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= 039806
(398 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 = 91.3 bits (225), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 47/99 (47%), Positives = 62/99 (62%), Gaps = 1/99 (1%)
Query: 1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
MWS + R SG+GN F+KNL +IDN L+ FS FG+I S KVV + G SKGYGFV
Sbjct: 85 MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFV 143
Query: 61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE 99
+ T E+A AIEK+ G + +++VG F R +R E
Sbjct: 144 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 76/158 (48%), Gaps = 18/158 (11%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTP---ESAL 69
+ + +V +L + L++ FS G I S +V +S GY +V + P E AL
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 70 DAI--EKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
D + + ++G V M P +R+ S N+++KNLD + + L + FS F
Sbjct: 70 DTMNFDVIKGKPVRIMWSQRDPSLRK-------SGVGNIFIKNLDKSIDNKALYDTFSAF 122
Query: 128 GKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
G I S + D NG SKG+G +V ++A +AI
Sbjct: 123 GNILSCKVVCDENG-SKGYG----FVHFETQEAAERAI 155
>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 = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 50/114 (43%), Positives = 68/114 (59%), Gaps = 2/114 (1%)
Query: 1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
MWS + R SG+GN F+KNL +IDN L+ FS FG+I S KVV + G SKGYGFV
Sbjct: 90 MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFV 148
Query: 61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE-GSSFNNLYVKNLDD 113
+ T E+A AIEK+ G + +++VG F R +R E G+ Y ++ D
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPD 202
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 76/158 (48%), Gaps = 18/158 (11%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTP---ESAL 69
+ + +V +L + L++ FS G I S +V +S GY +V + P E AL
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 70 DAI--EKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
D + + ++G V M P +R+ S N+++KNLD + + L + FS F
Sbjct: 75 DTMNFDVIKGKPVRIMWSQRDPSLRK-------SGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 128 GKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
G I S + D NG SKG+G +V ++A +AI
Sbjct: 128 GNILSCKVVCDENG-SKGYG----FVHFETQEAAERAI 160
>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 = 86.7 bits (213), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 47/103 (45%), Positives = 62/103 (60%), Gaps = 5/103 (4%)
Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI 72
G GN F+KNL +IDN L+ FS FG+I S KVV + G SKGYGFV + T E+A AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 73 EKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNL 111
EK+ G + +++VG F R +R E F N+Y+KN
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKA 164
N+++KNLD + + L + FS FG I S + D NG SKG+G +V ++A +A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYG----FVHFETQEAAERA 61
Query: 165 I 165
I
Sbjct: 62 I 62
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 82.0 bits (201), Expect = 5e-16, Method: Composition-based stats.
Identities = 44/90 (48%), Positives = 58/90 (64%), Gaps = 1/90 (1%)
Query: 10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESAL 69
R SG+GN F+KNL +IDN L+ FS FG+I S KVV + G SKGYGFV + T E+A
Sbjct: 7 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE 65
Query: 70 DAIEKLQGATVERMELYVGPFIRRADRIQE 99
AIEK+ G + +++VG F R +R E
Sbjct: 66 RAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 94 ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYV 153
AD S N+++KNLD + + L + FS FG I S + D NG SKG+G +V
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYG----FV 56
Query: 154 ARAQKKAERKAI 165
++A +AI
Sbjct: 57 HFETQEAAERAI 68
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/87 (43%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
N +VKNL ID+ +L + FS FG I S+KV++ + G+SKG+GFV +S+PE A A+ ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 76 QGATVERMELYVGPFIRRADRIQEGSS 102
G V LYV R+ +R Q G S
Sbjct: 76 NGRIVATKPLYVALAQRKEER-QSGPS 101
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 43/83 (51%), Gaps = 24/83 (28%)
Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----------------- 147
NLYVKNLDD + +E L + FS FG ITS + + G SKGFG
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 148 ------SKVLYVARAQKKAERKA 164
+K LYVA AQ+K ER++
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 174 RKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTS 232
R + LY KN++D +D+ L++ FS GTI+S K+M + G SKG + E T
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM-MEGGRSKGFGFVCFSSPEEATK 70
Query: 233 YLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAP 267
+ M + + +T P++ L QR + P
Sbjct: 71 AVTEMNGR----IVATK-PLYVALAQRKEERQSGP 100
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 44/134 (32%), Positives = 68/134 (50%), Gaps = 6/134 (4%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N V L + + +F GDI+S K+V + G+S GYGFV YS P A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 75 LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSL 133
L G ++ + V + I++ NLYV L M+++ + + FS++G+ ITS
Sbjct: 66 LNGLKLQTKTIKVSYARPSSASIRDA----NLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 134 VISKDANGTSKGFG 147
++ A G S+G G
Sbjct: 122 ILLDQATGVSRGVG 135
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N +V L T+ ++ Q+FS++G I +S++++ Q G S+G GF+++ A +AI+
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 75 LQG 77
L G
Sbjct: 152 LNG 154
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 43/134 (32%), Positives = 67/134 (50%), Gaps = 6/134 (4%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N V L + + +F G+I+S K+V + G+S GYGFV Y P+ A AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75 LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSL 133
L G ++ + V + I++ NLYV L MT++ L + FS++G+ ITS
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRDA----NLYVSGLPKTMTQKELEQLFSQYGRIITSR 119
Query: 134 VISKDANGTSKGFG 147
++ G S+G G
Sbjct: 120 ILVDQVTGVSRGVG 133
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N +V L T+ +L Q+FS++G I +S+++V Q G S+G GF+++ A +AI+
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 75 LQG 77
L G
Sbjct: 150 LNG 152
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 40/135 (29%), Positives = 59/135 (43%), Gaps = 22/135 (16%)
Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLYVARAQKKA 160
S NL V L +MT+E F G+I S + +D G S G+G +V K
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYG----FVNYIDPKD 56
Query: 161 ERKAI-----LRAQFERMRKE----------RAELY-KNINDEVDEIELKQYFSQCGTIS 204
KAI LR Q + ++ A LY + + + EL+Q FSQ G I
Sbjct: 57 AEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 205 SVKIMRTD-RGISKG 218
+ +I+ G+S+G
Sbjct: 117 TSRILVDQVTGVSRG 131
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 74/148 (50%), Gaps = 13/148 (8%)
Query: 11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESAL 69
L+ + +V ++ + + Q F+ FG I+S + S K KG+ FV+Y PE+A
Sbjct: 10 LAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 69
Query: 70 DAIEKLQGATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
A+E++ + + VG P I + +E +FN +YV ++ D++++ +
Sbjct: 70 LALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVHQDLSDDDI 127
Query: 121 VEKFSEFGKITSLVISKD-ANGTSKGFG 147
F FGKI S +++D G KG+G
Sbjct: 128 KSVFEAFGKIKSCTLARDPTTGKHKGYG 155
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKL 75
+V ++ + + + +F FG I+S + GK KGYGF++Y +S+ DA+ +
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
>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 = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 76/156 (48%), Gaps = 13/156 (8%)
