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= 033734
(112 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
+ + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R +FV
Sbjct: 125 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 12 VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
VTE ++Y F P P+ + + D RS GY YV F +A++AL
Sbjct: 22 VTEAMLYEKF--SPAGPI----------LSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 72 ADMNGKLLDGRVIFV 86
MN ++ G+ + +
Sbjct: 70 DTMNFDVIKGKPVRI 84
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
+ + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R +FV
Sbjct: 130 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 12 VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
VTE ++Y F P P+ + + D RS GY YV F +A++AL
Sbjct: 27 VTEAMLYEKF--SPAGPI----------LSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 72 ADMNGKLLDGRVIFV 86
MN ++ G+ + +
Sbjct: 75 DTMNFDVIKGKPVRI 89
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
+ + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R +FV R R +
Sbjct: 32 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG--RFKSRKERE 87
Query: 99 APLARQSAQ 107
A L ++ +
Sbjct: 88 AELGARAKE 96
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
+ + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R +FV
Sbjct: 38 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 32/49 (65%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
++ D+ RS+G+G+VTF ++A+ A+ MNGK +DGR I VD S
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 36/48 (75%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
+ +A ++M+ G RSKG+G+V FS+ EEA KA+ +MNG+++ + ++V
Sbjct: 42 ITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.8 bits (107), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 31/46 (67%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV 89
++MD RSKGYG++TFS E A+KAL +NG L GR + V +V
Sbjct: 58 LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
+A +I DK S GYG+V + T ++A++A+ +NG L + I V RPS DA
Sbjct: 31 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDAN 90
Query: 101 L 101
L
Sbjct: 91 L 91
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
+ + +++D+ S+G ++ F EA++A+ NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
+A +I DK S GYG+V + T ++A++A+ +NG L + I V RPS DA
Sbjct: 31 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDAN 90
Query: 101 L 101
L
Sbjct: 91 L 91
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
+ + +++D+ S+G ++ F EA++A+ NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV 89
++ D RSKGYG++TFS E A++AL +NG L GR + V +V
Sbjct: 36 VLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV 82
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+A +I DK S GYG+V + T ++A++A+ +NG L + I V RPS
Sbjct: 48 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+A +I DK S GYG+V + T ++A++A+ +NG L + I V RPS
Sbjct: 33 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 32/48 (66%)
Query: 40 FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+ ++ D S+GYG+V+F+++++AQ A+ M G+ L+GR + ++
Sbjct: 29 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 76
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 36 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 29/43 (67%)
Query: 40 FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
+ ++ D S+GYG+V+F+++++AQ A+ M G+ L+GR
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 45 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 45 ARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
A I+ D+ SKG+G+V F++EE+A+ A M +DG + +D +P
Sbjct: 42 ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
+ ++ DK +S GYG+V +S +A KA+ +NG L + I V RPS DA
Sbjct: 33 SCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIRDAN 92
Query: 101 L 101
L
Sbjct: 93 L 93
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 77
+ + I++D+ S+G G++ F EA++A+ +NG+
Sbjct: 117 IITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
++ D+ + KGYG+ + +E A A+ ++NG+ GR + VDN
Sbjct: 40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
+I D+ ++S+G+ ++TF +A+ A DMNGK L G+ I V+ +
Sbjct: 39 LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+ ++ DK +S GYG+V +S +A KA+ +NG L + I V RPS
Sbjct: 33 SCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
+ ++ DK +S GYG+V + ++A+KA+ +NG L + I V RPS DA
Sbjct: 31 SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDAN 90
Query: 101 L 101
L
Sbjct: 91 L 91
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
+ + I++D+ S+G G++ F EA++A+ +NG+ G
Sbjct: 115 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/32 (53%), Positives = 22/32 (68%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
SKGY YV F +EA+KAL M+G +DG+ I
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+I+ D+ RS+G+ +V F ++A++A NG LDGR I VD
Sbjct: 43 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+I+ D+ RS+G+ +V F ++A++A NG LDGR I VD
