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= 006316
(650 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 = 231 bits (589), Expect = 9e-61, Method: Compositional matrix adjust.
Identities = 108/172 (62%), Positives = 137/172 (79%), Gaps = 1/172 (0%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
SLYVGDL V ++ LY+ F+ G ++S+RVCRD+ TRRSLGY YVN+ +A RALD
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
+NF + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 130
Query: 160 ATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
D G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F ++ERE+
Sbjct: 131 VCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 64/189 (33%), Positives = 100/189 (52%), Gaps = 18/189 (9%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
++YV +L TE L + F G I S V RD +S + +VNF P DA R+++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
+N K + +Q+ + SL+++ N+++KNLD SI + L
Sbjct: 72 MNFDVIKGKPVRIMWSQR------------DPSLRKSGVG----NIFIKNLDKSIDNKAL 115
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
+ FS FG I SCKV+ D NG S+G GFV F T E A +A+ +MNG ++ + ++V +
Sbjct: 116 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 174
Query: 399 RKEERRARL 407
++ER A L
Sbjct: 175 SRKEREAEL 183
Score = 93.2 bits (230), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 55/181 (30%), Positives = 99/181 (54%), Gaps = 6/181 (3%)
Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAID 186
++++ +L + L++ FS G ILS +V D + + S GY +V F A+ A+D
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIIT 246
+N ++ K V + +R+ + K+ N+++KNL ++ L F FG I
Sbjct: 71 TMNFDVIKGKPVRI----MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNIL 126
Query: 247 STAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKG 306
S V+ D +G SK +GFV+F+ + A R++E +NG +D++ +VG+ + + ERE EL
Sbjct: 127 SCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA 185
Query: 307 K 307
+
Sbjct: 186 R 186
>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 = 231 bits (588), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 109/178 (61%), Positives = 139/178 (78%), Gaps = 1/178 (0%)
Query: 34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
A + SLYVGDL V ++ LY+ F+ G ++S+RVCRD+ TRRSLGY YVN+ +
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
A RALD +NF + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 70 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
ILSCKV D G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F ++ERE+
Sbjct: 130 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186
Score = 95.5 bits (236), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 64/189 (33%), Positives = 100/189 (52%), Gaps = 18/189 (9%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
++YV +L TE L + F G I S V RD +S + +VNF P DA R+++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
+N K + +Q+ + SL+++ N+++KNLD SI + L
Sbjct: 77 MNFDVIKGKPVRIMWSQR------------DPSLRKSGVG----NIFIKNLDKSIDNKAL 120
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
+ FS FG I SCKV+ D NG S+G GFV F T E A +A+ +MNG ++ + ++V +
Sbjct: 121 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 179
Query: 399 RKEERRARL 407
++ER A L
Sbjct: 180 SRKEREAEL 188
Score = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 56/193 (29%), Positives = 104/193 (53%), Gaps = 6/193 (3%)
Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDN 177
+P+ ++++ +L + L++ FS G ILS +V D + + S GY +V F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 178 EESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKK 237
A+ A+D +N ++ K V + +R+ + K+ N+++KNL ++ L
Sbjct: 67 PADAERALDTMNFDVIKGKPVRI----MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 238 IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
F FG I S V+ D +G SK +GFV+F+ + A R++E +NG +D++ +VG+ + +
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 298 YEREMELKGKFEQ 310
ERE EL + ++
Sbjct: 182 KEREAELGARAKE 194
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 139 bits (350), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 65/93 (69%), Positives = 80/93 (86%), Gaps = 1/93 (1%)
Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNE 178
DP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV D G S+GYGFV F+ +
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
E+A+ AI+K+NGMLLND++VFVG F ++ERE+
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 94
Score = 75.9 bits (185), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 37/83 (44%), Positives = 55/83 (66%), Gaps = 1/83 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
N+++KNLD SI + L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
NG ++ + ++V + ++ER A
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREA 94
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 54/89 (60%), Gaps = 1/89 (1%)
Query: 215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
K+ N+++KNL ++ L F FG I S V+ D +G SK +GFV+F+ + A R
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 66
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREME 303
