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= 014331
(426 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 7/73 (9%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRGLDRT 112
I+ GN D R D+E +F +YG + +D+K+ FAF+ +D RDAEDA+ G D
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 113 EFGRKGRRLRVEW 125
++ G RLRVE+
Sbjct: 85 DY--DGYRLRVEF 95
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKI--ISVRIRRN---FAFVQYEVQEDATRAL 203
++V N P RT+D+E F YG I I ++ RR FAFV++E DA A+
Sbjct: 25 IYVGNLPP-DIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 117
+ GN +L F YG V D+ +AF++M+ DA +AIRGLD TEF +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF--Q 70
Query: 118 GRRLRVEWT 126
G+R+ V+ +
Sbjct: 71 GKRMHVQLS 79
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRAL 203
+ S L V N P T ++L FE YG +I I +++AFV E EDA A+
Sbjct: 8 KASTKLHVGNISPTCTN-QELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAI 61
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEF 114
++ GN A + +LER F YG + V + GFAF+ +D RDAEDA+RGLD
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 115 GRKGRRLRVEWT 126
G R+RVE +
Sbjct: 63 --CGSRVRVELS 72
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 168 DLERHFEPYGKIISVRIRRN---FAFVQYE---VQEDATRALDATNMSKLTDRV 215
+LER F YG + +V I RN FAFV++E EDA R LD + RV
Sbjct: 16 ELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 114
M +F GN +A + ++ LF +YGKV D+ + F++++D+ AEDAIR L +
Sbjct: 8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 115 GRKGRRLRVEWTKHE 129
G + VE +K++
Sbjct: 68 --HGVNINVEASKNK 80
Score = 32.7 bits (73), Expect = 0.44, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 213
LF+ N P +++ FE YGK++ I +N+ FV E + A A+ + KL
Sbjct: 11 LFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 214 RVISVE 219
I+VE
Sbjct: 70 VNINVE 75
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 117
IF GN +L LF R G+V D+ +AF++M+ E DA+ AI L+ E K
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV--K 69
Query: 118 GRRLRVE 124
G+R+ VE
Sbjct: 70 GKRINVE 76
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%)
Query: 166 TRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR 223
+++L FE G++I + +++AFV E + DA A+ N ++ + I+VE + +
Sbjct: 23 SQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK 80
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 213
+F+ N + + D+E F YGKI+ + + FAFVQY + +A A+ + +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 214 RVISVEYA 221
+V+ + A
Sbjct: 78 QVLDINLA 85
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 53 AMMRPIFCGNFE-YDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD 110
+M +F GN ++SD+E +F +YGK+ + GFAF+ +ER+A A+ G D
Sbjct: 13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGED 71
>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 = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 75/181 (41%), Gaps = 37/181 (20%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 106
M ++ G+ D ++ L F G + + DM + G+A++ DAE
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE--- 71
Query: 107 RGLDRTEFGR-KGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKT--LFVINFDPYH 163
R LD F KG+ +R+ W++ + + R S +F+ N D
Sbjct: 72 RALDTMNFDVIKGKPVRIMWSQRD----------------PSLRKSGVGNIFIKNLDK-S 114
Query: 164 TRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 217
+ L F +G I+S ++ + + FV +E QE A RA++ N L DR +
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Query: 218 V 218
V
Sbjct: 175 V 175
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 9/90 (10%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 201
P +L+V + P T E+ F P G I+S+R+ R+ +A+V ++ DA R
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEK-FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 202 ALDATNMSKLTDRVISVEYAVRDDDDRRNG 231
ALD N + + + + ++ RD R++G
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSG 102
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 62 NFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTE 113
N D R++DL+ LFR +G + R+ + GFAFI DA AI G+ +
Sbjct: 22 NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV--SG 79
Query: 114 FGRKGRRLRVEWTK 127
FG L VEW K
Sbjct: 80 FGYDHLILNVEWAK 93
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 164 TRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRV 215
TR DL+ F P+G I + + ++ FAF+ + +EDA RA+ + +
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI 86
Query: 216 ISVEYA 221
++VE+A
Sbjct: 87 LNVEWA 92
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 114
++ GN + +++LER F YG + V + GFAF+ +D RDA DA+R LD
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLD---- 131
Query: 115 GRK--GRRLRVEWTKHE 129
GR G R+RVE + E
Sbjct: 132 GRTLCGCRVRVELSNGE 148
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYE---VQEDATRALDATN 207
++V N +T +LER F YG + SV + RN FAFV++E DA R LD
Sbjct: 76 VYVGNLGNNGNKT-ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 208 MSKLTDRV 215
+ RV
Sbjct: 135 LCGCRVRV 142
