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= 036791
(157 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF T ++ L FS++GQ++E ++ D RS+G+G+VT ++A+ A++ MNGK
Sbjct: 19 GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS 78
Query: 124 LDGRVIFVDNVRPS 137
+DGR I VD S
Sbjct: 79 VDGRQIRVDQAGKS 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 57.0 bits (136), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 30/71 (42%), Positives = 44/71 (61%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ F+ T++ML F FG++ ++MD RSKGYG++T S E A+KAL +NG
Sbjct: 33 SLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE 92
Query: 124 LDGRVIFVDNV 134
L GR + V +V
Sbjct: 93 LAGRPMKVGHV 103
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/60 (45%), Positives = 42/60 (70%), Gaps = 2/60 (3%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
E L AFS FG +T A ++M+ G RSKG+G+V S+ EEA KA+ +MNG+++ + ++V
Sbjct: 30 ERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>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 = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
S + L D FS FG + ++ D +N SKGYG+V T+E A++A+ MNG LL+ R
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Query: 128 VIFV 131
+FV
Sbjct: 167 KVFV 170
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T+ ML + FS G + + D+ RS GY YV +A++AL MN ++ G+
Sbjct: 22 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 81
Query: 129 I 129
+
Sbjct: 82 V 82
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
S + L D FS FG + ++ D +N SKGYG+V T+E A++A+ MNG LL+ R
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Query: 128 VIFV 131
+FV
Sbjct: 172 KVFV 175
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T+ ML + FS G + + D+ RS GY YV +A++AL MN ++ G+
Sbjct: 27 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 86
Query: 129 I 129
+
Sbjct: 87 V 87
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 40/60 (66%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T E + AF+ FG++++A ++ D+ +SKGYG+V+ + +A+ A+V M G+ L GR I
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
S + L D FS FG + ++ D +N SKGYG+V T+E A++A+ MNG LL+ R
Sbjct: 22 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 79
Query: 128 VIFV 131
+FV
Sbjct: 80 KVFV 83
>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 = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
S + L D FS FG + ++ D +N SKGYG+V T+E A++A+ MNG LL+ R
Sbjct: 16 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 73
Query: 128 VIFV 131
+FV
Sbjct: 74 KVFV 77
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.1 bits (126), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 43/71 (60%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ F+ T++ML F FG++ ++ D RSKGYG++T S E A++AL +NG
Sbjct: 12 SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE 71
Query: 124 LDGRVIFVDNV 134
L GR + V +V
Sbjct: 72 LAGRPMRVGHV 82
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A+ +
Sbjct: 20 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 78
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 79 VDGRV-----VEPKR------AVSREDSQRP 98
Score = 34.7 bits (78), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 97 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 152 TFDDHDSVDKIVI 164
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A+ +
Sbjct: 18 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 76
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 77 VDGRV-----VEPKR------AVSREDSQRP 96
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 95 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 149
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 150 TFDDHDSVDKIVI 162
>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 = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 16/93 (17%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK- 122
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A MN +
Sbjct: 13 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---MNARP 69
Query: 123 -LLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 70 HKVDGRV-----VEPKR------AVSREDSQRP 91
Score = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 90 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 144
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 145 TFDDHDSVDKIVI 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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 39/60 (65%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T E + AF+ FG++++A ++ D+ +SKGYG+V+ + +A+ A+ M G+ L GR I
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A+ +
Sbjct: 19 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 77
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 78 VDGRV-----VEPKR------AVSREDSQRP 97
Score = 33.9 bits (76), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 96 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 150