++E +NG +D++ +VG+ + + ERE E
Sbjct: 67 AIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 45/73 (61%), Gaps = 2/73 (2%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
++++ +LD S+++ LYD F+ G ++S +V D + S GYG+V++ A RA+++
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 70
Query: 101 LNFTPLNGKPIRI 113
+N LN + + +
Sbjct: 71 MNGMLLNDRKVFV 83
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 137 bits (346), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 68/108 (62%), Positives = 84/108 (77%), Gaps = 3/108 (2%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
G+GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV D G S+GYGFV F+ +E+A+ AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 186 DKLNGMLLNDKQVFVGPFLRKQEREST--ADKTRFNNVYVKNLSETTT 231
+K+NGMLLND++VFVG F ++ERE+ A F NVY+KN +T
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
Score = 77.4 bits (189), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 38/85 (44%), Positives = 56/85 (65%), Gaps = 1/85 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
N+++KNLD SI + L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 383 NGKMVVSKPLYVALAQRKEERRARL 407
NG ++ + ++V + ++ER A L
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAEL 90
Score = 65.5 bits (158), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 63/110 (57%), Gaps = 11/110 (10%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
N+++KNL ++ L F FG I S V+ D +G SK +GFV+F+ + A R++E +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNL 329
NG +D++ +VG+ + + ERE EL + A +F N+Y+KN
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGAR--------AKEF--TNVYIKNF 105
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S ++++ +LD S+++ LYD F+ G ++S +V D + S GYG+V++ A RA+
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAI 62
Query: 99 DELNFTPLNGKPIRI-MYSYRDPTIRKSGA-----GNIFIKNL 135
+++N LN + + + + R + GA N++IKN
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 132 bits (333), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 66/77 (85%), Positives = 70/77 (90%)
Query: 552 GALASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEAL 611
GALASALAN+ PE QR +LGENLYPLVDQLEHD AAKVTGMLLEMDQTEVLHLLESP+AL
Sbjct: 8 GALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDAL 67
Query: 612 KAKVAEAMEVLRNVAQQ 628
KAKVAEAMEVLR+ Q
Sbjct: 68 KAKVAEAMEVLRSAQQH 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 116 bits (290), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 56/88 (63%), Positives = 74/88 (84%), Gaps = 1/88 (1%)
Query: 318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK 377
+++ +NLYVKNLDD I D++L++ FS FGTITS KVM + G S+G GFV FS+ EEA+K
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATK 70
Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRA 405
A+TEMNG++V +KPLYVALAQRKEER++
Sbjct: 71 AVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 73.2 bits (178), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 41/94 (43%), Positives = 59/94 (62%), Gaps = 4/94 (4%)
Query: 211 STADK-TRFN--NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFD 267
S+ D+ TR+ N+YVKNL + ++ L+K F FG ITS VM + G+SK FGFV F
Sbjct: 5 SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFS 63
Query: 268 DPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
P++A ++V +NG+ K YV AQ+K ER+
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
N+++KNLD ID++ L FS FG I S KV + G+S+G+GFV F + E A A+ ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 189 NGMLLNDKQVFVGPFLRKQERES 211
NG ++ K ++V RK+ER+S
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 57/102 (55%), Gaps = 4/102 (3%)
Query: 26 ANNGGVGD-ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
++G GD ++ +LYV +LD ++D +L F+ G + S +V + RS G+G
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFG 58
Query: 85 YVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
+V +++ EAT+A+ E+N + KP+ + + R R+SG
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE-RQSG 99
>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 = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 56/152 (36%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ +L LF+ +G+V S ++ RD SLGYG+VNY A +A RA++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
LN L K I++ SY P+ N++I L +++ K + D FS FG I++ +V
Sbjct: 63 TLNGLRLQSKTIKV--SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 160 ATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
D + G SRG F++FD A+ AI NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 83.2 bits (204), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 22/186 (11%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+L+ +F G + S ++RD G S +GFVN+ DA R++
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
LNG + K V A + +++ + NLY+ L +++ +
Sbjct: 64 LNGLRLQSKTIKVSYA------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
+++FS FG I + +V+ D G+SRG F+ F EA +A+T NG S+P+ V
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVK 165
Query: 396 LAQRKE 401
A E
Sbjct: 166 FAANLE 171