Sbjct: 46 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 14 EDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALAD 73
EDL + PL LHY +D + KG+ +VTF E A KA A+
Sbjct: 23 EDLEKLFSAYGPLSELHY-------------PIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 74 MNGKLLDGRVIFV 86
++G++ GR++ V
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+I+ D+ RS+G+ +V F ++A++A NG LDGR I VD
Sbjct: 77 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 27 FPLHYFLISDSF-----LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
F + ++ D F + A I M+ GK SKG G V F + E A++A MNG L G
Sbjct: 18 FDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSG 75
Query: 82 RVIFV 86
R I V
Sbjct: 76 REIDV 80
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLDGRV 83
+ I+ D+ +S+GYG+V F + AQ+A+A +NG +L+ R+
Sbjct: 71 SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL 114
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 27 FPLHYFLISDSF-----LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
F + ++ D F + A I M+ GK SKG G V F + E A++A MNG L G
Sbjct: 15 FDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSG 72
Query: 82 RVIFV 86
R I V
Sbjct: 73 REIDV 77
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
SKG+G+VTF +A +A ++G +++GR I V+N
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
SKG+G+VTF +A +A ++G +++GR I V+N
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
A +I D+ +S+GYG+VT + A++A D N ++DGR
Sbjct: 47 AVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGR 86
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
KGY +V FST E A A+ +NG ++G V+
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 38 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 86
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 87 -AVSREDSQRP 96
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 40 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 88
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 89 -AVSREDSQRP 98
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 33 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 81
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 82 -AVSREDSQRP 91
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 40 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 88
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 89 -AVSREDSQRP 98
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 39 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 87
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 88 -AVSREDSQRP 97
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
K Y ++ F + A KA+ +MNGK L+G I + +P + + RQ+A P
Sbjct: 45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
+I+ D+ RS+G+ +V F ++A++A NG LDGR I V
Sbjct: 46 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
L ++ D RS+G+G+VT++T EE A+ K +DGRV V P R
Sbjct: 41 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV-----VEPKR----- 89
Query: 99 APLARQSAQSP 109
++R+ +Q P
Sbjct: 90 -AVSREDSQRP 99
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 34 ISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
+ + F AA I + +SKG Y+ F TE +A+K + G +DGR I
Sbjct: 110 LKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 34 ISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
ISD F ++D ++ +GYV F + E+ +KAL L G +F + ++ +
Sbjct: 28 ISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE------LTGLKVFGNEIKLEK 81
Query: 94 RYNTDAPLARQS 105
D+ R +
Sbjct: 82 PKGKDSKKERDA 93
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
TI+ DK +SKG ++ F ++ AQ +N K L GRVI
Sbjct: 46 VTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI 88
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
Y +V FS E+A +A+ +NGK+LDG I V +P
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 88
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.9 bits (76), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALA----DMNGKLLDGR 82
A ++ DK NR +G+G+VTF +E+ +K ++N K+++ +
Sbjct: 29 AMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECK 73
>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 = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
++ K + +GY ++ + E + A +GK +DGR + VD R
Sbjct: 134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
++ +SKGY V ++E K L + GK+L+G + +VRP+ R N
Sbjct: 92 NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV---DVRPATRQN 138
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 75
+ + I+DK N+ KGYG+V F + AQKA+ +
Sbjct: 32 IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 68
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
I D+ S+G+ +V F + +A+ A+ M+G +LDGR + V R R
Sbjct: 102 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 151
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 26/36 (72%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+SKGY ++ F++ E+A++AL N + ++GR I ++