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 151 TFDDHDSVDKIVI 163
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A+ +
Sbjct: 20 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 78
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 79 VDGRV-----VEPKR------AVSREDSQRP 98
Score = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 97 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 152 TFDDHDSVDKIVI 164
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT +T EE A+ +
Sbjct: 21 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 79
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
+DGRV V P R +++R+ +Q P
Sbjct: 80 VDGRV-----VEPKR------AVSREDSQRP 99
Score = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP + L ++ + V + T + L D F Q+G++ I+ D G + +G+ +V
Sbjct: 98 RPGAHLTVKKIFVG-----GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 152
Query: 105 TSSTEEEAQKALV 117
T + K ++
Sbjct: 153 TFDDHDSVDKIVI 165
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ + T+E L D FS+ G V ++ D + KGYG+ +E A A+ ++NG+
Sbjct: 15 NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74
Query: 124 LDGRVIFVDNV 134
GR + VDN
Sbjct: 75 FSGRALRVDNA 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 7/93 (7%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T ++ML F + G ++E +I D ++S+G+ ++T +A+ A DMNGK L G+
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA 77
Query: 129 IFVDNV-RPS-----RRYNTDASLARQPAQSPE 155
I V+ +PS RR +S R P+ S E
Sbjct: 78 IKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ L FS G+V A +I D S GYG+V T ++A++A+ +NG L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
V RPS DA+L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 34.7 bits (78), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RPSS++I + + + + + T++ + D FS+FG++ + +++D S+G ++
Sbjct: 80 RPSSEVIK---DANLY-ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 105 TSSTEEEAQKALVDMNG 121
EA++A+ NG
Sbjct: 136 RFDKRSEAEEAITSFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ L FS G+V A +I D S GYG+V T ++A++A+ +NG L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
V RPS DA+L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RPSS++I + + + + + T++ + D FS+FG++ + +++D S+G ++
Sbjct: 80 RPSSEVIK---DANLY-ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 105 TSSTEEEAQKALVDMNG 121
EA++A+ NG
Sbjct: 136 RFDKRSEAEEAITSFNG 152
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62 CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
C+ V S TT+ L + FS++G + + +I+ D RS+G+ +V ++A++A
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 119 MNGKLLDGRVIFVD 132
NG LDGR I VD
Sbjct: 74 ANGMELDGRRIRVD 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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62 CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
C+ V S TT+ L + FS++G + + +I+ D RS+G+ +V ++A++A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 119 MNGKLLDGRVIFVD 132
NG LDGR I VD
Sbjct: 77 ANGMELDGRRIRVD 90
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+S+ TTK+ L D FS+FG+V + T+ +D RS+G+G+V E K + D
Sbjct: 6 GLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQKEHK 64
Query: 124 LDGRVI 129
L+G+VI
Sbjct: 65 LNGKVI 70
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+S+ T+K+ L D F++FG+V + TI D RS+G+G++ +K L D
Sbjct: 18 GLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQKEHR 76
Query: 124 LDGRVI 129
LDGRVI
Sbjct: 77 LDGRVI 82
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62 CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
C+ V S TT+ L + FS++G + + +I+ D RS+G+ +V ++A++A
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 119 MNGKLLDGRVIFVD 132
NG LDGR I VD
Sbjct: 108 ANGMELDGRRIRVD 121
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DM 119
+S+ TT+E L + F QFG+V E ++ D RS+G+G+VT + K L ++
Sbjct: 32 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 91
Query: 120 NGKLLDGRVIFVDNVRP 136
+ K +D +V F +P
Sbjct: 92 DSKTIDPKVAFPRRAQP 108
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 47/95 (49%), Gaps = 17/95 (17%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR-----SKGYGYVTSSTEEEAQKALVDM 119
++FSTT+E L FS+ G + TI KN+ S G+G+V E+AQKAL +
Sbjct: 13 LNFSTTEETLKGVFSKVGAIKSCTISKK--KNKAGVLLSMGFGFVEYKKPEQAQKALKQL 70
Query: 120 NGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
G +DG + VR S R A +PA P
Sbjct: 71 QGHTVDGHKL---EVRISER-------ATKPASGP 95
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+SF TT+E L + + Q+G++T+ ++ D RS+G+G+VT S+ E A+
Sbjct: 34 GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHS 92
Query: 124 LDGRVI 129
+DGRV+
Sbjct: 93 IDGRVV 98
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 50/103 (48%), Gaps = 10/103 (9%)
Query: 52 MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEE 111
M V V F R +++ + T+E+L AFSQFG++ + D Y ++ +
Sbjct: 8 MAKVKVLFVR--NLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDG 57