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 114
++ GN + +++LER F YG + V + GFAF+ +D RDA DA+R LD
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELD---- 131
Query: 115 GRK--GRRLRVEWTKHE 129
GR G R+RVE + E
Sbjct: 132 GRTLCGCRVRVELSNGE 148
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYE---VQEDATRALDATN 207
++V N +T +LER F YG + SV + RN FAFV++E DA R LD
Sbjct: 76 VYVGNLGNNGNKT-ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 208 MSKLTDRV 215
+ RV
Sbjct: 135 LCGCRVRV 142
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 75/181 (41%), Gaps = 37/181 (20%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 106
M ++ G+ D ++ L F G + + DM + G+A++ DAE
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE--- 66
Query: 107 RGLDRTEFGR-KGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKT--LFVINFDPYH 163
R LD F KG+ +R+ W++ + + R S +F+ N D
Sbjct: 67 RALDTMNFDVIKGKPVRIMWSQRD----------------PSLRKSGVGNIFIKNLDK-S 109
Query: 164 TRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 217
+ L F +G I+S ++ + + FV +E QE A RA++ N L DR +
Sbjct: 110 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 218 V 218
V
Sbjct: 170 V 170
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 9/90 (10%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 201
P +L+V + P T E+ F P G I+S+R+ R+ +A+V ++ DA R
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEK-FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 202 ALDATNMSKLTDRVISVEYAVRDDDDRRNG 231
ALD N + + + + ++ RD R++G
Sbjct: 68 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSG 97
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 43/86 (50%), Gaps = 10/86 (11%)
Query: 51 EVAMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDA 102
+V M + N Y L R+F +YG+V DR +S GFAF+ D+RDA
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 103 EDAIRGLDRTEFGRKGRRLRVEWTKH 128
EDA+ +D GR LRV+ ++
Sbjct: 103 EDAMDAMDGAVL--DGRELRVQMARY 126
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 162 YHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTD 213
Y T L R FE YG++ V I R FAFV++ + DA A+DA + + L
Sbjct: 57 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116
Query: 214 RVISVEYA 221
R + V+ A
Sbjct: 117 RELRVQMA 124
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 169 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 220
L F P+G I ++I R FAFV++E+ EDA A+D N S+L R I V
Sbjct: 29 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 88
Query: 221 A 221
A
Sbjct: 89 A 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 11/77 (14%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMK-SGFAFIYMDDERDAEDAI 106
MR I+ GN Y A ++ LF ++GKV DR K GF F+ M +E +E AI
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AI 59
Query: 107 RGLDRTEFGRKGRRLRV 123
LD T+F GR +RV
Sbjct: 60 AKLDNTDF--MGRTIRV 74
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 169 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 220
L F P+G I ++I R FAFV++E+ EDA A+D N S+L R I V
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 221 A 221
A
Sbjct: 140 A 140
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 43/87 (49%), Gaps = 10/87 (11%)
Query: 50 FEVAMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERD 101
+V M + N Y L R+F +YG+V DR +S GFAF+ D+RD
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 102 AEDAIRGLDRTEFGRKGRRLRVEWTKH 128
AEDA+ +D GR LRV+ ++
Sbjct: 125 AEDAMDAMDGAVL--DGRELRVQMARY 149
Score = 35.0 bits (79), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 161 PYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLT 212
Y T L R FE YG++ V I R FAFV++ + DA A+DA + + L
Sbjct: 79 TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 138
Query: 213 DRVISVEYA 221
R + V+ A
Sbjct: 139 GRELRVQMA 147
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 169 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 220
L F P+G I ++I R FAFV++E+ EDA A+D N S+L R I V
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 221 A 221
A
Sbjct: 84 A 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 169 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 220
L F P+G I ++I R FAFV++E+ EDA A+D N S+L R I V
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 221 A 221
A
Sbjct: 82 A 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 169 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 220
L F P+G I ++I R FAFV++E+ EDA A+D N S+L R I V
Sbjct: 19 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 221 A 221
A
Sbjct: 79 A 79
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 58 IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRG 108
+F GN ++SD+E +F +YG+V + G+AF+ +ER A A+ G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLG 81
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 213
+F+ N + + D+E F YG++ + + +AFVQY + A A+ N L
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 214 RVISVEYA 221
+ + + A
Sbjct: 90 QTLDINMA 97