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 49/160 (30%), Positives = 80/160 (50%), Gaps = 8/160 (5%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSA 184
G N+ + L +++ L FS+ G + S K+ D + G S GYGFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
I+ LNG+ L K + V + E D N+Y+ L T T+ D++ +F FG
Sbjct: 61 INTLNGLRLQSKTIKVS--YARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
I ++ V+ D G S+ F+ FD +A ++ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
NL V L +++ D+L+ LFS G + S K++RD G S G GFV + TA++A +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 382 MNGKMVVSKPLYVALAQRKEE 402
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 56/152 (36%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ +L LF+ +G+V S ++ RD SLGYG+VNY A +A RA++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
LN L K I++ SY P+ N++I L +++ K + D FS FG I++ +V
Sbjct: 63 TLNGLRLQSKTIKV--SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 160 ATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
D + G SRG F++FD A+ AI NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 22/186 (11%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+L+ +F G + S ++RD G S +GFVN+ DA R++
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
LNG + K V A + +++ + NLY+ L +++ +
Sbjct: 64 LNGLRLQSKTIKVSYA------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
+++FS FG I + +V+ D G+SRG F+ F EA +A+T NG S+P+ V
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVX 165
Query: 396 LAQRKE 401
A E
Sbjct: 166 FAANLE 171
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 49/160 (30%), Positives = 80/160 (50%), Gaps = 8/160 (5%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSA 184
G N+ + L +++ L FS+ G + S K+ D + G S GYGFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
I+ LNG+ L K + V + E D N+Y+ L T T+ D++ +F FG
Sbjct: 61 INTLNGLRLQSKTIKVS--YARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
I ++ V+ D G S+ F+ FD +A ++ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
NL V L +++ D+L+ LFS G + S K++RD G S G GFV + TA++A +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 382 MNGKMVVSKPLYVALAQRKEE 402
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 95.5 bits (236), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 57/182 (31%), Positives = 96/182 (52%), Gaps = 22/182 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+ K +FG G I S ++RD G+S +GFVN+ DP+DA +++
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
LNG K K V A + ++ NLYV L ++S ++
Sbjct: 66 LNGLKLQTKTIKVSYA------------------RPSSASIRDANLYVSGLPKTMSQKEM 107
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGK--MVVSKPLYVA 395
++LFS++G I + +++ D G+SRG GF+ F EA +A+ +NG+ + ++P+ V
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVK 167
Query: 396 LA 397
A
Sbjct: 168 FA 169
Score = 93.2 bits (230), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 52/152 (34%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ + LF +G + S ++ RD T +SLGYG+VNY+ ++A +A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
LN L K I++ SY P+ N+++ L K++ K + FS +G I++ ++
Sbjct: 65 TLNGLKLQTKTIKV--SYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 160 ATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
D + G SRG GF++FD A+ AI LNG
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 89.0 bits (219), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 53/157 (33%), Positives = 88/157 (56%), Gaps = 8/157 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
N+ + L +++ F + G+I SCK+ D + GQS GYGFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IIT 246
LNG+ L K + V R S+A R N+YV L +T ++ +++++F ++G IIT
Sbjct: 66 LNGLKLQTKTIKVS-----YARPSSAS-IRDANLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 247 STAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
S ++ A G S+ GF+ FD +A +++ LNG+K
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
>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 = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ + LF +G++ S ++ RD T +SLGYG+VNY +A +A++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
LN L K I++ SY P+ N+++ L K++ K L FS +G I++ ++
Sbjct: 63 TLNGLRLQTKTIKV--SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 160 ATDSL-GQSRGYGFVQFDNEESAKSAIDKLNG 190
D + G SRG GF++FD A+ AI LNG
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 8/157 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
N+ + L +++ + F + G I SCK+ D + GQS GYGFV + + + A+ AI+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IIT 246
LNG+ L K + V R S+A R N+YV L +T T+ +L+++F ++G IIT
Sbjct: 64 LNGLRLQTKTIKVS-----YARPSSAS-IRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 247 STAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
S ++ G S+ GF+ FD +A +++ LNG+K
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Score = 89.4 bits (220), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 54/183 (29%), Positives = 94/183 (51%), Gaps = 22/183 (12%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVE 277
N+ V L + T+++ + +FG G I S ++RD G+S +GFVN+ DP DA +++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