Query: 112 AQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
A KA+ +MNGK L+G I + +P + + RQ A P
Sbjct: 58 AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ L FS G+V A +I D S GYG+V T ++A++A+ +NG L + I
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 130 FVDNVRPS 137
V RPS
Sbjct: 77 KVSYARPS 84
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ L FS G+V A +I D S GYG+V T ++A++A+ +NG L + I
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 130 FVDNVRPS 137
V RPS
Sbjct: 92 KVSYARPS 99
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+ + TT L F FG + EA +I D +S+GYG+VT + A++A D N +
Sbjct: 24 GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PI 82
Query: 124 LDGR 127
+DGR
Sbjct: 83 IDGR 86
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DM 119
+S+ TT+E L + F QFG+V E ++ D RS+G+G+VT + K L ++
Sbjct: 7 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 66
Query: 120 NGKLLDGRVIF 130
+ K +D +V F
Sbjct: 67 DSKTIDPKVAF 77
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 33/49 (67%)
Query: 81 FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
FG++++A ++ D+ +SKGYG+V+ + +A+ A+ M G+ L GR I
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 62 CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
C ++ T +++ FS FGQ+ E + + KGY +V ST E A A+V +NG
Sbjct: 30 CGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG 83
Query: 122 KLLDGRVI 129
++G V+
Sbjct: 84 TTIEGHVV 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 62 CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
C+ V S TT+ L + FS++G + + +I+ D RS+G+ +V ++A++A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 119 MNGKLLDGRVIFV 131
NG LDGR I V
Sbjct: 77 ANGMELDGRRIRV 89
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ F T +ML D F++ G V A I M+ GK SKG G V + E A++A MNG
Sbjct: 15 NLPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMK 72
Query: 124 LDGRVIFV 131
L GR I V
Sbjct: 73 LSGREIDV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ F T +ML D F++ G V A I M+ GK SKG G V + E A++A MNG
Sbjct: 12 NLPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMK 69
Query: 124 LDGRVIFV 131
L GR I V
Sbjct: 70 LSGREIDV 77
>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 = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
E L +AF F ++ D+ S+GYG+V+ +++++AQ A+ M G+ L+GR +
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
++ + E L +AF F ++ D+ S+GYG+V+ +++++AQ A+ M G+ L
Sbjct: 95 LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL 154
Query: 125 DGR 127
+GR
Sbjct: 155 NGR 157
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
+S+++++E L FS +G ++E +D + KG+ +VT E A KA +++G++
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF 75
Query: 125 DGRVIFV 131
GR++ V
Sbjct: 76 QGRMLHV 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA----LVDM 119
+S +TT E + F QFG+V +A ++ D NR +G+G+VT +E+ +K ++
Sbjct: 6 GLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEI 65
Query: 120 NGKLLDGR 127
N K+++ +
Sbjct: 66 NNKMVECK 73
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%)
Query: 52 MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEE 111
M + ++ + ++++ T+ + L F ++G+V + I D S+G+ +V + +
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 112 AQKALVDMNGKLLDGRVIFVDNVRPSR 138
A+ A+ M+G +LDGR + V R R
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMARYGR 151
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 67 FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
+S T E + + FSQFG+V +I D + KG+G+V EE +A+ ++ G
Sbjct: 11 YSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV-EMQEESVSEAIAKLDNTDFMG 69
Query: 127 RVIFVDNVRPSR 138
R I V P +
Sbjct: 70 RTIRVTEANPKK 81
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ FS T L FS++G+V + TI+ D +SKG ++ ++ AQ +N K
Sbjct: 23 NLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQ 82
Query: 124 LDGRVI 129
L GRVI
Sbjct: 83 LFGRVI 88
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
L F QFG++ + II + + SKG+G+VT +A +A ++G +++GR I V+N
Sbjct: 46 LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
L F QFG++ + II + + SKG+G+VT +A +A ++G +++GR I V+N
Sbjct: 32 LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
RP D+ ++ + ++++ T+ + L F ++G+V + I D S+G+ +V
Sbjct: 39 RPPPDV----EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 105 TSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR 138
+ +A+ A+ M+G +LDGR + V R R
Sbjct: 95 RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 14 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 74 LMGQPISVD 82
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
V++ TT+ L F +G + ++ + +GY ++ E + A +GK +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 125 DGRVIFVD 132
DGR + VD
Sbjct: 170 DGRRVLVD 177
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 16 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 75