>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 = 9e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 201
P +T ++N+ P + +L F G++ S ++ R+ + FV Y +DA R
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 202 ALDATNMSKLTDRVISVEYA 221
A++ N +L + I V YA
Sbjct: 62 AINTLNGLRLQSKTIKVSYA 81
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 51 EVAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV--------DMKSGFAFIYMDDERDA 102
+V M + N Y L R+F +YG+V V GFAF+ D RDA
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 103 EDAIRGLDRTEFGRKGRRLRVEWTKH 128
+DA +D E GR LRV+ ++
Sbjct: 69 QDAEAAMDGAEL--DGRELRVQVARY 92
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 153 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------NFAFVQYEVQEDATRALD 204
TL V N Y T L R FE YG++ V I R FAFV++ + DA A
Sbjct: 15 TLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 205 ATNMSKLTDRVISVEYA 221
A + ++L R + V+ A
Sbjct: 74 AMDGAELDGRELRVQVA 90
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFG 115
+F GN D + D +RLF RYG+ V + GF FI ++ AE A LD T
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL- 83
Query: 116 RKGRRLRVEWTKH 128
K R LR+ + H
Sbjct: 84 -KSRPLRIRFATH 95
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 10/75 (13%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 109
+F G +D + LE++F +YG++ DR +S GF F+ ++ DA+DA+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 110 DRTEFGRKGRRLRVE 124
+ GR++RV+
Sbjct: 75 NGKSV--DGRQIRVD 87
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDA 205
LFV + T + LE+ F YG+I V + R F FV +E +DA A+ A
Sbjct: 15 LFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 206 TNMSKLTDRVISVEYAVRDDDDR 228
N + R I V+ A + D+R
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNR 96
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 11/76 (14%)
Query: 56 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIR 107
R ++ GN +Y + DLE F G ++R+ + G+A+I ER++ DA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF-AERNSVDAAV 95
Query: 108 GLDRTEFGRKGRRLRV 123
+D T F +GR ++V
Sbjct: 96 AMDETVF--RGRTIKV 109
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQE 197
N P+ L V Y T RDL F YG I V I R FAFV +E +
Sbjct: 41 ANPDPNCCLGVFGLSLYTTE-RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 198 DATRALDATNMSKLTDRVISVEYAV 222
DA A + N +L R I V++++
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSI 124
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 10/64 (15%)
Query: 71 DLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR 122
DL +F +YG + V D +S GFAF+Y ++ DA++A + E GRR+R
Sbjct: 62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR 119
Query: 123 VEWT 126
V+++
Sbjct: 120 VDFS 123
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDA 205
+NTR LFV F P + +L F P+G + V+I FAFV++E E A +A++
Sbjct: 3 SNTR----LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEE 57
Query: 206 TNMSKLTDRVISVEYA 221
+ ++ + V Y+
Sbjct: 58 VHGKSFANQPLEVVYS 73
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 117
+F F D ++S+L +F +G + V + +GFAF+ ++ A AI + F +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 66
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFG 115
+F GN D + ++ +LF +YGK V + GF FI ++ AE A LD
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL- 83
Query: 116 RKGRRLRVEWTKH 128
+G++LRV + H
Sbjct: 84 -RGKQLRVRFACH 95
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQE 197
N P+ L V Y T RDL F YG I V I R FAFV +E +
Sbjct: 10 ANPDPNCCLGVFGLSLYTTE-RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 198 DATRALDATNMSKLTDRVISVEYAV 222
DA A + N +L R I V++++
Sbjct: 69 DAKEAKERANGMELDGRRIRVDFSI 93
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 10/64 (15%)
Query: 71 DLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR 122
DL +F +YG + V D +S GFAF+Y ++ DA++A + E GRR+R
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR 88
Query: 123 VEWT 126
V+++
Sbjct: 89 VDFS 92
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMK-SGFAFIYMDDERDAEDAI 106
+R +F GN Y+A + L+ +F G V DR K G+ F D+ A A+
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 107 RGLDRTEFGRKGRRLRVEWTKHE 129
R L+ EF GR LRV+ E
Sbjct: 68 RNLNGREF--SGRALRVDNAASE 88
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQE 197
N P+ L V Y T RDL F YG I V I R FAFV +E +
Sbjct: 7 ANPDPNCCLGVFGLSLYTTE-RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 198 DATRALDATNMSKLTDRVISVEYAV 222
DA A + N +L R I V++++
Sbjct: 66 DAKEAKERANGMELDGRRIRVDFSI 90
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 10/64 (15%)
Query: 71 DLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR 122
DL +F +YG + V D +S GFAF+Y ++ DA++A + E GRR+R
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR 85
Query: 123 VEWT 126
V+++
Sbjct: 86 VDFS 89
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 147 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 204
N P LF+ N + DL R F PYG I+ + I+ F F+Q++ + A++