LNG + K V A + ++ NLYV L +++ +
Sbjct: 63 TLNGLRLQTKTIKVSYA------------------RPSSASIRDANLYVSGLPKTMTQKE 104
Query: 338 LKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYV 394
L++LFS++G I + +++ D G+SRG GF+ F EA +A+ +NG+ ++P+ V
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
Query: 395 ALA 397
A
Sbjct: 165 KFA 167
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
NL V L +++ ++ + LF G I SCK++RD G S G GFV + ++A KA+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 382 MNGKMVVSKPLYVALAQ 398
+NG + +K + V+ A+
Sbjct: 64 LNGLRLQTKTIKVSYAR 80
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 85.5 bits (210), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 46/154 (29%), Positives = 86/154 (55%), Gaps = 2/154 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG+LD ++ + L F G + ++++ D +++ Y +V Y+ +H+A AL L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
N + ++I ++++ N+F+ +L+ ++D++ L + F F + LS V
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 162 D-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN 194
D G SRGYGFV F +++ A++A+D + G LN
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
Score = 85.1 bits (209), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 53/180 (29%), Positives = 93/180 (51%), Gaps = 17/180 (9%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+YV NL + TED LK+ F G I + +M D + K+ + FV + DA +++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 281 GKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKE 340
GK+ ++ +++ F+ + D F NL+V +L+ ++ D+ L+
Sbjct: 63 GKQIENN-------------IVKINWAFQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 341 LFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR 399
F +F + S VM D G SRG GFV+F++ ++A A+ M G+ + +PL + A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 67.4 bits (163), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 84/168 (50%), Gaps = 5/168 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+++ NLDK+I L F G I + K+ D ++ Y FV++ A A+ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
G + + V + Q ++S++D T N++V +L+ ++ L+ F +F S
Sbjct: 63 GKQIENNIVKINWAF--QSQQSSSDDTF--NLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK 296
VM D G S+ +GFV+F DDA +++++ G+ + + + A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 47/76 (61%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
+L+VGDL+++V+D L + F +S V D+ T S GYG+V++ + +A A+D
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 101 LNFTPLNGKPIRIMYS 116
+ LNG+P+RI ++
Sbjct: 149 MQGQDLNGRPLRINWA 164
>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 = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 48/155 (30%), Positives = 81/155 (52%), Gaps = 3/155 (1%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+T+L V L D +LY LF +G + + R+ RD T S GY +V++ + ++ RA+
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 99 DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
LN + K R+ SY P N+++ NL ++I + L F +G+I+
Sbjct: 74 KVLNGITVRNK--RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 131
Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGML 192
+ D L G+ RG FV+++ E A+ AI LN ++
Sbjct: 132 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 80.1 bits (196), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 58/183 (31%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+ +L +F G I + + RD G S + FV+F D+ R+++
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
LNG +K V A+ E S+K+T NLYV NL +I+DD+L
Sbjct: 76 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
+F ++G+I ++RD G RG FV ++ EEA +A++ +N + S+PL V
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 396 LAQ 398
LA+
Sbjct: 178 LAE 180
Score = 79.3 bits (194), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 81/154 (52%), Gaps = 8/154 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+ + L + ++ L+ F G I +C++ D G S GY FV F +E ++ AI
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS 247
LNG+ + +K++ V + ES D N+YV NL T T+D L IFG++G I
Sbjct: 76 LNGITVRNKRLKVS--YARPGGESIKD----TNLYVTNLPRTITDDQLDTIFGKYGSIVQ 129
Query: 248 TAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
++RD G+ + FV ++ ++A ++ ALN
Sbjct: 130 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 82.0 bits (201), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 47/155 (30%), Positives = 83/155 (53%), Gaps = 3/155 (1%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+T+L V L + D +LY LF +G + + R+ RD T S GY +V++ + ++ RA+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 99 DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
LN + K +++ SY P N+++ NL ++I + L F +G+I+
Sbjct: 63 KVLNGITVRNKRLKV--SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGML 192
+ D L G+ RG FV+++ E A+ AI LN ++
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 82.0 bits (201), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 59/182 (32%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+ +L +F G I + +MRD G S + FV+F D+ R+++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
LNG +K V A+ E S+K+T NLYV NL +I+DD+L