Query: 3 STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQ 61
S + L+ + +V ++ + + Q F+ FG I+S + S K KG+ FV+
Sbjct: 17 SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 62 YSTPESALDAIEKLQGATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLD 112
Y PE+A A+E++ + + VG P I + +E +FN +YV ++
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVH 134
Query: 113 DDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
D++++ + F FGKI S +++D G KG+G
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKL 75
+V ++ + + + +F FG I+S+ + GK KGYGF++Y +S+ DA+ +
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
>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 = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/141 (28%), Positives = 69/141 (48%), Gaps = 13/141 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQS-SKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
+V ++ + + Q F+ FG I+S S K KG+ FV+Y PE+A A+E+
Sbjct: 16 YVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXN 75
Query: 77 GATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
+ + VG P I + +E +FN +YV ++ D++++ + F F
Sbjct: 76 SVXLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 128 GKITSLVISKD-ANGTSKGFG 147
GKI S +++D G KG+G
Sbjct: 134 GKIKSCTLARDPTTGKHKGYG 154
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAI 72
+V ++ + + + +F FG I+S + GK KGYGF++Y +S+ DA+
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>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 = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
G N V L + +L +FS G+++S+K++ + G S GYGFV Y T + A A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 IEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-I 130
I L G ++ + V ++ I++ NLY+ L MT++ + + FS FG+ I
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 131 TSLVISKDANGTSKG 145
S V+ G S+G
Sbjct: 117 NSRVLVDQTTGLSRG 131
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
G N V L + +L +FS G+++S+K++ + G S GYGFV Y T + A A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 IEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-I 130
I L G ++ + V ++ I++ NLY+ L MT++ + + FS FG+ I
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 131 TSLVISKDANGTSKG 145
S V+ G S+G
Sbjct: 117 NSRVLVDQTTGLSRG 131
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEK 74
N V + +T+D ++L Q+F ++G I+S K+V +E + S+GYGFV++ + SA AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 75 LQGATVERMELYV 87
L G + L V
Sbjct: 104 LNGFNILNKRLKV 116
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDR 213
I VDE++L+Q F + G I SVKI+ DR
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIV-CDR 78
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 42/151 (27%), Positives = 72/151 (47%), Gaps = 19/151 (12%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV NL + I ++F ++G + S+V ++ + +G+GF++ + A A +L G
Sbjct: 26 FVGNLPTDITEEDFKRLFERYG--EPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDG 80
Query: 78 ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
++ L RI+ + L VKNL ++ E+L + FS+FG + V+
Sbjct: 81 TILKSRPL----------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 138 DANGTSKGFGSKVLYVARAQKKAERKAILRA 168
D G + G G +V A K RKA+ R
Sbjct: 131 DDRGRATGKG----FVEFAAKPPARKALERC 157
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 37/122 (30%), Positives = 61/122 (50%), Gaps = 17/122 (13%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG-----SKVL-YVARAQKK 159
L+V NL D+TEE F +G+ + + I++D +GFG S+ L +A+A+
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 79
Query: 160 AERKAILRAQFERMR---KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGIS 216
IL+++ R+R A KN++ V L+Q FSQ G + ++ DRG +
Sbjct: 80 G---TILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRA 136
Query: 217 KG 218
G
Sbjct: 137 TG 138
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 19/151 (12%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV NL I ++ ++F K+G ++ +V + K KG+GF++ +E
Sbjct: 26 FVGNLPPDITEEEMRKLFEKYG--KAGEVFIH---KDKGFGFIR----------LETRTL 70
Query: 78 ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
A + ++EL P + R++ +L V+NL ++ E+L E FS FG++ V+
Sbjct: 71 AEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV 130
Query: 138 DANGTSKGFGSKVLYVARAQKKAERKAILRA 168
D G G G V + K A RKA+ R
Sbjct: 131 DDRGRPSGKG----IVEFSGKPAARKALDRC 157
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 54/121 (44%), Gaps = 11/121 (9%)
Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVL---YVARAQKKA 160
+ L+V NL D+TEE + + F ++GK + I KD KGFG L +A K
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 77
Query: 161 ERKAILRAQFERMR---KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISK 217
LR + R+R + +N+ V L++ FS G + ++ DRG
Sbjct: 78 LDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPS 137
Query: 218 G 218
G
Sbjct: 138 G 138
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
+V +L I L IF FG I+S ++++ S+ G+SKGYGF+ +S E A A+E+L
Sbjct: 30 YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN 89
Query: 77 GATVERMELYVGPFIRRAD 95
G + + VG R D
Sbjct: 90 GFELAGRPMKVGHVTERTD 108
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 95 DRIQEGSSF-NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLY 152
+ +Q+GS+ LYV +L ++TE++L F FG+I S+ + D+ G SKG+G
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 153 VARAQKKA 160
+ KKA
Sbjct: 77 DSECAKKA 84
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK----SKGYGFVQYSTPES 67
SG F+KNL + L +FSK G I+S + + S G+GFV+Y PE
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 68 ALDAIEKLQGATVERMELYV 87
A A+++LQG TV+ +L V
Sbjct: 63 AQKALKQLQGHTVDGHKLEV 82
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT----SKGFG 147
S + L++KNL+ TEE L FS+ G I S ISK N S GFG
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFG 53
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY 86
+H+IFSKFG I ++ ++GK+KGY F++Y++P A+DA++ G +++ +
Sbjct: 38 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY 86
+H+IFSKFG I ++ ++GK+KGY F++Y++P A+DA++ G +++ +
Sbjct: 24 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/125 (32%), Positives = 64/125 (51%), Gaps = 12/125 (9%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG-------SKVLYVARAQ 157
+++ L+ D TE+ L E F ++G +T L I KD A G S+GFG S V V + Q
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 158 KKAERKAI--LRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIM-RTDR 213
+ K I RA + + +++ I +V E +++FSQ GTI ++M D
Sbjct: 66 HILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT 125
Query: 214 GISKG 218
G S+G
Sbjct: 126 GQSRG 130
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 79/162 (48%), Gaps = 12/162 (7%)
Query: 21 NLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQGAT 79
N +T DNL+ + F K+G + K++ G+S+G+GF+ + P S++D + K Q
Sbjct: 12 NWDTTEDNLR--EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKP-SSVDEVVKTQHIL 68
Query: 80 VERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS--LVISK 137
++ + P +RA E ++V + D+ + E FS++G I L++ K
Sbjct: 69 DGKV---IDP--KRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 138 DANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAE 179
D G S+GFG A A + + + + ++ +RAE
Sbjct: 124 DT-GQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE 164
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/133 (28%), Positives = 66/133 (49%), Gaps = 7/133 (5%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+V NL I L Q F G I + K+++ + K+ Y FV+Y A A++ L G
Sbjct: 4 YVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNG 63
Query: 78 ATVERMELYVGPFIRRADRIQEGSSFN--NLYVKNLDDDMTEEILVEKFSEF-GKITSLV 134
