 GMDGKF----LDGWVIFVEYAK 115
+ +DG I V++AK
Sbjct: 72 ILQSLHPPLKIDGKTIGVDFAK 93
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L++ LS T + LR F + +++ G+ FV Y A +AIE +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETL 64
Query: 100 DGKF-LDGWVIFVEYAKPRQ 118
GK L G ++ V+Y+ ++
Sbjct: 65 SGKVELHGKIMEVDYSVSKK 84
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
+ VSGL + + L+D G+V +A + K G G V+Y E A+ +
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKL 70
Query: 100 D 100
D
Sbjct: 71 D 71
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L L + T + L++ F E+ ++V G SKG ++++ T A K E
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEI---RLVSK--DGKSKGIAYIEFKTEADAEKTFEEK 150
Query: 100 DGKFLDGWVIFVEY 113
G +DG I + Y
Sbjct: 151 QGTEIDGRSISLYY 164
>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 = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 40 LFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIEGM 99
L LS T++ L++ F + + ++V G SKG ++++ + A K +E
Sbjct: 102 LLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 100 DGKFLDGWVIFVEY 113
G +DG + + Y
Sbjct: 157 QGAEIDGRSVSLYY 170
>pdb|1WTD|A Chain A, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Dna- Free Form
pdb|1WTD|B Chain B, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Dna- Free Form
pdb|1WTE|A Chain A, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Complexed With Cognate Dna
pdb|1WTE|B Chain B, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Complexed With Cognate Dna
Length = 272
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 57 TFSAFGEVVHAKIVKHRESGYSKGFG 82
+ + F E+V A I KH +G+ GFG
Sbjct: 48 SLNDFDELVEAIIAKHLMTGHDTGFG 73
>pdb|2HLY|A Chain A, The Crystal Structure Of Genomics Apc5867
Length = 207
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 72 HRESGYSKGFGFVKYATLEAAGKAIEGMDGKFLDG 106
HRE GY G G + +EA G AI+ M F +G
Sbjct: 75 HREDGYVTGAGENFHCWVEADGWAIDFMAPAFSEG 109
>pdb|4AAH|A Chain A, Methanol Dehydrogenase From Methylophilus W3a1
pdb|4AAH|C Chain C, Methanol Dehydrogenase From Methylophilus W3a1
pdb|2AD6|A Chain A, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C)
pdb|2AD6|C Chain C, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C)
pdb|2AD7|A Chain A, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C) In The Presence Of Methanol
pdb|2AD7|C Chain C, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C) In The Presence Of Methanol
pdb|2AD8|A Chain A, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C) In The Presence Of Ethanol
pdb|2AD8|C Chain C, Crystal Structure Of Methanol Dehydrogenase From M. W3a1
(Form C) In The Presence Of Ethanol
Length = 571
Score = 26.9 bits (58), Expect = 3.7, Method: Composition-based stats.
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 77 YSKGFGFVKYATLEAAGKAIEGMDGKFL 104
Y+KG G V YATL+ KA++ DGK L
Sbjct: 472 YTKG-GLVWYATLDGYLKALDNKDGKEL 498
>pdb|1G72|A Chain A, Catalytic Mechanism Of Quinoprotein Methanol
Dehydrogenase: A Theoretical And X-Ray Crystallographic
Investigation
pdb|1G72|C Chain C, Catalytic Mechanism Of Quinoprotein Methanol
Dehydrogenase: A Theoretical And X-Ray Crystallographic
Investigation
Length = 573
Score = 26.9 bits (58), Expect = 3.7, Method: Composition-based stats.