Sbjct: 65 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
+F ++G+I ++RD G RG FV ++ EEA +A++ +N + S+PL V
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 396 LA 397
LA
Sbjct: 167 LA 168
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 82/154 (53%), Gaps = 8/154 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+ + L + + ++ L+ F G I +C++ D G S GY FV F +E ++ AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS 247
LNG+ + +K++ V + ES D N+YV NL T T+D L IFG++G I
Sbjct: 65 LNGITVRNKRLKVS--YARPGGESIKD----TNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 248 TAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
++RD G+ + FV ++ ++A ++ ALN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 58/76 (76%)
Query: 548 PMQTGALASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLES 607
P+ + AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LES
Sbjct: 2 PLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLES 61
Query: 608 PEALKAKVAEAMEVLR 623
PE+L++KV EA+ VL+
Sbjct: 62 PESLRSKVDEAVAVLQ 77
>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 = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 58/76 (76%)
Query: 548 PMQTGALASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLES 607
P+ + AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LES
Sbjct: 2 PLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLES 61
Query: 608 PEALKAKVAEAMEVLR 623
PE+L++KV EA+ VL+
Sbjct: 62 PESLRSKVDEAVAVLQ 77
>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 = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 93/176 (52%), Gaps = 15/176 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKL 188
+++ ++ + + F+ FG I S ++ DS+ + +G+ FV+++ E+A+ A++++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 189 NGMLLNDKQVFVG---------PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIF 239
N ++L + + VG P + + E+ A FN +YV ++ + ++DD+K +F
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----FNRIYVASVHQDLSDDDIKSVF 146
Query: 240 GEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
FG I S + RD GK K +GF+ ++ + +V ++N + VGKA
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 47/169 (27%), Positives = 83/169 (49%), Gaps = 11/169 (6%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSV 276
+ VYV ++ ED +++ F FG I S + D+ K K F FV ++ P+ A ++
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISD 335
E +N + VG+ G+ + + + A++ N +YV ++ +SD
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139
Query: 336 DKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
D +K +F FG I S + RDP G +G GF+ + A+ + A++ MN
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
+AR F +YV + ++D + +F G++ S + RD +T + GYG++ Y A
Sbjct: 121 EARAF--NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ 178
Query: 93 EATRALDELNFTPLNGKPIRI 113
+ A+ +N L G+ +R+
Sbjct: 179 SSQDAVSSMNLFDLGGQYLRV 199
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 37/69 (53%), Positives = 55/69 (79%)
Query: 555 ASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAK 614
AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LESPE+L++K
Sbjct: 55 ASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 114
Query: 615 VAEAMEVLR 623
V EA+ VL+
Sbjct: 115 VDEAVAVLQ 123
>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 = 80.1 bits (196), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 58/76 (76%)
Query: 548 PMQTGALASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLES 607
P+ + AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LES
Sbjct: 2 PLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLES 61
Query: 608 PEALKAKVAEAMEVLR 623
PE+L++KV EA+ VL+
Sbjct: 62 PESLRSKVDEAVAVLQ 77
>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 = 79.7 bits (195), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 37/69 (53%), Positives = 55/69 (79%)
Query: 555 ASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAK 614
AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LESPE+L++K
Sbjct: 8 ASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 67
Query: 615 VAEAMEVLR 623
V EA+ VL+
Sbjct: 68 VDEAVAVLQ 76
>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 = 79.3 bits (194), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 93/176 (52%), Gaps = 15/176 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKL 188
+++ ++ + + F+ FG I S ++ DS+ + +G+ FV+++ E+A+ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 189 NGMLLNDKQVFVG---------PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIF 239
N ++L + + VG P + + E+ A FN +YV ++ + ++DD+K +F
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----FNRIYVASVHQDLSDDDIKSVF 131
Query: 240 GEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
FG I S + RD GK K +GF+ ++ + +V ++N + VGKA
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 48/166 (28%), Positives = 83/166 (50%), Gaps = 11/166 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
VYV ++ ED +++ F FG I S + D+ K K F FV ++ P+ A ++E +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISDDKL 338
N + VG+ G+ + + + A++ N +YV ++ +SDD +