+E + I A + Q+ SS + NL+V +L+ ++ +E L F +F ++ V
Sbjct: 64 KQIENNIVK----INWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 135 ISKDANGTSKGFG 147
+ G+S+G+G
Sbjct: 120 MWDMQTGSSRGYG 132
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFV 60
W+ + ++ N FV +L +D+ L F F S V+ Q G S+GYGFV
Sbjct: 75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134
Query: 61 QYSTPESALDAIEKLQG 77
+++ + A +A++ +QG
Sbjct: 135 SFTSQDDAQNAMDSMQG 151
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 21/35 (60%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
LYV NLD +TE+IL + F G I ++ I D N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN 37
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
+ FV N+ +L IFS+ G + S ++V +E GK KGYGF +Y E+AL A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 75 LQG 77
L G
Sbjct: 70 LNG 72
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
S +++V N+ + TEE L + FSE G + S + D G KG+G
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYG 53
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALD 70
SG +V +L I L IF FG I + ++ S G+SKGYGF+ +S E A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 71 AIEKLQGATVERMELYVGPFIRRAD 95
A+E+L G + + VG R D
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTERLD 87
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKK 159
S + LYV +L ++TE++L F FGKI ++V+ KD++ G SKG+G ++ + +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYG----FITFSDSE 58
Query: 160 AERKAI 165
R+A+
Sbjct: 59 CARRAL 64
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIE 73
G FV L+ + L Q+FSK+G I VV +E +S+G+GFV + + A DA+
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 74 KLQGATVERMELYV 87
+ G +V+ ++ V
Sbjct: 73 AMNGKSVDGRQIRV 86
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
L+V L D E+ L + FS++G+I+ +V+ KD S+GFG
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N V L + + +F GDI+S K+V + G+S GYGFV YS P A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 75 LQGATVERMELYV 87
L G ++ + V
Sbjct: 66 LNGLKLQTKTIKV 78
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
V N+ + L Q+F +FG I +++ ++ G SKG+GFV + A A EKL G
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 92
Query: 79 TVERMELYV 87
VE ++ V
Sbjct: 93 VVEGRKIEV 101
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
V N+ + L Q+F +FG I +++ ++ G SKG+GFV + A A EKL G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 79 TVERMELYV 87
VE ++ V
Sbjct: 79 VVEGRKIEV 87
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
N F+ +L + L Q+F FG++ S+KV + Q SK +GFV Y P SA AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 75 LQGATVERMELYV 87
+ G + L V
Sbjct: 87 MNGFQIGMKRLKV 99
>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 = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
N FV +L +D+ L F F S V+ Q G S+GYGFV +++ + A +A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 75 LQG 77
+QG
Sbjct: 63 MQG 65
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N +V L T+ ++ Q+FS++G I +S++++ Q G S+G GF+++ A +AI+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 75 LQG 77
L G
Sbjct: 63 LNG 65
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 105 NLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDANGTSKGFG 147
NLYV L M+++ + + FS++G+ ITS ++ A G S+G G
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVG 46
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 9 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 67
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 68 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 127
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 128 QYGKIEVIEIM-TDRGSGK 145
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 18 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 77
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 78 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 132
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 133 EVIEIMTDRGSGKKRGF 149
>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 = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 7 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 65
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 66 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 125
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 126 QYGKIEVIEIM-TDRGSGK 143
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 16 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 75
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 76 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 130
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 131 EVIEIMTDRGSGKKRGF 147
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 66
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 67 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 127 QYGKIEVIEIM-TDRGSGK 144
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 77 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 132 EVIEIMTDRGSGKKRGF 148
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
FV +L +D+ L++ F K + + KVV+ Q G SKGYGFV+++ A+ + Q
Sbjct: 13 FVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQ 72
Query: 77 GA 78
GA
Sbjct: 73 GA 74
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 6 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 64
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 65 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 124
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 125 QYGKIEVIEIM-TDRGSGK 142
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 15 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 74
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 75 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 129
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 130 EVIEIMTDRGSGKKRGF 146
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+ +AS + + + Q FS FG I +V KGY FV++ST ESA AI + G
Sbjct: 29 YCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNG 83
Query: 78 ATVE 81
T+E
Sbjct: 84 TTIE 87
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 66
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 67 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 127 QYGKIEVIEIM-TDRGSGK 144
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 77 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 132 EVIEIMTDRGSGKKRGF 148
>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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
+E L++ L + T+E L F ++G +T V+ +D N S+GFG V Y
Sbjct: 1 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 59
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
AR K R +A+ R +R + I ++ +E L+ YF
Sbjct: 60 EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119
Query: 199 QCGTISSVKIMRTDRGISK 217
Q G I ++IM TDRG K
Sbjct: 120 QYGKIEVIEIM-TDRGSGK 137
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
F+ L+ + L F ++G + V+ K S+G+GFV Y+T E A+
Sbjct: 10 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69
Query: 73 EKLQGATVERMELYVGPFIRRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKI 130
K+ G VE + R D + G+ + ++V + +D E L + F ++GKI
Sbjct: 70 HKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 124
Query: 131 TSLVISKD-ANGTSKGF 146
+ I D +G +GF
Sbjct: 125 EVIEIMTDRGSGKKRGF 141
>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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
G N V L + +L +FS G+++S+K++ + G S GYGFV Y T + A A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 72 IEKLQG 77
I L G
Sbjct: 63 INTLNG 68
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDI-QSSKVVVSQE-GKSKGYGFVQYSTPESAL 69