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 58 IFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR-TEFG 115
+F GN + + DL R+F YG + ++++K+ F FI D+ + DAI + FG
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFG 72
Query: 116 RK 117
+K
Sbjct: 73 KK 74
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 202
SKT ++N+ P + + + F G I S ++ R+ + FV Y DA +A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 203 LDATNMSKLTDRVISVEYA 221
++ N KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 69 QSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGLD 110
Q ++E+LF +YG++ + G FI D +AE+AI+GL+
Sbjct: 104 QKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
>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 = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRAL 203
+T ++N+ P + +L F G++ S ++ R+ + FV Y +DA RA+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 204 DATNMSKLTDRVISVEYA 221
+ N +L + I V YA
Sbjct: 62 NTLNGLRLQSKTIKVSYA 79
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 69 QSDLERLFRRYGKVDR----VDMKSGF----AFIYMDDERDAEDAIRGLD 110
Q D+E +F R+G++ VD +G AFI D +AE+AI +
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRAL 203
+T ++N+ P + +L F G++ S ++ R+ + FV Y +DA RA+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 204 DATNMSKLTDRVISVEYA 221
+ N +L + I V YA
Sbjct: 62 NTLNGLRLQSKTIKVSYA 79
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 69 QSDLERLFRRYGKVDR----VDMKSGF----AFIYMDDERDAEDAIRGLD 110
Q D+E +F R+G++ VD +G AFI D +AE+AI +
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 204
P LF+ N + DL R F PYG I+ + I+ F F+Q++ + A++
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 55
Score = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 58 IFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR-TEFG 115
+F GN + + DL R+F YG + ++++K+ F FI D+ + DAI + FG
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFG 64
Query: 116 RK 117
+K
Sbjct: 65 KK 66
>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 = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 14/80 (17%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
+ +F YD +S L R F YG + R+ M G+AFI + ERD A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 107 RGLDRTEFGRK--GRRLRVE 124
+ D G+K GRR+ V+
Sbjct: 162 KHAD----GKKIDGRRVLVD 177
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRAL 203
KTLFV + Y T L R FE YG I + + R +AF++YE + D A
Sbjct: 103 KTLFVARVN-YDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 204 DATNMSKLTDRVISVE 219
+ K+ R + V+
Sbjct: 162 KHADGKKIDGRRVLVD 177
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDA 205
+NTR LFV F P + +L F P+G + V+I FAFV++E E A +A++
Sbjct: 30 SNTR----LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEE 84
Query: 206 TNMSKLTDRVISVEYA 221
+ ++ + V Y+
Sbjct: 85 VHGKSFANQPLEVVYS 100
Score = 32.3 bits (72), Expect = 0.56, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 117
+F F D ++S+L +F +G + V + +GFAF+ ++ A AI + F +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 93
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 54 MMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR- 111
M +F GN + + DL R+F YG + ++++K+ F FI D+ + DAI +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQE 80
Query: 112 TEFGRK 117
FG+K
Sbjct: 81 MNFGKK 86
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 204
LF+ N + DL R F PYG I+ + I+ F F+Q++ + A++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 201
PSK+ ++ P+ DL R F YGK++ V I ++ AF+ + ++ A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 202 ALDATNMSKLTDRVISVEYAV 222
A N +L RVI A+
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
Score = 36.6 bits (83), Expect = 0.027, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 109
++ N + +DL R+F +YGKV +V + G AFI D+ A++ R +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 110 DRTE-FGR 116
+ + FGR
Sbjct: 79 NNKQLFGR 86
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 54 MMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR- 111
M +F GN + + DL R+F YG + ++++K+ F FI D+ + DAI +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQE 80
Query: 112 TEFGRK 117
FG+K
Sbjct: 81 MNFGKK 86
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 204
LF+ N + DL R F PYG I+ + I+ F F+Q++ + A++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 34/81 (41%), Gaps = 9/81 (11%)
Query: 146 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQE 197
N P+ L V Y T RDL F YG I V I R FAFV +E +
Sbjct: 10 ANPDPNCCLGVFGLSLYTTE-RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 198 DATRALDATNMSKLTDRVISV 218
DA A + N +L R I V
Sbjct: 69 DAKEAKERANGMELDGRRIRV 89
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 10/61 (16%)
Query: 71 DLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR 122
DL +F +YG + V D +S GFAF+Y ++ DA++A + E GRR+R
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR 88
Query: 123 V 123
V
Sbjct: 89 V 89
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDAT 200