Sbjct: 51 KSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE 86
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
L ++ D RS+G+G+VTFS+ E A+A +DGRV+
Sbjct: 54 LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVV 98
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 43 TIIMDKGKNR-----SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT 97
+ + K KN+ S G+G+V + E+AQKAL + G +DG + VR S R
Sbjct: 34 SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKL---EVRISERATK 90
Query: 98 DA 99
A
Sbjct: 91 PA 92
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
I D+ S+G+ +V F + +A+ A+ M+G +LDGR + V R R
Sbjct: 79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
+ +A + +DK + SK +G+V+F + AQ A+ MNG
Sbjct: 67 VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+ DK +SKG+ +++F E+A +A+A ++G D ++ V+ +PS
Sbjct: 47 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
>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 = 32.7 bits (73), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+ KG+ +V + E AQ AL MN +L GR I V RPS
Sbjct: 53 KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG--RPS 91
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 75
+ T+ D + KGYG++ + + +Q A++ MN
Sbjct: 139 SCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
+G+ +V F +AQ A A M+G LDGR + V R RR
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRR 95
>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 = 32.3 bits (72), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
+ KG+ +V + E AQ AL MN +L GR I V RPS
Sbjct: 68 KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG--RPS 106
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 75
+AT+ D + KGYG++ + + +Q A++ MN
Sbjct: 154 SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.3 bits (72), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
I +D + +G+ +V F E+A A+ +MN L GR I V+ +P R
Sbjct: 44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 93
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
+SKG Y+ F +E +A+K L + G +DGR +
Sbjct: 134 KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
>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 = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 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 = 32.0 bits (71), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
+ +A + +DK N SK +G+V++ AQ A+ MNG
Sbjct: 52 VVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.0 bits (71), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
+SKG Y+ F +E +A+K L + G +DGR +
Sbjct: 51 KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83
>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 = 32.0 bits (71), Expect = 0.083, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
++ K + +GY ++ + E + A +GK +DGR + VD R
Sbjct: 134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 43 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 32.0 bits (71), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 57 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
++ + +SKGYG+ + ++ A +A +D+ GK L R ++V
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
++ + +SKGYG+ + ++ A +A +D+ GK L R ++V
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
++ + +SKGYG+ + ++ A +A +D+ GK L R ++V
Sbjct: 125 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKAL------ADMNGKLLDGRVIFVD 87
+++ SKG + F T+E AQK L A+ G LDGR + VD
Sbjct: 47 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVD 96
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ KGY V + T +EAQ A+ +NG+ L G+ I VD
Sbjct: 56 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 97
>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 = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
TI+ DK KG+ Y+ FS +E + +LA ++ L GR I V R +R
Sbjct: 36 TILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKRTNR 85
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
TI+ DK KG+ Y+ FS +E + +LA ++ L GR I V R +R
Sbjct: 37 TILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKRTNR 86
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
TI D RS+G+G++ F +K L D LDGRVI
Sbjct: 41 CTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQKEHRLDGRVI 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
I+ D SKGY ++ F++ + + A+ MNG+ L R I V
Sbjct: 38 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV 80
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.8 bits (68), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 55 GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
G YV F EE+A+KA+ D+N + +G+ I +
Sbjct: 69 GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 77
+ + I++D+ S+G G++ F EA++A+ +NG+
Sbjct: 28 IITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 66
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
L+ + L TI D+ + + K +G+V F E A+A +NG L GR I V
Sbjct: 33 LYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 31/94 (32%)