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 77 YSKGFGFVKYATLEAAGKAIEGMDGKFL 104
Y+KG G V YATL+ KA++ DGK L
Sbjct: 474 YTKG-GLVWYATLDGYLKALDNKDGKEL 500
>pdb|3D9D|A Chain A, Nitroalkane Oxidase: Mutant D402n Crystallized With
1-Nitrohexane
pdb|3D9D|B Chain B, Nitroalkane Oxidase: Mutant D402n Crystallized With
1-Nitrohexane
pdb|3D9D|C Chain C, Nitroalkane Oxidase: Mutant D402n Crystallized With
1-Nitrohexane
pdb|3D9D|D Chain D, Nitroalkane Oxidase: Mutant D402n Crystallized With
1-Nitrohexane
pdb|3D9E|A Chain A, Nitroalkane Oxidase: Active Site Mutant D402n Crystallized
With 1- Nitrooctane
pdb|3D9E|B Chain B, Nitroalkane Oxidase: Active Site Mutant D402n Crystallized
With 1- Nitrooctane
pdb|3D9E|C Chain C, Nitroalkane Oxidase: Active Site Mutant D402n Crystallized
With 1- Nitrooctane
pdb|3D9E|D Chain D, Nitroalkane Oxidase: Active Site Mutant D402n Crystallized
With 1- Nitrooctane
pdb|3FCJ|A Chain A, Nitroalkane Oxidase: Mutant402n Crystallized With
Nitroethane
pdb|3FCJ|B Chain B, Nitroalkane Oxidase: Mutant402n Crystallized With
Nitroethane
pdb|3FCJ|C Chain C, Nitroalkane Oxidase: Mutant402n Crystallized With
Nitroethane
pdb|3FCJ|D Chain D, Nitroalkane Oxidase: Mutant402n Crystallized With
Nitroethane
Length = 438
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 196 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 230
>pdb|2ZAF|A Chain A, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2ZAF|B Chain B, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2ZAF|C Chain C, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2ZAF|D Chain D, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
Length = 439
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 197 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 231
>pdb|2REH|A Chain A, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2REH|B Chain B, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2REH|C Chain C, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
pdb|2REH|D Chain D, Mechanistic And Structural Analyses Of The Roles Of Arg409
And Asp402 In The Reaction Of The Flavoprotein
Nitroalkane Oxidase
Length = 439
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 197 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 231
>pdb|2C12|A Chain A, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
pdb|2C12|B Chain B, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
pdb|2C12|C Chain C, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
pdb|2C12|D Chain D, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
pdb|2C12|E Chain E, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
pdb|2C12|F Chain F, Crystal Structure Of Nitroalkane Oxidase In Complex With
Spermine, A Competitive Inhibitor
Length = 439
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 197 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 231
>pdb|3D9F|A Chain A, Nitroalkane Oxidase: Active Site Mutant S276a Crystallized
With 1- Nitrohexane
pdb|3D9F|B Chain B, Nitroalkane Oxidase: Active Site Mutant S276a Crystallized
With 1- Nitrohexane
pdb|3D9F|C Chain C, Nitroalkane Oxidase: Active Site Mutant S276a Crystallized
With 1- Nitrohexane
pdb|3D9F|D Chain D, Nitroalkane Oxidase: Active Site Mutant S276a Crystallized
With 1- Nitrohexane
Length = 438
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 196 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 230
>pdb|3D9G|A Chain A, Nitroalkane Oxidase: Wild Type Crystallized In A Trapped
State Forming A Cyanoadduct With Fad
pdb|3D9G|B Chain B, Nitroalkane Oxidase: Wild Type Crystallized In A Trapped
State Forming A Cyanoadduct With Fad
pdb|3D9G|C Chain C, Nitroalkane Oxidase: Wild Type Crystallized In A Trapped
State Forming A Cyanoadduct With Fad
pdb|3D9G|D Chain D, Nitroalkane Oxidase: Wild Type Crystallized In A Trapped
State Forming A Cyanoadduct With Fad
Length = 438
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 196 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 230