R S T ++N+ P R+L F G I + RI R+ +AFV + + D+
Sbjct: 11 RASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQ 70
Query: 201 RALDATNMSKLTDRVISVEYA 221
RA+ N + ++ + V YA
Sbjct: 71 RAIKVLNGITVRNKRLKVSYA 91
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 41/158 (25%), Positives = 64/158 (40%), Gaps = 35/158 (22%)
Query: 66 DARQSDLERLFRRYGKVDRV----DMKSGF----AFIYMDDERDAEDAIRGLDRTEFGRK 117
D +L LFR G ++ D K+G+ AF+ E D++ AI+ L+ +
Sbjct: 25 DXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITV--R 82
Query: 118 GRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG 177
+RL+V + + TN L+V N P L+ F YG
Sbjct: 83 NKRLKVSYAR----------PGGESIKDTN------LYVTNL-PRTITDDQLDTIFGKYG 125
Query: 178 KIISVRIRRN--------FAFVQYEVQEDATRALDATN 207
I+ I R+ AFV+Y +E+A A+ A N
Sbjct: 126 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 11/79 (13%)
Query: 53 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAED 104
A R I+ GN +Y A +LE F G V+RV + GFA+I D+
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 105 AIRGLDRTEFGRKGRRLRV 123
++ LD + F +GR+++V
Sbjct: 64 SL-ALDESLF--RGRQIKV 79
>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 = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 153 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 204
T ++N+ P + +L F G++ S ++ R+ + FV Y +DA RA++
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 205 ATNMSKLTDRVISVEYA 221
N +L + I V YA
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 11/76 (14%)
Query: 56 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIR 107
R I+ GN +Y A +LE F G V+RV + GFA+I D+ ++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 64
Query: 108 GLDRTEFGRKGRRLRV 123
LD + F +GR+++V
Sbjct: 65 ALDESLF--RGRQIKV 78
>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 = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 115
+F GN D + ++ +LF +YGK V + GF FI ++ AE A LD
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL- 76
Query: 116 RKGRRLRVEWTKH 128
+G++LRV + H
Sbjct: 77 -RGKQLRVRFACH 88
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALD 204
+ L+V N D T L+++F+ G I +++I N+AFV+Y DA AL
Sbjct: 1 RVLYVGNLDKAITEDI-LKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 205 ATNMSKLTDRVISVEYAVR 223
N ++ + ++ + +A +
Sbjct: 60 TLNGKQIENNIVKINWAFQ 78
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 202
SKT ++N+ P + + + F G I S ++ R+ + FV Y DA +A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 203 LDATNMSKLTDRVISVEYA 221
++ N KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT 206
R TL+V D T R F P+G II + + RN AFV YE E A +A+
Sbjct: 13 RKGNTLYVYGEDMTPTLLRG---AFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 69
Query: 207 NMSKLTDRVISVEYA 221
N +++ + V A
Sbjct: 70 NGTQVESVQLKVNIA 84
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 109
+F YD +S L R F YG + R+ M G+AFI + ERD A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 110 DRTEFGRKGRRLRVE 124
D + GRR+ V+
Sbjct: 165 DGKKI--DGRRVLVD 177
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRAL 203
KTLFV + Y T L R FE YG I + + R +AF++YE + D A
Sbjct: 103 KTLFVARVN-YDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 204 DATNMSKLTDRVISVE 219
+ K+ R + V+
Sbjct: 162 KHADGKKIDGRRVLVD 177
>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 = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 202
SKT ++N+ P + + F G+I S ++ R+ + FV Y +DA +A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 203 LDATNMSKLTDRVISVEYA 221
++ N +L + I V YA
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 8/50 (16%)
Query: 69 QSDLERLFRRYGK-------VDRVDMKS-GFAFIYMDDERDAEDAIRGLD 110
Q +LE+LF +YG+ VD+V S G FI D +AE+AI+GL+
Sbjct: 102 QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 40/167 (23%), Positives = 67/167 (40%), Gaps = 47/167 (28%)
Query: 66 DARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRK 117
+ Q + LF G++ D++ +S G+ F+ D +DAE AI L+
Sbjct: 13 NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN------- 65
Query: 118 GRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKT------LFVINFDPYHTRTRDLER 171
G RL+ + K + RPS L+V P ++LE+
Sbjct: 66 GLRLQTKTIK-----------------VSYARPSSASIRDANLYVSGL-PKTMTQKELEQ 107
Query: 172 HFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSK 210
F YG+II+ RI R F++++ + +A A+ N K
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 105 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 163
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 103 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 161
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 102 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 160
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 162
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 162
>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 = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT 206
R TL+V D T R F P+G II + + RN AFV YE E A +A+