SG F+ NL ID L+ FS FG I Q+ K++ + G SKGY F+ +++ +++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 70 DAIEKLQG 77
AIE + G
Sbjct: 63 AAIEAMNG 70
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKI--TSLVISKDANGTSKGF 146
+++ NLD ++ E++L + FS FG I T ++ G SKG+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGY 50
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 1/86 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
FV+NL+ T L ++FS +G + + S K KG+ FV + PE A+ A ++
Sbjct: 12 FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71
Query: 77 GATVERMELYVGPFIRRADRIQEGSS 102
G + L+V P + + Q G S
Sbjct: 72 GQVFQGRMLHVLPSTIKKEASQSGPS 97
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEK 74
N F+ +L + L F FG++ S+KV + Q SK +GFV + P+SA AI+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 75 LQGATVERMELYV 87
+ G V L V
Sbjct: 102 MNGFQVGTKRLKV 114
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV+NLA+T+ L + FS+FG ++ K K K Y F+ + + A+ A+E++ G
Sbjct: 15 FVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNG 67
Query: 78 ATVE 81
+E
Sbjct: 68 KDLE 71
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
L+V+NL + +TEEIL + FS+FGK+ + KD
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
FV +L+ I + F+ FG I ++VV GKSKGYGFV + A +AI+++
Sbjct: 19 FVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG 78
Query: 77 G 77
G
Sbjct: 79 G 79
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 13 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 70
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 71 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 96
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
V NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y +SA A L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 78 ATVERMELYV 87
+ LYV
Sbjct: 160 KPLGPRTLYV 169
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
V NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y +SA A L G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
Query: 78 ATVERMELYV 87
+ LYV
Sbjct: 160 KPLGPRTLYV 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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
V NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y +SA A L G
Sbjct: 98 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 157
Query: 78 ATVERMELYV 87
+ LYV
Sbjct: 158 KPLGPRTLYV 167
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 13 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 70
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 71 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 96
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKL 75
+V LA +D+ LH F FGDI ++ + E K +G+ FV++ E A AI+ +
Sbjct: 67 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 69
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 70 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 95
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 69
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 70 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 95
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 10 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 67
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 68 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 93
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
M P + ++ KNL+ I +L ++F +I+ +VSQ+GKSKG ++
Sbjct: 3 MLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYI 58
Query: 61 QYSTPESALDAIEKLQGATVE 81
++ + A +E+ QGA ++
Sbjct: 59 EFKSEADAEKNLEEKQGAEID 79
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +D ++ F+++G ++ K++ + G SKGYGFV + +E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 77 GATVERMELYVGPFIRRAD 95
++++L GP IR+ +
Sbjct: 72 NFHGKKLKL--GPAIRKQN 88
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH 219
I+ +DE E++ +F++ G++ VKI+ G+SKG+
Sbjct: 17 IDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGY 52
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 9 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 66
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 67 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 92
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 69
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 70 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 95
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 8 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 65
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 66 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 91
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV NL + + L+++F + G + + +EGK K +GFV + PES AI L G
Sbjct: 20 FVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNG 79
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
++V NL+ + EEIL E F + G +T + I KD G K FG
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +D ++ F+++G ++ K++ + G SKGYGFV + +E
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 72
Query: 77 GATVERMELYVGPFIRRAD 95
++++L GP IR+ +
Sbjct: 73 NFHGKKLKL--GPAIRKQN 89
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH 219
I+ +DE E++ +F++ G++ VKI+ G+SKG+
Sbjct: 18 IDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGY 53
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKL 75
+V LA +D+ LH F FGDI ++ + E K +G+ FV++ E A AI+ +
Sbjct: 16 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 7 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 64
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
+QG PF + RIQ + +++ K
Sbjct: 65 SMQGF----------PFYDKPMRIQYAKTDSDIIAK 90
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
N V L +L +FS G+++S+K++ + G S GYGFV Y T + A AI
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 75 LQG 77
L G
Sbjct: 81 LNG 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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
FV + +D ++ F+++G ++ K++ + G SKGYGFV + +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 76 QGATVERMELYVGPFIRR 93
++++L GP IR+
Sbjct: 71 INFHGKKLKL--GPAIRK 86
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH 219
I+ +DE E++ +F++ G++ VKI+ G+SKG+
Sbjct: 17 IDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGY 52
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 10 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR 67
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
QG PF + RIQ + +++ K
Sbjct: 68 SXQGF----------PFYDKPXRIQYAKTDSDIIAK 93
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR 69
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
QG PF + RIQ + +++ K
Sbjct: 70 SXQGF----------PFYDKPXRIQYAKTDSDIIAK 95
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
++ NL I D LK LH IFS+FG I ++VS+ K +G FV + SA +A+
Sbjct: 13 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR 70
Query: 74 KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVK 109
QG PF + RIQ + +++ K
Sbjct: 71 SXQGF----------PFYDKPXRIQYAKTDSDIIAK 96
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 69/157 (43%), Gaps = 8/157 (5%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG---KSKGYGFVQYSTPESALDAIEK 74
FV + T L ++F ++G + V+ + +SKG FV + T ++AL+A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 75 LQGATVERMELYVGPFIRRADRIQEGSSFNN--LYVKNLDDDMTEEILVEKFSEFGKITS 132
L V + P + ++ ++ + L++ + TE + FS FG+I
Sbjct: 67 LHNXKV--LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEE 124
Query: 133 LVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQ 169
I + +G S+G V + RA + KA +AQ
Sbjct: 125 CRILRGPDGLSRGCAF-VTFTTRAXAQTAIKAXHQAQ 160
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 20/141 (14%)