Query: 2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
L + F QFG+V E LV + D RS+G+G+VTF
Sbjct: 42 LREYFGQFGEVKECLV---------------------------MRDPLTKRSRGFGFVTF 74
Query: 62 STEEEAQKALA----DMNGKLLDGRVIFVDNVRP 91
+ K LA +++ K +D +V F +P
Sbjct: 75 MDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQP 108
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
KGY +V +S E A+ A+ NG++L G+ + ++
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
I+ D S GY +V F++E ++Q+A+ +NG + + + V RP
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
A I+ DK +S+G G VTF EA +A++ NG+LL R + V
Sbjct: 45 ADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
+F +I D+ + KG+G+V EE +A+A ++ GR I V P +
Sbjct: 28 VFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMGRTIRVTEANPKK 81
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL 78
+++D+ SKGYG+V F+ E E ++AL + G +
Sbjct: 39 GGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAV 75
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR-VIFVDNVRPSRRYNTD 98
+D+ ++KG+ +V + +A+K + +GK LD + +F+ ++ RYN+D
Sbjct: 46 IDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSD 99
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
I+ D S GY +V F++E ++Q+A+ +NG + + + V RP
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 31/83 (37%)
Query: 2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
L D FS+FG+V + T+ +D RS+G+G+V F
Sbjct: 16 LKDYFSKFGEVVD---------------------------CTLKLDPITGRSRGFGFVLF 48
Query: 62 STEEEAQKAL----ADMNGKLLD 80
E K + +NGK++D
Sbjct: 49 KESESVDKVMDQKEHKLNGKVID 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 = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 31 YFLISDSFLFAATII-MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
Y L S S I+ +DK K + G+ +V + + +A+ A+ +NG LD R+I D
Sbjct: 57 YELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 114
>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 = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 55 GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
GY +V F++E ++Q+A+ +NG + + + V RP
Sbjct: 57 GYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARP 93
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 95 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 5/60 (8%)
Query: 33 LISDSFLFAATII-----MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
L+ + FL A ++ D+ + +GYG+V F +EE+A A+ M+ L G+ I V+
Sbjct: 31 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90
>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 = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
++ D RSKGY ++ F E + A+ ++NG L R +
Sbjct: 36 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 76
>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 = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
TI+ DK KGY Y+ F+ A+A M+ + GR I V
Sbjct: 67 TILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKV 109
>pdb|1Q5X|A Chain A, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|B Chain B, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|C Chain C, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|2YJT|A Chain A, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|B Chain B, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|C Chain C, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJV|A Chain A, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|B Chain B, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|C Chain C, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|D Chain D, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|E Chain E, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|F Chain F, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|G Chain G, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|H Chain H, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|I Chain I, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|J Chain J, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|K Chain K, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|L Chain L, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
Length = 161
Score = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 71 LADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
L + NG+ GRV+ VD RR DA LAR + Q+ E
Sbjct: 51 LLEQNGR---GRVLVVDGGGSVRRALVDAELARLAVQNEWEG 89
>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 = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 34 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 77
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 31/88 (35%)
Query: 2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
L + F QFG+V E LV + D RS+G+G+VTF
Sbjct: 17 LREYFGQFGEVKECLV---------------------------MRDPLTKRSRGFGFVTF 49
Query: 62 STEEEAQKALA----DMNGKLLDGRVIF 85
+ K LA +++ K +D +V F
Sbjct: 50 MDQAGVDKVLAQSRHELDSKTIDPKVAF 77