Sbjct: 37 RKGNTLYVYGEDMTPTLLRG---AFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 93
Query: 207 NMSKLTDRVISVEYA 221
N +++ + V A
Sbjct: 94 NGTQVESVQLKVNIA 108
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 152 KTLFVINFDPYHTRTRD-LERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSK 210
K LFV N +T T + LE+ F +GK+ V+ +++AF+ ++ ++ A +A++ N
Sbjct: 12 KVLFVRNLA--NTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKD 69
Query: 211 LTDRVISVEYAVRDDDDRR 229
L I + +A D R+
Sbjct: 70 LEGENIEIVFAKPPDQKRK 88
Score = 32.0 bits (71), Expect = 0.61, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 32/59 (54%)
Query: 52 VAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD 110
+A ++ +F N + LE+ F ++GK++RV +AFI+ D+ A A+ ++
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMN 66
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 55 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 106
++ IF G + D + L F +YGK++ +++ K GFAF+ DD D+ D I
Sbjct: 97 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 155
>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 = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 162 YHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTD 213
Y + + F P+G I S+ + + FAFV+YEV E A AL+ N L
Sbjct: 38 YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97
Query: 214 RVISV 218
R I V
Sbjct: 98 RNIKV 102
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.4 bits (80), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 110
+F G + + L+ +F ++G + DR GFAFI ++ DA++A + ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 111 RTEFGRKGRRLRVEWTK 127
G+ ++VE K
Sbjct: 70 GKSL--HGKAIKVEQAK 84
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.0 bits (79), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 202
S T ++N+ P R+L F G I + RI R+ +AFV + + D+ RA
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 203 LDATNMSKLTDRVISVEYA 221
+ N + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 41/158 (25%), Positives = 64/158 (40%), Gaps = 35/158 (22%)
Query: 66 DARQSDLERLFRRYGKVDRV----DMKSGF----AFIYMDDERDAEDAIRGLDRTEFGRK 117
D +L LFR G ++ D K+G+ AF+ E D++ AI+ L+ +
Sbjct: 14 DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--R 71
Query: 118 GRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG 177
+RL+V + + TN L+V N P L+ F YG
Sbjct: 72 NKRLKVSYAR----------PGGESIKDTN------LYVTNL-PRTITDDQLDTIFGKYG 114
Query: 178 KIISVRIRRN--------FAFVQYEVQEDATRALDATN 207
I+ I R+ AFV+Y +E+A A+ A N
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
>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 = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFA--------FVQYEVQEDATRALDA 205
+FV + P T T D++ F P+G+I R+ ++ A FV + + DA A+
Sbjct: 18 VFVGDLSPEIT-TEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 206 TNMSKLTDRVISVEYAVR 223
L R I +A R
Sbjct: 77 MGGQWLGGRQIRTNWATR 94
>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 = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALD 204
S +F+ N D + L F +G I+S ++ + + FV +E QE A RA++
Sbjct: 5 SGNIFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 63
Query: 205 ATNMSKLTDRVISV 218
N L DR + V
Sbjct: 64 KMNGMLLNDRKVFV 77
>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 = 34.7 bits (78), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 162 YHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTD 213
Y + + F P+G I S+ + + FAFV+YEV E A AL+ N L
Sbjct: 23 YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 82
Query: 214 RVISV 218
R I V
Sbjct: 83 RNIKV 87
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 34.7 bits (78), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 201
S T ++N+ P R+L F G I + RI R+ +AFV + + D+ R
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 202 ALDATNMSKLTDRVISVEYA 221
A+ N + ++ + V YA
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFA--------FVQYEVQEDATRALDA 205
+FV + P T T D++ F P+GKI R+ ++ A FV + + DA A+
Sbjct: 18 VFVGDLSPEIT-TEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 206 TNMSKLTDRVISVEYAVR 223
L R I +A R
Sbjct: 77 MGGQWLGGRQIRTNWATR 94
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 10/90 (11%)
Query: 150 PSKTLFVINFDPYHTRTRDLERHF----EPYGKIISVRIR----RNFAFVQYEVQEDATR 201
P+K L++ N P T RDL F E G I R+ R AF+ + +E A +
Sbjct: 24 PNKVLYLKNLSPRVTE-RDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 202 ALDATNMSKLTDRVISVEYAVRDDDDRRNG 231
AL N KL +++ +E+ ++ R +G
Sbjct: 83 ALHLVNGYKLYGKILVIEFG-KNKKQRSSG 111
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 162 YHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTD 213
Y + + F P+G I S+ + FAFV+YEV E A AL+ N L
Sbjct: 22 YELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGG 81
Query: 214 RVISV 218
R I V
Sbjct: 82 RNIKV 86
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATN 207
+F+ N D + L F +G I+S ++ + + FV +E QE A RA++ N
Sbjct: 14 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 208 MSKLTDRVISV 218
L DR + V