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 76 LMGQPISVD 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 14 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 74 LMGQPISVD 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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 30 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 89
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 90 LMGQPISVD 98
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
+ TK+ + + FS +G++ + ++ + + SKGY YV +EA+KAL M+G +DG
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 127 RVI 129
+ I
Sbjct: 75 QEI 77
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 14 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 74 LMGQPISVD 82
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T+E F G++ ++ D +S GYG+V ++A+KA+ +NG L + I
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
V RPS DA+L
Sbjct: 75 KVSYARPSSASIRDANL 91
Score = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
+ T++ L FSQ+G++ + I++D S+G G++ EA++A+ +NG+ G
Sbjct: 99 TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
V T+E + D F+++G++ + +D KGY V T +EAQ A+ +NG+
Sbjct: 29 GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 88
Query: 124 LDGRVIFVD 132
L G+ I VD
Sbjct: 89 LMGQPISVD 97
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
E+L AFSQFG V +A +++D + R+ G G+V + + A+KAL + DG +
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE----RCGDGAFLLT 165
Query: 132 DNVRP 136
RP
Sbjct: 166 TTPRP 170
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T+E F ++G+ +E I NR +G+G++ + A+ A +++G +L R +
Sbjct: 35 TEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPL 88
Query: 130 FV 131
+
Sbjct: 89 RI 90
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 28/41 (68%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
+ +STT+E L FSQ+G+V + I+ D N+S+G+G+V
Sbjct: 23 GLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
++L AF FG +T+ I +D + +G+ +V E+A A+ +MN L GR I V
Sbjct: 27 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
Query: 132 DNVRPSR 138
+ +P R
Sbjct: 87 NLAKPMR 93
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ F G + ++ D +S GYG+V S +A KA+ +NG L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 130 FVDNVRPSRRYNTDASL 146
V RPS DA+L
Sbjct: 77 KVSYARPSSASIRDANL 93
Score = 34.3 bits (77), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 71 KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
KEM FSQ+G++ + I++D S+G G++ EA++A+ +NG+
Sbjct: 105 KEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
L + F +FG VTE +I D K R +G+G++T E+ +A V+M+ + G+ + V
Sbjct: 27 LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNMHFHDIMGKKVEVKR 85
Query: 134 VRP 136
P
Sbjct: 86 AEP 88
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVT---SSTEEEAQKALVDMN 120
+++ TT++ L + F ++G VT+ I+ D RS+G+G+++ S+ +E K ++
Sbjct: 10 GLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILD 69
Query: 121 GKLLD 125
GK++D
Sbjct: 70 GKVID 74
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVT 105
FSQ+G + +A +++D +S+G+G+VT
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVT 135
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 3/85 (3%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++SF TT+E + + FS+ G + + + +D K + G+ +V + +A+ A+ +NG
Sbjct: 46 NLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR 105
Query: 124 LDGRVIFVD---NVRPSRRYNTDAS 145
LD R+I D + R+Y S
Sbjct: 106 LDDRIIRTDWDAGFKEGRQYGRGRS 130
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 14/102 (13%)
Query: 44 VRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGY 103
V+ +SDLI+ + + + TT++ L + FS FG+V + D+ SKG+G+
Sbjct: 12 VQKTSDLIV----------LGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 104 VTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDAS 145
V TE E Q ++ ++DGR + D P+ + + D+
Sbjct: 62 V-RFTEYETQVKVMSQR-HMIDGR--WCDCKLPNSKQSQDSG 99
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL------V 117
++SF + +E L + QFG + +++ SKG + T+E AQK L
Sbjct: 22 NLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA 81
Query: 118 DMNGKLLDGRVIFVD 132
+ G LDGR + VD
Sbjct: 82 EGGGLKLDGRQLKVD 96
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
V++ TT+ L F +G + ++ + +GY ++ E + A +GK +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 125 DGRVIFVD 132
DGR + VD
Sbjct: 170 DGRRVLVD 177
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T++ F G + ++ D +S GYG+V S +A KA+ +NG L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 130 FVDNVRPS 137
V RPS
Sbjct: 77 KVSYARPS 84
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 62 CISVSFST-------TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQK 114
C S S + + E+L +AFS FGQV A +I+D + R G G V S + A+K
Sbjct: 94 CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARK 152
Query: 115 AL 116
AL
Sbjct: 153 AL 154
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T+E + F ++G+ E I ++ KG+G++ T A+ A V+++ L G+ +