Query: 107 YVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT---SKGFGSKVLYVARAQKKAER- 162
+V + +E+ L E F ++G + + + +D + SKG Y +A +A+
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 163 ---KAILRAQFERMRKERAELYKN------------INDEVDEIELKQYFSQCGTISSVK 207
+L ++ + A+ KN I+ + E +++ FS G I +
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 208 IMRTDRGISKGHCMAIAQTKR 228
I+R G+S+G C + T R
Sbjct: 127 ILRGPDGLSRG-CAFVTFTTR 146
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKL 75
+V LA +D+ LH F FGDI ++ + E K +G+ FV++ E A AI+ +
Sbjct: 6 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKL 75
+V LA +D+ LH F FGDI ++ + E K +G+ FV++ E A AI+ +
Sbjct: 9 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
>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 = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKL 75
+V LA +D+ LH F FGDI ++ + E K +G+ FV++ E A AI+ +
Sbjct: 11 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
+ FV +L+ I + F+ FG I ++VV GKSKGYGFV + A +AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 75 LQG 77
+ G
Sbjct: 77 MGG 79
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
NLY+ NL M E+ L FG++ S I +D++GTS+G G
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG 69
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 30/62 (48%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
N ++ NL ++D +L + FG + S++++ G S+G GF + + E I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 76 QG 77
G
Sbjct: 87 NG 88
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALD 70
SG +++ L + L ++ +G I S+K ++ + K KGYGFV + +P +A
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 71 AIEKLQGATVE-RMELYVGP 89
A+ L+ + V+ +M GP
Sbjct: 63 AVTALKASGVQAQMAKQSGP 82
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFV 60
FV L + L + F FGDI+ + V+ Q GKS+GYGFV
Sbjct: 21 FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKS-KGYGFVQYSTPESALDAIEK 74
N +V NL + + ++ ++FS+FG + + K++ +E K KG+GFV+ ES +AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 75 L 75
L
Sbjct: 62 L 62
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTS-KGFG 147
N+YV NL T E + E FS+FGK+ ++ + D KGFG
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG 46
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV+ + +L++IF FG ++ K++ G+ FV++ ESA AIE++ G
Sbjct: 35 FVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHG 87
Query: 78 ATVERMELYV 87
+ L V
Sbjct: 88 KSFANQPLEV 97
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV L + ++F FG+I+ ++ +G SKG FV+YS+ A AI L G
Sbjct: 19 FVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALHG 78
Query: 78 A 78
+
Sbjct: 79 S 79
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAE 161
S L+V L+ +E+ + F FG I I + +G SKG + V Y + A+ +A
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGC-AFVKYSSHAEAQAA 72
Query: 162 RKAILRAQ 169
A+ +Q
Sbjct: 73 INALHGSQ 80
>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 = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
KNL+ I +L ++F +I+ +VSQ+GKSKG ++++ + A +E+ QG
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 78 ATVE 81
A ++
Sbjct: 159 AEID 162
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV+NLA+T+ L + FS+FG ++ K K K Y FV + +A+ A++++ G
Sbjct: 19 FVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEDRGAAVKAMDEMNG 71
Score = 34.7 bits (78), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
L+V+NL +TEEIL + FSEFGK+ + KD
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD 50
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV+ + +L++IF FG ++ K++ G+ FV++ ESA AIE++ G
Sbjct: 8 FVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHG 60
Query: 78 ATVERMELYV 87
+ L V
Sbjct: 61 KSFANQPLEV 70
>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 = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESAL 69
+ G+ + V NL L ++F K+G + + + K S+G+ FV++ A
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103
Query: 70 DAIEKLQGATVERMELYV 87
DA++ + GA ++ EL V
Sbjct: 104 DAMDAMDGAVLDGRELRV 121
>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 = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV ++ ++ + F +G+I++ + + + G SKGY V+Y T + AL A E L
Sbjct: 76 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 135
Query: 77 GATV 80
GA +
Sbjct: 136 GAEI 139
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 57/112 (50%), Gaps = 12/112 (10%)
Query: 55 KGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDD 114
KG GF S A+ + E+++ + EL GP R EG L+V ++ ++
Sbjct: 34 KGRGFGSDSNTREAIHSYERVRNEDDD--ELEPGP-----QRSVEGWI---LFVTSIHEE 83
Query: 115 MTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKAI 165
E+ + EKF ++G+I ++ ++ D G SKG+ + V Y Q A ++A+
Sbjct: 84 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY-ALVEYETHKQALAAKEAL 134
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
L+VK L +D TEE L E F G + + +++ G+SKGFG V + + KA ++A+
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGF-VDFNSEEDAKAAKEAM 74
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 3 STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
S PN+ ++ S FVK L+ L + F G +++ V + G SKG+GFV +
Sbjct: 6 SGPNARSQPSK--TLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDF 61
Query: 63 STPESALDAIEKLQGATVE 81
++ E A A E ++ ++
Sbjct: 62 NSEEDAKAAKEAMEDGEID 80
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
+ NL+ + L ++F K I KV +Q GKSKGY F+++++ E A +A+
Sbjct: 20 LSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 79 TVE----RMELYVGP 89
+E R+EL GP
Sbjct: 77 EIEGRAIRLELQ-GP 90
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 98 QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
+E F L++ L + TEE L + ++GK+T V+ +D A+ S+GFG
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 35.8 bits (81), Expect = 0.042, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV ++ ++ + F +G+I++ + + + G SKGY V+Y T + AL A E L
Sbjct: 30 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 89
Query: 77 GATV 80
GA +
Sbjct: 90 GAEI 93
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKA 164
L+V ++ ++ E+ + EKF ++G+I ++ ++ D G SKG+ + V Y Q A ++A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY-ALVEYETHKQALAAKEA 87
Query: 165 ILRAQ 169
+ A+
Sbjct: 88 LNGAE 92
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+V NL + + +L + F +G ++S V + G+ FV++ P A DA+ +L G
Sbjct: 77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDG 132
Query: 78 ATV 80
T+
Sbjct: 133 RTL 135
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 33/73 (45%)
Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
G F+ L + L +F K G I ++ + KS+G+ F+ + P A +A +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 75 LQGATVERMELYV 87
+ G ++ + V
Sbjct: 68 MNGKSLHGKAIKV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.4 bits (80), Expect = 0.056, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
SG FV+NL L F++ G + + + + + GKSKG G V++ +PE A A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERA 61
Query: 72 IEKLQGATVERMELYVGPFIRRADRIQEGSS 102
+ G + E+ V R DR G S
Sbjct: 62 CRMMNGMKLSGREIDV-----RIDRNASGPS 87
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
S + ++V+NL D T ++L +KF+E G + I K NG SKG G
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCG 48
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
SG FV+NL L F++ G + + + + + GKSKG G V++ +PE A A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERA 64
Query: 72 IEKLQGATVERMELYVGPFIRRADRIQEGSS 102
+ G + E+ V R DR G S
Sbjct: 65 CRMMNGMKLSGREIDV-----RIDRNASGPS 90
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
++V+NL D T ++L +KF+E G + I K NG SKG G
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCG 51
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESAL 69