Sbjct: 73 GMLLNDRKVFV 83
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATN 207
L+V N D R L + F P+G I S ++ + F FV + E+AT+A+ N
Sbjct: 18 LYVKNLDDGIDDER-LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 208 MSKLTDRVISVEYAVRDDD 226
+ + + V A R ++
Sbjct: 77 GRIVATKPLYVALAQRKEE 95
>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 = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTDSD 92
>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 = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTDSD 92
>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 = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 1 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYAKTDSD 87
>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 = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 2 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYAKTDSD 88
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 58 IFCGNFEYDARQSDLERLFRRYG-------KVDRVDMK-SGFAFIYMDDERDAEDAIRGL 109
+F N Y + + DLE+LF YG +D + K GFAF+ A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 110 DRTEFGRKGRRLRV 123
D F +GR L V
Sbjct: 71 DGQVF--QGRMLHV 82
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAI 106
IF G ++ +++L F+++G V V M GF FI +DE+ + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 33.1 bits (74), Expect = 0.28, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV--------RIRRNFAFVQYEVQEDAT 200
+ S TL+V N Y T + E F G I + + F FV+Y + DA
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYE-LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 201 RALDATNMSKLTDRVISVEY 220
A+ N ++L DR+I ++
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 57 PIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRG 108
++ GN + + + LF + G + ++ M GF F+ DAE+A+R
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 109 LDRTEFGRKGRRLRVEW 125
++ T R +R +W
Sbjct: 101 INGTRL--DDRIIRTDW 115
>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 = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 33.1 bits (74), Expect = 0.34, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYAKTDSD 89
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN 207
K LFV N T LE+ F +GK+ V+ +++AFV +E + A +A+D N
Sbjct: 16 KVLFVRNLATTVTE-EILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMN 70
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%)
Query: 52 VAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAI 106
+A ++ +F N + LE+ F +GK++RV +AF++ +D A A+
Sbjct: 12 MAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAM 66
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 155 FVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDAT 206
++N+ P L + FE YG I SV+I R + FV+++ A +A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 207 NMSKLTDRVISVEYA 221
N + ++ + V A
Sbjct: 105 NGFNILNKRLKVALA 119
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ + ++YA D D
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 0.59, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 110
++ GN + + + LF + G + D++ GF F+ DAE+A+R ++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 111 RTEFGRKGRRLRVEW 125
T R +R +W
Sbjct: 81 GTRL--DDRIIRTDW 93
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 149 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV-------RIRRNFAFVQYEVQEDATR 201
+ S TL+V N Y T + E F G I + + F FV+Y + DA
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYEL-FSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAEN 74
Query: 202 ALDATNMSKLTDRVISVEY 220
A+ N ++L DR+I ++
Sbjct: 75 AMRYINGTRLDDRIIRTDW 93
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ ++YA D D
Sbjct: 65 TNALRSXQGFPFYDKPXRIQYAKTDSD 91
>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 = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ ++YA D D
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 31.6 bits (70), Expect = 0.92, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 148 TRPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDA 199
TRP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 200 TRALDATNMSKLTDRVISVEYAVRDDD 226
T AL + D+ ++YA D D
Sbjct: 63 TNALRSXQGFPFYDKPXRIQYAKTDSD 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 69 QSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGLD 110
Q ++E+LF +YG++ + G FI D +AE+AI+GL+
Sbjct: 15 QKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 64
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 10/71 (14%)
Query: 161 PYHTRTRDLERHFEPYGKIISVRI---------RRNFAFVQYEVQEDATRALDA-TNMSK 210
P+ R++ F +G++ +VR+ R F FV + ++DA +A +A + +
Sbjct: 24 PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH 83
Query: 211 LTDRVISVEYA 221
L R + +E+A
Sbjct: 84 LYGRRLVLEWA 94
>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 = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 149 RPSKTLFVINFDPYHTR---TRDLERHFEPYGKIISVRIRRNF-----AFVQYEVQEDAT 200
RP+ T+++ N + + + L F +G+I+ + + R+ AFV ++ AT