Sbjct: 76 NSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 127
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
K +F FG I SC + RDP G +G GF+ + A+ + A++ MN
Sbjct: 128 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
+AR F +YV + ++D + +F G++ S + RD +T + GYG++ Y A
Sbjct: 106 EARAF--NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQ 163
Query: 93 EATRALDELNFTPLNGKPIRI 113
+ A+ +N L G+ +R+
Sbjct: 164 SSQDAVSSMNLFDLGGQYLRV 184
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 79.0 bits (193), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 37/69 (53%), Positives = 55/69 (79%)
Query: 555 ASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAK 614
AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LESPE+L++K
Sbjct: 8 ASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 67
Query: 615 VAEAMEVLR 623
V EA+ VL+
Sbjct: 68 VDEAVAVLQ 76
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 79.0 bits (193), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 37/69 (53%), Positives = 55/69 (79%)
Query: 555 ASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAK 614
AS LA+A P++Q+ +LGE L+PL+ + A K+TGMLLE+D +E+LH+LESPE+L++K
Sbjct: 7 ASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 66
Query: 615 VAEAMEVLR 623
V EA+ VL+
Sbjct: 67 VDEAVAVLQ 75
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 74.7 bits (182), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 39/69 (56%), Positives = 51/69 (73%)
Query: 554 LASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKA 613
L++ LAN +PEQQ+ +LGE LY + + AAKVTGMLLEMD E+L+LL++P L A
Sbjct: 11 LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 614 KVAEAMEVL 622
KV EA+EVL
Sbjct: 71 KVQEALEVL 79
>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 = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 89/176 (50%), Gaps = 15/176 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
+++ ++ + + F+ FG I S + DS+ + +G+ FV+++ E+A+ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 189 NGMLLNDKQVFVG---------PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIF 239
N + L + + VG P + + E+ A FN +YV ++ + ++DD+K +F
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----FNRIYVASVHQDLSDDDIKSVF 130
Query: 240 GEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
FG I S + RD GK K +GF+ ++ + +V + N + VGKA
Sbjct: 131 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 47/166 (28%), Positives = 80/166 (48%), Gaps = 11/166 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
VYV ++ ED +++ F FG I S D+ K K F FV ++ P+ A ++E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISDDKL 338
N + VG+ G+ + + + A++ N +YV ++ +SDD +
Sbjct: 75 NSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 126
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
K +F FG I SC + RDP G +G GF+ + A+ + A++ N
Sbjct: 127 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
+AR F +YV + ++D + +F G++ S + RD +T + GYG++ Y A
Sbjct: 105 EARAF--NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQ 162
Query: 93 EATRALDELNFTPLNGKPIRI 113
+ A+ N L G+ +R+
Sbjct: 163 SSQDAVSSXNLFDLGGQYLRV 183
>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|B Chain B, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|C Chain C, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|D Chain D, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
Length = 98
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 37/77 (48%), Positives = 55/77 (71%)
Query: 555 ASALANASPEQQRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAK 614
AS LA+A P++Q+ LGE L+PL+ A K+TG LLE+D +E+L+ LESPE+L++K
Sbjct: 9 ASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESLRSK 68
Query: 615 VAEAMEVLRNVAQQQAT 631
V EA+ VL+ ++AT
Sbjct: 69 VDEAVAVLQAHQAKEAT 85
>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 = 71.6 bits (174), Expect = 1e-12, Method: Composition-based stats.
Identities = 47/162 (29%), Positives = 83/162 (51%), Gaps = 28/162 (17%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDP---DDAARSV 276
+++ L+ TTED+L++ FG++G +T +M+D A G+S+ FGF++F+ P D+ ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
L+GK D K Q K GK ++V + +
Sbjct: 66 HILDGKVIDPKRAIPRDEQDK-------TGK----------------IFVGGIGPDVRPK 102
Query: 337 KLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASK 377
+ +E FS++GTI ++M D + G SRG GFV + +A+ +
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Score = 63.9 bits (154), Expect = 3e-10, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 76/145 (52%), Gaps = 9/145 (6%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +++G L+ + L + F + G V +++ +D +T RS G+G++++ E ++
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF----EKPSSV 58
Query: 99 DELNFTP--LNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS 156
DE+ T L+GK I + P + G IF+ + + K + FS +G I+
Sbjct: 59 DEVVKTQHILDGKVIDPKRAI--PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIID 116
Query: 157 CKVATDS-LGQSRGYGFVQFDNEES 180
++ D GQSRG+GFV +D+ ++
Sbjct: 117 AQLMLDKDTGQSRGFGFVTYDSADA 141
Score = 56.2 bits (134), Expect = 5e-08, Method: Composition-based stats.