+ G+ + V NL L ++F K+G + + + K S+G+ FV++ A
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 70 DAIEKLQGATVERMELYV 87
DA++ + GA ++ EL V
Sbjct: 127 DAMDAMDGAVLDGRELRV 144
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+V NL + + +L + F +G ++S V + G+ FV++ P A DA+ L G
Sbjct: 77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRDLDG 132
Query: 78 ATV 80
T+
Sbjct: 133 RTL 135
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.0 bits (79), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
KNL + +L ++F +I+ +VS++GKSKG ++++ T A E+ QG
Sbjct: 97 LAKNLPYKVTQDELKEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQG 152
Query: 78 ATVE 81
++
Sbjct: 153 TEID 156
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
F+ ++ + +FS FG I+ +++ +G S+G FV ++T A AI+ +
Sbjct: 111 FIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 170
Query: 78 ATVERMELYVGPFI 91
A + ME P +
Sbjct: 171 A--QTMEGCSSPMV 182
Score = 32.0 bits (71), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 31/155 (20%), Positives = 65/155 (41%), Gaps = 19/155 (12%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT---SKGFGSKVLYVARAQKKAER 162
++V + +E+ L E F ++G + + + +D + SKG Y +A +A+
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 163 K----AILRAQFERMRKERAELYKN------------INDEVDEIELKQYFSQCGTISSV 206
+L ++ + A+ KN I+ + E +++ FS G I
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 137
Query: 207 KIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQ 241
+I+R G+S+G T+ + ++ M+ Q
Sbjct: 138 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 172
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQGATVERMELYV-G 88
L ++FSK+G I +V Q+ +S+G+ FV + + A +A E+ G ++ + V G
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG 91
Query: 89 P 89
P
Sbjct: 92 P 92
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
F+ ++ + +FS FG I+ +++ +G S+G FV ++T A AI+ +
Sbjct: 99 FIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 158
Query: 78 ATVERMELYVGPFI 91
A + ME P +
Sbjct: 159 A--QTMEGCSSPMV 170
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 31/155 (20%), Positives = 65/155 (41%), Gaps = 19/155 (12%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT---SKGFGSKVLYVARAQKKAER 162
++V + +E+ L E F ++G + + + +D + SKG Y +A +A+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 163 K----AILRAQFERMRKERAELYKN------------INDEVDEIELKQYFSQCGTISSV 206
+L ++ + A+ KN I+ + E +++ FS G I
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 207 KIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQ 241
+I+R G+S+G T+ + ++ M+ Q
Sbjct: 126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
FV NL + KL ++FS G + + ++ ++GKS+G G V + A+ AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 76 QG 77
G
Sbjct: 77 NG 78
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 97 IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGS 148
+Q G + ++V NLD + + L E FS G + I +D +G S+G G+
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 34.7 bits (78), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 55 ASMLASAPPQEQKQMLGERLFPLIQAM 81
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 34.7 bits (78), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQGATVERMELYV 87
L ++FSK+G I +V Q+ +S+G+ FV + + A +A E+ G ++ + V
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 34.7 bits (78), Expect = 0.099, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
L+V LD T+E L FS++G++ VI KD S+GFG
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTP 65
IG FV L + L FS++G++ ++ + +S+G+GFV++ P
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESA 68
F++NL+ + L ++ +FGD++ +VV+ + + SKG F Q+ T E+A
Sbjct: 19 FIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQGATVE 81
L ++FSK+G I +V Q+ +S+G+ FV + + A +A E+ G ++
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 80
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAIEKL 75
V NL+ L ++F FG I S++ ++++ G+SKG+ F+ + E A AI +
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSI--SRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 76 QGATVERMELYV 87
G + + L V
Sbjct: 78 SGFGYDHLILNV 89
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
+ V NL +D E L E F FG I+ + ++KD G SKGF
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF 59
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
IGN +KN++ L +IFS +G I + +GF+Q+ P+S DAIE
Sbjct: 15 IGNLPLKNVSKE----DLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 63
>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 = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
+ FV +L+ I + F+ FG I ++VV GKSKGYGFV + A +AI++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 75 LQG 77
+ G
Sbjct: 68 MGG 70
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip1
Length = 98
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 9 ASMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
IGN +KN++ L +IFS +G I + +GF+Q+ P+S DAIE
Sbjct: 7 IGNLPLKNVSKE----DLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 55
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 7 ASMLASAPPQEQKQMLGERLFPLIQAM 33
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
IGN +KN++ L +IFS +G I + +GF+Q+ P+S DAIE
Sbjct: 27 IGNLPLKNVSKE----DLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related Protein
4 (Larp4)
Length = 88
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 9 ASMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQGATVE 81
L ++FSK+G I +V Q+ +S+G+ FV + + A +A E+ G ++
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 83
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
IGN +KN++ L +IFS +G I + +GF+Q+ P+S DAIE
Sbjct: 27 IGNLPLKNVSKE----DLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 34/64 (53%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
V NL + + + ++F++FG ++ + V + G+S G V + AL A+++ +G
Sbjct: 92 LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 151
Query: 78 ATVE 81
++
Sbjct: 152 VPLD 155
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG 145
L V NLD +++ + E F+EFG + + D +G S G
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 130
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 8 ASMLASAPPQEQKQMLGERLFPLIQAM 34
>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
Length = 80
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 8 ASMLASAPPQEQKQMLGERLFPLIQAM 34
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYS 63
P+ L G F+ L + +++ ++ ++ + FG +++ +V S G SKGY F +Y
Sbjct: 87 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 146
Query: 64 TPESALDAIEKLQGATVERMELYV 87
AI L G + +L V
Sbjct: 147 DINVTDQAIAGLNGMQLGDKKLLV 170
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/107 (24%), Positives = 49/107 (45%), Gaps = 16/107 (14%)
Query: 46 VVVSQEGKSKGYGFVQY-----STPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG 100
V+ Q + K + F+++ +T A D I QG +++ IRR Q
Sbjct: 44 VLAVQINQDKNFAFLEFRSVDETTQAMAFDGI-IFQGQSLK---------IRRPHDYQPL 93
Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
+ L++ L + + ++ + E + FG + + + KD A G SKG+
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY 140
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYS 63
P+ L G F+ L + +++ ++ ++ + FG +++ +V S G SKGY F +Y
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144
Query: 64 TPESALDAIEKLQGATVERMELYV 87
AI L G + +L V
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLV 168
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 26/107 (24%), Positives = 49/107 (45%), Gaps = 16/107 (14%)
Query: 46 VVVSQEGKSKGYGFVQY-----STPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG 100
V+ Q + K + F+++ +T A D I QG +++ IRR Q
Sbjct: 42 VLAVQINQDKNFAFLEFRSVDETTQAMAFDGI-IFQGQSLK---------IRRPHDYQPL 91
Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
+ L++ L + + ++ + E + FG + + + KD A G SKG+
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY 138
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 355 SSMLVATSPDERKDILGQRLYPLVKKL 381
+SML + P E+K +LG+RL+PL++ +
Sbjct: 9 ASMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 23/28 (82%)
Query: 348 AASNENLSSMLVATSPDERKDILGQRLY 375
A+ +NLS++L +P+++K++LG+RLY
Sbjct: 5 ASQGQNLSTVLANLTPEQQKNVLGERLY 32
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 33 QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
++F FG I V+ +G SKG FV++S+ A AI L G+
Sbjct: 34 RLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 34/64 (53%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
V NL + + + ++F++FG ++ + V + G+S G V + AL A+++ +G
Sbjct: 39 LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 98
Query: 78 ATVE 81
++
Sbjct: 99 VPLD 102
Score = 28.1 bits (61), Expect = 9.3, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG 145
L V NLD +++ + E F+EFG + + D +G S G
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 34/64 (53%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
V NL + + + ++F++FG ++ + V + G+S G V + AL A+++ +G
Sbjct: 39 LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 98
Query: 78 ATVE 81
++
Sbjct: 99 VPLD 102
Score = 28.1 bits (61), Expect = 9.4, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG 145
L V NLD +++ + E F+EFG + + D +G S G
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
+ L+V NL D+TEE + + F ++GK + I KD KGFG
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFG 54
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+++NL I +++ IF K+G I+ +V + E ++G +V Y A +A++ L G
Sbjct: 12 YIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLSG 69
Query: 78 ATVERMELYV 87
V L V
Sbjct: 70 FNVSNRYLVV 79
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+V NL + +L + FS +G +++ + + G+ FV++ P A DA+ L G
Sbjct: 4 YVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDG 59
Query: 78 ATV----ERMELYVG-PFIRRADR 96
+ R+EL G P R DR
Sbjct: 60 KVICGSRVRVELSTGMPRRSRFDR 83
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESA 68
+V NL ++ N L++IFSK+G + ++ ++ KSKG F+ + +SA
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.7 bits (73), Expect = 0.36, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
V NL + + + ++F++FG ++ + V + G+S G V + AL A+++ G
Sbjct: 32 LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNG 91
Query: 78 ATVE 81
++
Sbjct: 92 VPLD 95
>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 = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 1 MWSTPNSE-ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYG 58
MW N A+ FV + KL + F +G I+ +V S+ GK +GY
Sbjct: 88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 59 FVQYSTPESALDAIEKLQGATVE 81
F++Y A + G ++
Sbjct: 148 FIEYEHERDMHSAYKHADGKKID 170
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 28/61 (45%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
FV L + + ++F FG I V+ +G SKG FV++ T A AI L
Sbjct: 16 FVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHS 75
Query: 78 A 78
+
Sbjct: 76 S 76
Score = 28.1 bits (61), Expect = 9.9, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 187 EVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQG-PGL 245
+ DE ++++ F GTI ++R G SKG QT E + + +++ + PG
Sbjct: 24 QTDE-DVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHSSRTLPGA 82
Query: 246 ASTI 249
+S++
Sbjct: 83 SSSL 86
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.0 bits (71), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKV--VVSQEGKSKGYGFVQYSTPESALDAIEKL 75
V+N+ + ++ ++FS FG++++ ++ ++ G +G+GFV + T + A A L
Sbjct: 19 LVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNAL 78
Query: 76 QGAT 79
+T
Sbjct: 79 CHST 82
>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 = 32.0 bits (71), Expect = 0.65, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 36/64 (56%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+V NL+ +++++FSK GDI+ + + + + G+ FV+Y + A +A+ + G
Sbjct: 22 YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYING 81
Query: 78 ATVE 81
++
Sbjct: 82 TRLD 85
Score = 31.6 bits (70), Expect = 0.73, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
LYV NL TEE + E FS+ G I +++ D T+ GF V Y +RA + + I
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF-CFVEYYSRADAENAMRYI 79
>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 = 0.66, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 77 G 77
G
Sbjct: 71 G 71
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 51
>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 = 31.6 bits (70), Expect = 0.76, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 77 G 77
G
Sbjct: 71 G 71
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 51
>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 = 31.6 bits (70), Expect = 0.76, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 13 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 72
Query: 77 G 77
G
Sbjct: 73 G 73
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 53
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+++NL I +++ IF K+G I+ +V + E ++G +V Y A +A + L G
Sbjct: 22 YIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLSG 79
Query: 78 ATV 80
V
Sbjct: 80 FNV 82
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 31.6 bits (70), Expect = 0.77, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 77 G 77
G
Sbjct: 71 G 71
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 51
>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 = 0.77, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 26 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 85
Query: 77 G 77
G
Sbjct: 86 G 86
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
>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 = 31.6 bits (70), Expect = 0.78, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
V NL + + + ++F++FG ++ + V + G+S G V + AL A ++ G
Sbjct: 33 LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNG 92
Query: 78 ATVE 81
++
Sbjct: 93 VPLD 96
>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 = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 4 TPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQY 62
P+S +L F+ L + +++ ++ ++ + FG +++ +V S G SKGY F +Y
Sbjct: 110 VPDSAHKL------FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
Query: 63 STPESALDAIEKLQGATVERMELYV 87
AI L G + +L V
Sbjct: 164 VDINVTDQAIAGLNGMQLGDKKLLV 188
>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 = 0.90, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
FV + +H F+++G+I++ + + + G KGY V+Y T + A A+E L
Sbjct: 27 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 86
Query: 77 G 77
G
Sbjct: 87 G 87
Score = 28.5 bits (62), Expect = 6.2, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGF 146
L+V + ++ TEE + +KF+E+G+I ++ ++ D G KG+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67
>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 = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 86 YVGPFIRRADRIQEGSS---FNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
++GPF RR+D E + N LYV +DMT +L FS FG I L + N
Sbjct: 20 HMGPF-RRSDSFPERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRN 74
>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 = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPES---ALDAIE 73
F+ L+ L FSKFG++ + + G+S+G+GFV + ES +D E
Sbjct: 3 FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 62
Query: 74 -KLQGATVE 81
KL G ++
Sbjct: 63 HKLNGKVID 71