Sbjct: 35 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 88
Query: 130 FV 131
V
Sbjct: 89 RV 90
>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 = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + ++ + AF+ FG + + D + KG+ +V E AQ AL MN +
Sbjct: 20 SIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVM 79
Query: 124 LDGRVIFVDNVRPS 137
L GR I V RPS
Sbjct: 80 LGGRNIKVG--RPS 91
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
F FG++ T+ D + KGYG++ + +Q A+ MN L G+ + V
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+S TT+E L ++F G V A I+ D SKG+G+V ++EE+A+ A M
Sbjct: 22 GLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE 78
Query: 124 LDGRVIFVDNVRP 136
+DG + +D +P
Sbjct: 79 IDGNKVTLDWAKP 91
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S K+ L FS+ G+V +D ++KG+ +V + +A+K + +GK
Sbjct: 19 SAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR 78
Query: 124 LDGRV-IFVDNVRPSRRYNTD 143
LD + +F+ ++ RYN+D
Sbjct: 79 LDLKHRLFLYTMKDVERYNSD 99
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++++ T+ + L F ++G+V + I + +G+ +V +AQ A M+G
Sbjct: 20 NLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAE 79
Query: 124 LDGRVIFVDNVRPSRR 139
LDGR + V R RR
Sbjct: 80 LDGRELRVQVARYGRR 95
>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 = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 42/70 (60%), Gaps = 3/70 (4%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSK-GYGYVTSSTEEEAQKALVDMNGK 122
++SF TT+E + + FS+ G + + IIM + K ++ G+ +V + +A+ A+ +NG
Sbjct: 25 NLSFYTTEEQIYELFSKSGDIKK--IIMGLDKMKTACGFCFVEYYSRADAENAMRYINGT 82
Query: 123 LLDGRVIFVD 132
LD R+I D
Sbjct: 83 RLDDRIIRTD 92
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++NG
Sbjct: 11 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 124 LDGRVI 129
L R +
Sbjct: 71 LGSRFL 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
++L AF FG +T+ I +D + +G+ +V E+A A+ +MN L GR I V
Sbjct: 78 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
Query: 132 D 132
+
Sbjct: 138 N 138
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + ++ + AF+ FG + + D + KG+ +V E AQ AL MN +
Sbjct: 35 SIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVM 94
Query: 124 LDGRVIFVDNVRPS 137
L GR I V RPS
Sbjct: 95 LGGRNIKVG--RPS 106
Score = 33.5 bits (75), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
F FG++ AT+ D + KGYG++ + +Q A+ MN
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++NG
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 124 LDGRVI 129
L R +
Sbjct: 69 LGSRFL 74
>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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++NG
Sbjct: 10 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 124 LDGRVI 129
L R +
Sbjct: 70 LGSRFL 75
>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 = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
++L AF FG +T+ I +D + +G+ +V E+A A+ +MN L GR I V
Sbjct: 17 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 76
Query: 132 D 132
+
Sbjct: 77 N 77
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 71 KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
+E+ + ++G+V E + ++G + G YV EE+A+KA++D+N + +G+ I
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 131 VD 132
+
Sbjct: 100 AE 101
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 71 KEMLADAFSQFGQVTEATIIM-DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
+++L D FS FG + + IM D SKGY ++ ++ + + A+ MNG+ L R I
Sbjct: 19 EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI 78
Query: 130 FV 131
V
Sbjct: 79 TV 80
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
++L AF FG +T+ I +D + +G+ +V E+A A+ +MN L GR I V
Sbjct: 20 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 79
Query: 132 D 132
+
Sbjct: 80 N 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 = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
++L AF FG +T+ I +D + +G+ +V E+A A+ +MN L GR I V
Sbjct: 22 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 81
Query: 132 D 132
+
Sbjct: 82 N 82
>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 = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 64 SVSFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
S S+ TT + L G V E + +SKGY V ++E K L + G
Sbjct: 62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG 121
Query: 122 KLLDGRVIFVDNVRPSRRYN 141
K+L+G + +VRP+ R N
Sbjct: 122 KVLNGEKV---DVRPATRQN 138
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 49 DLIMQLVNVSFWRCIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSS 107
+L +QL C++ + S T++ + FG + ++ +SKGYG+
Sbjct: 86 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 145
Query: 108 TEEEAQKALVDMNGKLLDGRVIFV 131
++ A +A D+ GK L R ++V
Sbjct: 146 KKDSAARAKSDLLGKPLGPRTLYV 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 = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 49 DLIMQLVNVSFWRCIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSS 107