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.9 bits (63), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
R +G ++TF +E A +AL +NG L G+++ ++
Sbjct: 65 RMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 100
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.9 bits (63), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
++ D RSKGY ++ F E + A+ ++NG L R +
Sbjct: 34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 37 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 80
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82
>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 = 28.5 bits (62), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
++ D RSKGY ++ F E + A+ ++NG L R +
Sbjct: 35 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 75
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
+D+ SKGY V + T ++A A +NG + G+ I VD
Sbjct: 60 LDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
K Y +V E +A+ A+A +NGK + G+ I V+
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE 76
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
I+ DK N+S+G+G+V F LA LDGR I
Sbjct: 46 CVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP-HTLDGRNI 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
NR +G+G++ + A+ A A+++G +L R + +
Sbjct: 55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRI 90
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 32/91 (35%)
Query: 1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
+L AFSQFG V + A ++ D+G R+ G G+V
Sbjct: 112 LLEQAFSQFGPVEK--------------------------AVVVVDDRG--RATGKGFVE 143
Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
F+ + A+KAL + DG + RP
Sbjct: 144 FAAKPPARKALE----RCGDGAFLLTTTPRP 170
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
KG+ +V + E A+ A+A +G+++ G+V+ + N+ + N P
Sbjct: 50 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI-NLAAEPKVNRSGP 95
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
+I D K R +G+G++TF E+ +A+ +M+ + G+ + V P
Sbjct: 40 VVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEP 88
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 7/56 (12%)
Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
+H +I++S +A + +G + S YVT+ E+A +A+ +N ++DGR +
Sbjct: 45 IHKVVINNSTSYAGS----QGPSAS---AYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
+ + II ++ GY +V F+ A+K L +NGK L G P++R+ +
Sbjct: 37 VMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG-------ATPAKRFKLN 89
>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 = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
SKGY V + T ++A A +NG + G+ I VD
Sbjct: 113 SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
II D+ RSKG YV F + A+ + G+ L G I V
Sbjct: 57 IISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIV 98
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Rna-Binding Protein 19
Length = 91
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
A I+ + N++ GY +V FS EEE ++AL N + + GR I V
Sbjct: 38 AIRIVRNAHGNKT-GYIFVDFSNEEEVKQAL-KCNREYMGGRYIEV 81
>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 = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 44 IIMDKGKNRSKGYGYVTF---STEEEAQKALADMNGKLLD 80
I+ D RS+G+G+++F S+ +E K ++GK++D
Sbjct: 35 IMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVID 74
Score = 25.4 bits (54), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 8/33 (24%), Positives = 20/33 (60%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
+ A +++DK +S+G+G+VT+ + + +
Sbjct: 114 IIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVI 84
++ F E A KA+ D+NG+ GRV+
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVV 86
>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 = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 44 IIMDKGKNRSK-GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
IIM K ++ G+ +V + + +A+ A+ +NG LD R+I D
Sbjct: 48 IIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 92
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 219
>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 = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 19/35 (54%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 75
+ T+ D + KGYG++ + + +Q A++ N
Sbjct: 138 SCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
RS G V F + +A KA+ NG LDGR
Sbjct: 67 RSLGTADVHFERKADALKAMKQYNGVPLDGR 97
>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 = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV--DNVRPS 92
+ KG YV + E +A +A+ M+G + +I V N PS
Sbjct: 55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 110
>pdb|3RMX|A Chain A, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|B Chain B, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|C Chain C, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|D Chain D, Crystal Structure Of HcrD F1240A MUTANT
Length = 415
Score = 25.8 bits (55), Expect = 6.0, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 10 GQVTEDLVYFYFKSQPLFPLHYFLISDSFL------FAATIIMDKGKNRSKGYGYVTFST 63