Sbjct: 1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60
Query: 201 RALDATNMSKLTDRVISVEYAVRDDD 226
AL + D+ + ++YA D D
Sbjct: 61 NALRSMQGFPFYDKPMRIQYAKTDSD 86
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 152 KTLFVINFDPYHTRTRDLERHFEPY--GKIISVRIRRNFAFVQYEVQEDATRALDATNMS 209
K L+V N T +E+ F G + V+ R++AFV + +EDA A+ A N
Sbjct: 16 KILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGK 74
Query: 210 KLTDRVISVEYA 221
L I V A
Sbjct: 75 VLDGSPIEVTLA 86
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 55 MRPIFCGNFEYDARQSDLERLF--RRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD-R 111
M ++ GN DL +LF R+ +V +KSG+AF+ D+ A AI L +
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67
Query: 112 TEFGRKGRRLRVEWT 126
E G+ + V+++
Sbjct: 68 VEL--HGKIMEVDYS 80
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 58 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRTEFG 115
++ G + + L R F R+G + +D G FA+I + A+ A + G
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLG 79
Query: 116 RKGRRLRVEWTK 127
RRLRV++ K
Sbjct: 80 GPDRRLRVDFAK 91
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 59 FCGNFEYDARQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEF 114
+ GN + A ++DL LF+ +G + +D K G FI D A I L F
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFI--LDFKHYPEKGCCFIKYDTHEQAAVCIVAL--ANF 86
Query: 115 GRKGRRLRVEWTK 127
+GR LR W K
Sbjct: 87 PFQGRNLRTGWGK 99
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.6 bits (65), Expect = 3.7, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 10/84 (11%)
Query: 151 SKTLFVINFDPYHTRTRDLERHFEPYGKIISV-RIRRN--------FAFVQYEVQEDATR 201
S +F+ N DP + L F +G I+ +I R+ +AF+ + + +
Sbjct: 5 SSGIFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 202 ALDATNMSKLTDRVISVEYAVRDD 225
A++A N L +R I+V YA + D
Sbjct: 64 AIEAMNGQYLCNRPITVSYAFKKD 87
>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 = 29.3 bits (64), Expect = 4.7, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 168 DLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 219
D+ F YG+I ++ + + + V+YE ++A A++ N L + ISV+
Sbjct: 23 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
Query: 220 Y 220
+
Sbjct: 83 W 83
>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 = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 53 AMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDA 105
M +F G + ++++ F RYG V DR + G+ F+ ++ D +
Sbjct: 7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKI 66
Query: 106 IRGLDRTEFGRKGRRLRV 123
+ ++ G++L++
Sbjct: 67 V----ESQINFHGKKLKL 80
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 168 DLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 219
D+ F YG+I ++ + + + V+YE ++A A++ N L + ISV+
Sbjct: 23 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
Query: 220 Y 220
+
Sbjct: 83 W 83
>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 = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 154 LFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDA 205
LF+ + P +DL + F P+G ++S ++ + F FV Y+ A A+ +
Sbjct: 28 LFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 206 TNMSKLTDRVISVEYAVRDDDDRRNG 231
N ++ + + V+ R +D ++G
Sbjct: 87 MNGFQIGMKRLKVQLK-RSKNDSKSG 111
>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 = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 168 DLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 219
D+ F YG+I ++ + + + V+YE ++A A++ N L + ISV+
Sbjct: 25 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
Query: 220 Y 220
+
Sbjct: 85 W 85
>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 = 28.1 bits (61), Expect = 9.7, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 11/69 (15%)
Query: 59 FCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGLD 110
F G +D + DL+ F ++G+V +K GF FI D E LD
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV---LD 71
Query: 111 RTEFGRKGR 119
+ E GR
Sbjct: 72 QKEHRLDGR 80
>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 = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 168 DLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 219
D+ F YG+I ++ + + + V+YE ++A A++ N L + ISV+
Sbjct: 23 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
Query: 220 Y 220
+
Sbjct: 83 W 83
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,332,701
Number of Sequences: 62578
Number of extensions: 429049
Number of successful extensions: 962
Number of sequences better than 100.0: 118
Number of HSP's better than 100.0 without gapping: 52
Number of HSP's successfully gapped in prelim test: 66
Number of HSP's that attempted gapping in prelim test: 814
Number of HSP's gapped (non-prelim): 176
length of query: 426
length of database: 14,973,337
effective HSP length: 102
effective length of query: 324
effective length of database: 8,590,381
effective search space: 2783283444
effective search space used: 2783283444
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: 53 (25.0 bits)