+L +QL C++ + S T++ + FG + ++ +SKGYG+
Sbjct: 84 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 143
Query: 108 TEEEAQKALVDMNGKLLDGRVIFV 131
++ A +A D+ GK L R ++V
Sbjct: 144 KKDSAARAKSDLLGKPLGPRTLYV 167
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 49 DLIMQLVNVSFWRCIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSS 107
+L +QL C++ + S T++ + FG + ++ +SKGYG+
Sbjct: 86 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 145
Query: 108 TEEEAQKALVDMNGKLLDGRVIFV 131
++ A +A D+ GK L R ++V
Sbjct: 146 KKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
LA F FG V A + +D + SK +G+V+ + AQ A+ MNG
Sbjct: 57 LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 10/85 (11%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKN---RSKGYGYVTSSTEEEAQKALVDMN 120
++S+S T+E L + F E + + +N +SKGY ++ ++ E+A++AL N
Sbjct: 22 NLSYSATEETLQEVF-------EKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 121 GKLLDGRVIFVDNVRPSRRYNTDAS 145
+ ++GR I ++ P N+ S
Sbjct: 75 KREIEGRAIRLELQGPRGSPNSGPS 99
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 40/77 (51%)
Query: 61 RCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
R ++S T + L + F FG ++ + D +SKG+ +++ E+A +A+ ++
Sbjct: 19 RVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS 78
Query: 121 GKLLDGRVIFVDNVRPS 137
G D ++ V+ +PS
Sbjct: 79 GFGYDHLILNVEWAKPS 95
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
L F ++G + I+ D +S+GYG+V + AQ+A+ +NG
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 71 KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
KEM FSQ+G++ + I++D S+G G++ EA++A+ +NG+
Sbjct: 16 KEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 66
>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 = 0.028, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 67 FSTTKEMLADAFSQF--GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
ST++EM+ F+ G V I D Y +V S E+A +A+ +NGK+L
Sbjct: 25 LSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVL 76
Query: 125 DGRVIFVDNVRP 136
DG I V +P
Sbjct: 77 DGSPIEVTLAKP 88
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 34.3 bits (77), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
VS + T + L F + G+V E ++ D Y +V E +A+ A+ +NGK +
Sbjct: 17 VSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEV 68
Query: 125 DGRVIFVD 132
G+ I V+
Sbjct: 69 KGKRINVE 76
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 71 KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
+E+L + F Q G +T+ TI D + + K +G+V E A+ +NG L GR I
Sbjct: 30 EEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN 88
Query: 131 VDN 133
V
Sbjct: 89 VSG 91
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 51 IMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEE 110
+M V V F R ++ + T+E+L +FS+FG++ + D Y +V
Sbjct: 11 VMAKVKVLFVRNLATT--VTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRG 60
Query: 111 EAQKALVDMNGK 122
A KA+ +MNGK
Sbjct: 61 AAVKAMDEMNGK 72
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 33.9 bits (76), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+V + T E L F G V TI+ D KG+ Y+ S +E + +L ++ L
Sbjct: 12 NVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESL 70
Query: 124 LDGRVIFVDNVRPSR 138
GR I V R +R
Sbjct: 71 FRGRQIKVIPKRTNR 85
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ + ++ + AF+ FG + D + KG+ +V E AQ AL N
Sbjct: 19 SIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVX 78
Query: 124 LDGRVIFVDNVRPS 137
L GR I V RPS
Sbjct: 79 LGGRNIKVG--RPS 90
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA-----LVD 118
SV + + + F FG++ T+ D + KGYG++ + +Q A L D
Sbjct: 116 SVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFD 175
Query: 119 MNGKLL 124
+ G+ L
Sbjct: 176 LGGQYL 181
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD 132
FS++G+V ++ KGY +V S E A+ A++ NG++L G+ + ++
Sbjct: 49 FSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 33.5 bits (75), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+V + T E L F G V TI+ D KG+ Y+ S +E + +L ++ L
Sbjct: 13 NVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESL 71
Query: 124 LDGRVIFVDNVRPSR 138
GR I V R +R
Sbjct: 72 FRGRQIKVIPKRTNR 86
>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 = 0.062, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
+V + +T + L FS G + TI+ D KGY Y+ + E + A V M+ +
Sbjct: 43 NVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAMDETV 101
Query: 124 LDGRVIFV 131
GR I V
Sbjct: 102 FRGRTIKV 109
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.7 bits (73), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
+S T +E + + F FG+V + MD N+ +G+ ++T EE +K +
Sbjct: 6 GLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 32.7 bits (73), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
L F FG V A + +D N SK +G+V+ AQ A+ MNG
Sbjct: 42 LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 32.7 bits (73), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