>pdb|2C0U|A Chain A, Crystal Structure Of A Covalent Complex Of Nitroalkane
Oxidase Trapped During Substrate Turnover
pdb|2C0U|B Chain B, Crystal Structure Of A Covalent Complex Of Nitroalkane
Oxidase Trapped During Substrate Turnover
pdb|2C0U|C Chain C, Crystal Structure Of A Covalent Complex Of Nitroalkane
Oxidase Trapped During Substrate Turnover
pdb|2C0U|D Chain D, Crystal Structure Of A Covalent Complex Of Nitroalkane
Oxidase Trapped During Substrate Turnover
Length = 439
Score = 26.6 bits (57), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 PQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGE 63
PQ P +P+T + V +++ T +D + GE
Sbjct: 197 PQDPNVDPATQIAVLLVTRETIANNKKDAYQILGE 231
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 26.2 bits (56), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 38 TNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAAGKAIE 97
+ +FV ++ T E L+ F +GEVV I K + F FV +A + A +++
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVA-QSLC 65
Query: 98 GMDGKFLDGWVIFVEYAKPRQ 118
G D + G + + A+P+
Sbjct: 66 GED-LIIKGISVHISNAEPKH 85
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 37 STNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIV--KHRESGYSKGFGFVKYATLEAAGK 94
+ LF+ G+ K E + + + E V IV + ++GF FV+Y + AA
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 95 AIEG-MDGKF-LDGWVIFVEYAKP 116
A M G+ L G I V++A+P
Sbjct: 68 ARRKLMPGRIQLWGHQIAVDWAEP 91
>pdb|1NX8|A Chain A, Structure Of Carbapenem Synthase (Carc) Complexed With
N-Acetyl Proline
pdb|1NX8|B Chain B, Structure Of Carbapenem Synthase (Carc) Complexed With
N-Acetyl Proline
pdb|1NX8|C Chain C, Structure Of Carbapenem Synthase (Carc) Complexed With
N-Acetyl Proline
Length = 273
Score = 25.8 bits (55), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 52 ETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA-GKAIEG 98
+T RD +SA+G IV++ + GFG+ LE GK + G
Sbjct: 52 DTFRDIYSAYG-----TIVEYADEKIGVGFGYRDTLKLEGEKGKIVTG 94
>pdb|1YQ2|A Chain A, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|B Chain B, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|C Chain C, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|D Chain D, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|E Chain E, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
pdb|1YQ2|F Chain F, Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme
C2- 2-1)
Length = 1024
Score = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 22/51 (43%)
Query: 78 SKGFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQPPTLPSQNNT 128
++ + + TL + G DGK+ V+Y P PP +P N T
Sbjct: 69 AESYDDAAWDTLPVPSHWVMGQDGKYGRPIYTNVQYPFPIDPPHVPDANPT 119
>pdb|1NX4|A Chain A, The Crystal Structure Of Carbapenem Synthase (Carc)
pdb|1NX4|B Chain B, The Crystal Structure Of Carbapenem Synthase (Carc)
pdb|1NX4|C Chain C, The Crystal Structure Of Carbapenem Synthase (Carc)
Length = 273
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 52 ETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKYATLEAA-GKAIEG 98
+T RD +SA+G IV++ + GFG+ LE GK + G
Sbjct: 52 DTFRDIYSAYG-----TIVEYADEKIGVGFGYRDTLKLEGEKGKIVTG 94
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 27 NPPQRPQAEPSTNLFVSGLSKRTTDETLRDTFSAFGEVVHAKIVKHRESGYSKGFGFVKY 86
+P + ++ NLF+ L+ + L+ S +V R +G ++ FG+V +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDF 65
Query: 87 ATLEAAGKAIEGMDGKFLDGWVIFVEYAKPRQP 119
+ E KA+E L G +F K +P
Sbjct: 66 ESAEDLEKALE------LTGLKVFGNEIKLEKP 92
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 80 GFGFVKYATLEAAGKAIEGMDGKFLDGWVIFVE 112
GF FV++ A A+ +DG+ L G + VE
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVE 143
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,226,388
Number of Sequences: 62578
Number of extensions: 166605
Number of successful extensions: 542
Number of sequences better than 100.0: 178
Number of HSP's better than 100.0 without gapping: 152
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 335
Number of HSP's gapped (non-prelim): 203
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)