GQ+ +++ Y+ + F Y++I+D+++ + +++ + +RSK Y +
Sbjct: 217 GQILRNVIKDYWGNPLKFDTEYYIINDNYIDRYIAPESNVLVLVQYPDRSKLY-----TG 271
Query: 64 EEEAQKALADMN--GKLLDGRVIFVDNVRPSRRY----NTDAPLARQSAQSPE 110
K+++D N ++L+G I + + SR+Y +TD A Q + +
Sbjct: 272 NPITIKSVSDKNPYSRILNGDNIILHMLYNSRKYMIIRDTDTIYATQGGECSQ 324
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKAL 71
MD N+ +G+ ++TF EE +K +
Sbjct: 33 MDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKAL 71
MD N+ +G+ ++TF EE +K +
Sbjct: 35 MDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 115
>pdb|3OBR|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype D
Binding Domain
pdb|3OBT|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype D
Ligand Binding Domain In Complex With N-Acetylneuraminic
Acid
Length = 434
Score = 25.8 bits (55), Expect = 7.1, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 10 GQVTEDLVYFYFKSQPLFPLHYFLISDSFL------FAATIIMDKGKNRSKGYGYVTFST 63
GQ+ +++ Y+ + F Y++I+D+++ + +++ + +RSK Y +
Sbjct: 223 GQILRNVIKDYWGNPLKFDTEYYIINDNYIDRYIAPESNVLVLVQYPDRSKLY-----TG 277
Query: 64 EEEAQKALADMN--GKLLDGRVIFVDNVRPSRRY----NTDAPLARQSAQSPE 110
K+++D N ++L+G I + + SR+Y +TD A Q + +
Sbjct: 278 NPITIKSVSDKNPYSRILNGDNIILHMLYNSRKYMIIRDTDTIYATQGGECSQ 330
>pdb|3OGG|A Chain A, Crystal Structure Of The Receptor Binding Domain Of
Botulinum Neurotoxin D
Length = 414
Score = 25.8 bits (55), Expect = 7.1, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 10 GQVTEDLVYFYFKSQPLFPLHYFLISDSFL------FAATIIMDKGKNRSKGYGYVTFST 63
GQ+ +++ Y+ + F Y++I+D+++ + +++ + +RSK Y +
Sbjct: 216 GQILRNVIKDYWGNPLKFDTEYYIINDNYIDRYIAPESNVLVLVQYPDRSKLY-----TG 270
Query: 64 EEEAQKALADMN--GKLLDGRVIFVDNVRPSRRY----NTDAPLARQSAQSPE 110
K+++D N ++L+G I + + SR+Y +TD A Q + +
Sbjct: 271 NPITIKSVSDKNPYSRILNGDNIILHMLYNSRKYMIIRDTDTIYATQGGECSQ 323
>pdb|3RMY|A Chain A, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|B Chain B, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|C Chain C, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|D Chain D, Crystal Structure Of HcrD W1238A MUTANT
Length = 415
Score = 25.4 bits (54), Expect = 7.3, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 10 GQVTEDLVYFYFKSQPLFPLHYFLISDSFL------FAATIIMDKGKNRSKGYGYVTFST 63
GQ+ +++ Y+ + F Y++I+D+++ + +++ + +RSK Y +
Sbjct: 217 GQILRNVIKDYWGNPLKFDTEYYIINDNYIDRYIAPESNVLVLVQYPDRSKLY-----TG 271
Query: 64 EEEAQKALADMN--GKLLDGRVIFVDNVRPSRRY----NTDAPLARQSAQSPE 110
K+++D N ++L+G I + + SR+Y +TD A Q + +
Sbjct: 272 NPITIKSVSDKNPYSRILNGDNIILHMLYNSRKYMIIRDTDTIYATQGGECSQ 324
>pdb|3N7J|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype D
Binding Domain
Length = 415
Score = 25.4 bits (54), Expect = 7.3, Method: Composition-based stats.
Identities = 24/113 (21%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 10 GQVTEDLVYFYFKSQPLFPLHYFLISDSFL------FAATIIMDKGKNRSKGYGYVTFST 63
GQ+ +++ Y+ + F Y++I+D+++ + +++ + +RSK Y +
Sbjct: 217 GQILRNVIKDYWGNPLKFDTEYYIINDNYIDRYIAPESNVLVLVQYPDRSKLY-----TG 271
Query: 64 EEEAQKALADMN--GKLLDGRVIFVDNVRPSRRY----NTDAPLARQSAQSPE 110
K+++D N ++L+G I + + SR+Y +TD A Q + +
Sbjct: 272 NPITIKSVSDKNPYSRILNGDNIILHMLYNSRKYMIIRDTDTIYATQGGECSQ 324
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 25.4 bits (54), Expect = 7.8, Method: Composition-based stats.
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGK 77
+K Y + + T EE+++A +NGK
Sbjct: 55 NKPYSFARYRTTEESKRAYVTLNGK 79
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 25.4 bits (54), Expect = 7.9, Method: Composition-based stats.
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 53 SKGYGYVTFSTEEEAQKALADMNGK 77
+K Y + + T EE+++A +NGK
Sbjct: 55 NKPYSFARYRTTEESKRAYVTLNGK 79
>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 = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD 80
+D+ ++KG+ +V + +A+K + +GK LD
Sbjct: 46 IDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 24/55 (43%)
Query: 32 FLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
L S L A ++ D SKGY + + +A+A +NG L + + V
Sbjct: 134 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188
>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 = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 24/55 (43%)
Query: 32 FLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
L S L A ++ D SKGY + + +A+A +NG L + + V
Sbjct: 116 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
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
0.320 0.136 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,233,919
Number of Sequences: 62578
Number of extensions: 119007
Number of successful extensions: 403
Number of sequences better than 100.0: 148
Number of HSP's better than 100.0 without gapping: 138
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 243
Number of HSP's gapped (non-prelim): 169
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)