+S T +E + + F FG+V + MD N+ +G+ ++T EE +K +
Sbjct: 8 GLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.7 bits (73), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 62 CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
C+ ++ L D FS G+V + II D RSKG YV E ++ + + G
Sbjct: 30 CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV-EFCEIQSVPLAIGLTG 88
Query: 122 KLLDGRVIFV 131
+ L G I V
Sbjct: 89 QRLLGVPIIV 98
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S K+ L FS+ G+V +D ++KG+ +V + +A+K + +GK
Sbjct: 19 SAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR 78
Query: 124 LD 125
LD
Sbjct: 79 LD 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
TT + L +G++ I+D N+ KGYG+V + AQKA+ +
Sbjct: 16 GTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 68
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T +E+ A F G + I+ D S GY +V ++E ++Q+A+ +NG + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 129 IFVDNVRPS 137
+ V RP
Sbjct: 75 LKVSYARPG 83
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ ++ + + F +G++ + +D SKGY V T ++A A +NG
Sbjct: 33 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE 92
Query: 124 LDGRVIFVD 132
+ G+ I VD
Sbjct: 93 IMGQTIQVD 101
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T +E+ A F G + I+ D S GY +V ++E ++Q+A+ +NG + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 129 IFVDNVRPSRRYNTDASL 146
+ V RP D +L
Sbjct: 75 LKVSYARPGGESIKDTNL 92
>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 = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 67 FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
FS TKE L + G V + ++ + + KG YV E +A +A++ M+G +
Sbjct: 27 FSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKMDGMTIKE 85
Query: 127 RVIFV--DNVRPS 137
+I V N PS
Sbjct: 86 NIIKVAISNSGPS 98
>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 = 31.2 bits (69), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA 115
N F I V T+ + F+++G V E II D SKGYG+V+ + + QK
Sbjct: 10 NTVFVGGIDVRMDETE--IRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKI 66
Query: 116 L---VDMNGKLL 124
+ ++ +GK L
Sbjct: 67 VESQINFHGKKL 78
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
F FG + E TI+ N SKG +V S+ EAQ A+ ++G
Sbjct: 36 FEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAINALHG 78
>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 = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++SF+ T++ L + F E ++ GK SKG Y+ +E +A+K L + G
Sbjct: 106 NLSFNITEDELKEVFED---ALEIRLVSQDGK--SKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 124 LDGRVI 129
+DGR +
Sbjct: 161 IDGRSV 166
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++SF+ T++ L + F E ++ GK SKG Y+ +E +A+K L + G
Sbjct: 23 NLSFNITEDELKEVFED---ALEIRLVSQDGK--SKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 124 LDGRVI 129
+DGR +
Sbjct: 78 IDGRSV 83
>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 = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA 115
N F I V T+ + F+++G V E II D SKGYG+V+ + + QK
Sbjct: 10 NTVFVGGIDVRMDETE--IRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKI 66
Query: 116 L---VDMNGKLL 124
+ ++ +GK L
Sbjct: 67 VESQINFHGKKL 78
>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 = 30.4 bits (67), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T +E+ A F G + I D S GY +V ++E ++Q+A+ +NG + +
Sbjct: 27 TDRELYA-LFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKR 85
Query: 129 IFVDNVRPSRRYNTDASL 146
+ V RP D +L
Sbjct: 86 LKVSYARPGGESIKDTNL 103
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ F + + + F++FG + +A + D RS G V + +A KA+ NG
Sbjct: 35 NLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVP 93
Query: 124 LDGR 127
LDGR
Sbjct: 94 LDGR 97
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
S+ ++ + + F +G++ + +D SKGY V T ++A A +NG
Sbjct: 79 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE 138
Query: 124 LDGRVIFVD 132
+ G+ I VD
Sbjct: 139 IMGQTIQVD 147
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 30.0 bits (66), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA 115
N F I V T+ + F+++G V E II D SKGYG+V+ + + QK
Sbjct: 11 NTVFVGGIDVRMDETE--IRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 67
Query: 116 L---VDMNGKLL 124
+ ++ +GK L
Sbjct: 68 VESQINFHGKKL 79
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 30.0 bits (66), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
L + FS G V A I+ D +S+G G VT EA +A+ NG+LL R + V
Sbjct: 32 LKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++ F + + + F++FG + +A + D RS G V + +A KA NG
Sbjct: 36 NLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQYNGVP 94
Query: 124 LDGR 127
LDGR
Sbjct: 95 LDGR 98
>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 = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 116 LVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
L++ NG+ GRV+ VD RR DA LAR Q+ E
Sbjct: 51 LLEQNGR---GRVLVVDGGGSVRRALVDAELARLAVQNEWEG 89