Score = 28.9 bits (63), Expect = 5.0, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFG 147
+++ L D T++ L + FS+FG++ + D G S+GFG
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFG 44
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
V+NL + LHQIFSKFG + +++ ++ +QY+ P SA A L G
Sbjct: 38 VENLFYPVTLDVLHQIFSKFGTVLK---IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 94
Query: 79 TV 80
+
Sbjct: 95 NI 96
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
++L V L TE+ L E FS FG++ + + KD G SKGFG
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Score = 28.5 bits (62), Expect = 6.8, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 31 LHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
L + FS FG++ +V + G SKG+GFV+++ E+ + + +
Sbjct: 32 LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 1 MWSTPNSE-ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYG 58
MW N A+ FV + KL + F +G I+ +V S+ GK +GY
Sbjct: 88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 59 FVQYSTPESALDAIEKLQGATVE 81
F++Y A + G ++
Sbjct: 148 FIEYEHERDMHSAYKHADGKKID 170
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
V+NL + LHQIFSKFG + +++ ++ +QY+ P SA A L G
Sbjct: 33 VENLFYPVTLDVLHQIFSKFGTVLK---IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89
Query: 79 TV 80
+
Sbjct: 90 NI 91
>pdb|1XMC|A Chain A, C323m Mutant Structure Of Mouse Carnitine
Octanoyltransferase
pdb|1XMC|B Chain B, C323m Mutant Structure Of Mouse Carnitine
Octanoyltransferase
Length = 612
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 152 YVARAQKKAERKAILRAQ----FERMRKERAELYKNINDEVDEIELKQYFSQCGT--ISS 205
+ AR + ER +++ ++ +R+E+ ++K+ N +D + + FS C I+
Sbjct: 114 WPAREGTQLERGSMMLWHNLNYWQLLRREKLPVHKSGNTPLDMNQFRMLFSTCKVPGITR 173
Query: 206 VKIMRTDRGISKGHC-MAIAQTKRERTSYLRIMY 238
IM + S+GHC IA R R +++
Sbjct: 174 DSIMNYFKTESEGHCPTHIAVLCRGRAFVFDVLH 207
>pdb|1XMD|A Chain A, M335v Mutant Structure Of Mouse Carnitine
Octanoyltransferase
pdb|1XMD|B Chain B, M335v Mutant Structure Of Mouse Carnitine
Octanoyltransferase
Length = 612
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 152 YVARAQKKAERKAILRAQ----FERMRKERAELYKNINDEVDEIELKQYFSQCGT--ISS 205
+ AR + ER +++ ++ +R+E+ ++K+ N +D + + FS C I+
Sbjct: 114 WPAREGTQLERGSMMLWHNLNYWQLLRREKLPVHKSGNTPLDMNQFRMLFSTCKVPGITR 173
Query: 206 VKIMRTDRGISKGHC-MAIAQTKRERTSYLRIMY 238
IM + S+GHC IA R R +++
Sbjct: 174 DSIMNYFKTESEGHCPTHIAVLCRGRAFVFDVLH 207
>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 = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQY---STPESALD 70
G FV L+ L F+KFG++ + G+S+G+GF+ + ++ E LD
Sbjct: 12 GKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
Query: 71 AIE-KLQGATVE 81
E +L G ++
Sbjct: 72 QKEHRLDGRVID 83
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 107 YVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
+V L D +++ L + F++FG++ I D N G S+GFG
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFG 56
>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 = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 5/67 (7%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSK---GYGFVQYSTPESALDAIEK 74
+V NL+ +++++FSK GDI+ K+++ + K G+ FV+Y + A +A+
Sbjct: 43 YVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 75 LQGATVE 81
+ G ++
Sbjct: 101 INGTRLD 107
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 18 FVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI 72
F+ NL + + + IFSK+G + V KGY FVQYS A A+
Sbjct: 31 FIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAV 79
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
V+NL + LHQIFSKFG + +++ ++ +QY+ P SA A L G
Sbjct: 51 VENLFYPVTLDVLHQIFSKFGTVLK---IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107
Query: 79 TV 80
+
Sbjct: 108 NI 109
>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 = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 50 QEGKSKGYGFVQYSTPESALDAIEKLQG 77
Q G+SKGY F+++ ES+ A+ L G
Sbjct: 41 QTGRSKGYAFIEFRDLESSASAVRNLNG 68
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
++NL I +++ IF K+G I+ +V + E ++G +V Y A +A + L G
Sbjct: 22 MIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLSG 79
Query: 78 ATV 80
V
Sbjct: 80 FNV 82
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 50 QEGKSKGYGFVQYSTPESALDAIEKLQG 77
Q G+SKGY F+++ ES+ A+ L G
Sbjct: 39 QTGRSKGYAFIEFRDLESSASAVRNLNG 66
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
F+ L + +++ ++ ++ + FG +++ +V S G SKGY F +Y AI L
Sbjct: 5 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64
Query: 77 GATVERMELYV 87
G + +L V
Sbjct: 65 GMQLGDKKLLV 75
>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 = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 50 QEGKSKGYGFVQYSTPESALDAIEKLQG 77
Q G+SKGY F+++ ES+ A+ L G
Sbjct: 40 QTGRSKGYAFIEFRDLESSASAVRNLNG 67
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
+++NL I +++ IF K+G I+ ++ V +++G +V Y A +A + L G
Sbjct: 16 YIRNLPYKITAEEMYDIFGKYGPIR--QIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 73
Query: 78 ATV 80
V
Sbjct: 74 FNV 76
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 100 GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFG 147
GSS +++ L T+E L E F +FG++ ++ +D S+GFG
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 29.6 bits (65), Expect = 3.5, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 3 STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSK---GYGF 59
S+ +S + G+ V NL L ++F K+G + V + +E +K G+ F
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRV--GDVYIPREPHTKAPRGFAF 59
Query: 60 VQYSTPESALDAIEKLQGATVERMELYV 87
V++ A DA + GA ++ EL V
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRV 87
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
SG+ F+ NL ++ +F ++G + ++ K YGFV +A DA
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 72 IEKLQ 76
I L
Sbjct: 59 IRNLH 63
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 354 LSSMLVATSPDERKDILGQRLYPLVKKLK 382
L+S L + P+ ++ +LG+ LYPLV +L+
Sbjct: 10 LASALANSPPETQRMMLGENLYPLVDQLE 38
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 97 IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
I E + +YV LD+ ++E +L E F + G + + + KD G +G+G
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
SG+ ++ NL+ + L Q+F + +V++ GY FV Y A+ A
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----GYAFVDYPDQNWAIRA 60
Query: 72 IEKLQG 77
IE L G
Sbjct: 61 IETLSG 66
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K
PROTEIN
Length = 143
Score = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS------KVVVSQEGKSKGYGFV 60
+VKNLA + L IF ++ D S + + +EG+ KG F+
Sbjct: 49 YVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFI 97
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.1 bits (61), Expect = 9.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 99 EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVI 135
E + LYV L D +TE L F +FG+I ++ +
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITV 44
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 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,843,120
Number of Sequences: 62578
Number of extensions: 414065
Number of successful extensions: 1341
Number of sequences better than 100.0: 172
Number of HSP's better than 100.0 without gapping: 105
Number of HSP's successfully gapped in prelim test: 67
Number of HSP's that attempted gapping in prelim test: 1067
Number of HSP's gapped (non-prelim): 293
length of query: 398
length of database: 14,973,337
effective HSP length: 101
effective length of query: 297
effective length of database: 8,652,959
effective search space: 2569928823
effective search space used: 2569928823
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: 52 (24.6 bits)