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
++ +L + F Q G V + D + +GYG+V +EE+A A+ M+ L G+
Sbjct: 27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86
Query: 129 IFVD 132
I V+
Sbjct: 87 IRVN 90
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 96 NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
+SKG Y+ TE +A+K + G +DGR I
Sbjct: 127 GKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 35/69 (50%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
++S T+ L F++F + I + R +G ++T +E A +AL +NG
Sbjct: 32 NLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYK 91
Query: 124 LDGRVIFVD 132
L G+++ ++
Sbjct: 92 LYGKILVIE 100
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
T +L AFS FG I+D+ + + +VT E A +A+ ++NG
Sbjct: 50 TPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNG 95
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
T +L AFS FG I+D+ + + +VT E A +A+ ++NG
Sbjct: 26 TPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNG 71
>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 = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 70 TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
T+E + F ++G+ E I ++ KG+G++ T A+ A V+++ L G+ +
Sbjct: 28 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81
Query: 130 FV 131
V
Sbjct: 82 RV 83
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
F FG + E T++ SKG +V S+ EAQ A+ ++G
Sbjct: 36 FQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD 132
FS++G++ ++ KG+ +V E A+ A+ +G+++ G+V+ ++
Sbjct: 37 FSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN 83
>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 = 4.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 110 EEAQKALVDMNGKLLDGRVI 129
E A KA+VD+NG+ GRV+
Sbjct: 67 ESAIKAVVDLNGRYFGGRVV 86
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
+ S ++ L + FGQV I+ D S+G G+ + E+ + + NGK +
Sbjct: 33 LPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFI 91
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 64 SVSFSTTKEMLADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKAL 116
++ F + + + FS FG++ + + G +G+G+V T+++A+KA
Sbjct: 22 NIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>pdb|2PYX|A Chain A, Crystal Structure Of Tryptophan Halogenase (Yp_750003.1)
From Shewanella Frigidimarina Ncimb 400 At 1.50 A
Resolution
pdb|2PYX|B Chain B, Crystal Structure Of Tryptophan Halogenase (Yp_750003.1)
From Shewanella Frigidimarina Ncimb 400 At 1.50 A
Resolution
Length = 526
Score = 26.6 bits (57), Expect = 6.4, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 75 ADAFSQFGQVTEATI-----IMDIGKNRSKGYGYVTSSTEE---EAQKALVDMNG 121
+DA S T +T I DIG KG GYV SS+ +AQK L + G
Sbjct: 264 SDANSPIASCTHSTAQPNGWIWDIGLPTRKGVGYVYSSSHTNDIDAQKTLFNYLG 318
>pdb|3L20|A Chain A, Crystal Structure Of A Hypothetical Protein From
Staphylococcus Aureus
pdb|3L20|B Chain B, Crystal Structure Of A Hypothetical Protein From
Staphylococcus Aureus
Length = 172
Score = 26.6 bits (57), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 10/84 (11%)
Query: 65 VSFSTTKEMLADAFSQFGQVTEATII--MDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
++F +KE LA + +V AT + +++G+ ++ +G T+EEAQ+A +
Sbjct: 31 IAFENSKEALA----YYEEVFGATDVKRLEVGEEQASHFG----XTKEEAQEATXHAEFE 82
Query: 123 LLDGRVIFVDNVRPSRRYNTDASL 146
+L +V+ D+ + + N SL
Sbjct: 83 VLGVKVLCSDSFGRADKINNGISL 106
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 26.6 bits (57), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI-FVD 132
L + F FG + E I+ G+ +V E A KA+ +++GK + + V
Sbjct: 48 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Query: 133 NVRPSRRY 140
+ P++RY
Sbjct: 100 SKLPAKRY 107
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 26.2 bits (56), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
T++ + F Q+G+V E II K YG+V + A+ A+ +++ L G
Sbjct: 20 ATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71
Query: 129 IFVD 132
I V+
Sbjct: 72 INVE 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/86 (18%), Positives = 39/86 (45%), Gaps = 1/86 (1%)
Query: 41 HCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKG 100
H +V + ++ L + W + S T+ + D V + + + N S+
Sbjct: 65 HKVVGQNEIIVSHLTECTLW-MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 123
Query: 101 YGYVTSSTEEEAQKALVDMNGKLLDG 126
+ Y+ +++E+A+ + +NG ++G
Sbjct: 124 FAYIDVTSKEDARYCVEKLNGLKIEG 149
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
0.318 0.129 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,049,782
Number of Sequences: 62578
Number of extensions: 141909
Number of successful extensions: 572
Number of sequences better than 100.0: 146
Number of HSP's better than 100.0 without gapping: 121
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 417
Number of HSP's gapped (non-prelim): 166
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
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: 47 (22.7 bits)