Identities = 40/174 (22%), Positives = 81/174 (46%), Gaps = 17/174 (9%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK- 187
+FI L+ L + F +G + K+ D + G+SRG+GF+ F+ S +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 188 --LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGII 245
L+G +++ K+ + + E++ T ++V + + ++ F ++G I
Sbjct: 66 HILDGKVIDPKRA-----IPRDEQDKTG------KIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 246 TSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY 298
+M D D G+S+ FGFV +D D R + F D++ + +A+ ++
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPRH 167
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 46/75 (61%), Gaps = 4/75 (5%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAF---STAEEA 375
E +++ L+ ++D L+E F ++GT+T K+M+DP G SRG GF++F S+ +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 376 SKALTEMNGKMVVSK 390
K ++GK++ K
Sbjct: 62 VKTQHILDGKVIDPK 76
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++VG + V + + F+Q G ++ ++ D T +S G+G+V Y++A R
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 75/150 (50%), Gaps = 14/150 (9%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
+ L+VG+L + + ++ LF + G+ V + +D G+G++ A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
EL+ PL GK +R+ ++ + ++ ++NL + + N+ L + FS FG + V
Sbjct: 77 ELDNMPLRGKQLRVRFA--------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 160 ATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
D G+ G G V+F + +A+ A+D+ +
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 75/166 (45%), Gaps = 33/166 (19%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
T+ + ++V NL TE++++K+F ++G + +D K FGF+ + R+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLE-----TRT 69
Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKF--EGLNLYVKNLDDSI 333
+ + + D+ M L+GK + +F +L V+NL +
Sbjct: 70 LAEIAKVELDN---------------MPLRGK------QLRVRFACHSASLTVRNLPQYV 108
Query: 334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
S++ L+E FS FG + V+ D G G G V FS A KAL
Sbjct: 109 SNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 68.9 bits (167), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 20/183 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSVE 277
++V + T +E DL+++F ++G + V+RD +SK FV F A +
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
AL+ K M + + + E + E L++ + +++
Sbjct: 78 ALHNMKVLPG--------------MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEND 123
Query: 338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYV 394
++ +FS FG I C+++R P+G+SRG FV F+T A+ A KA+ + S P+ V
Sbjct: 124 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 183
Query: 395 ALA 397
A
Sbjct: 184 KFA 186
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/159 (28%), Positives = 72/159 (45%), Gaps = 12/159 (7%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNY---NAAHE 93
+ ++VG + + ++ L +LF Q G V + V RD S +S G +V + AA E
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGA---GNIFIKNLDKSIDNKALHDTFST 150
A AL + P PI++ + K+ A +FI + K + FS+
Sbjct: 75 AQNALHNMKVLPGMHHPIQM----KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS 130
Query: 151 FGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
FG I C++ G SRG FV F A++AI ++
Sbjct: 131 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFST---A 372
+ + ++V + + S+ L+ELF ++G + V+RD + S+G FV F T A
Sbjct: 13 LDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 72
Query: 373 EEASKALTEM 382
EA AL M
Sbjct: 73 LEAQNALHNM 82
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 20/183 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSVE 277
++V + T +E DL+++F ++G + V+RD +SK FV F A +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
AL+ K M + + + E + E L++ + +++
Sbjct: 66 ALHNMKVLPG--------------MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEND 111
Query: 338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYV 394
++ +FS FG I C+++R P+G+SRG FV F+T A+ A KA+ + S P+ V
Sbjct: 112 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
Query: 395 ALA 397
A
Sbjct: 172 KFA 174
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/159 (28%), Positives = 72/159 (45%), Gaps = 12/159 (7%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNY---NAAHE 93
+ ++VG + + ++ L +LF Q G V + V RD S +S G +V + AA E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGA---GNIFIKNLDKSIDNKALHDTFST 150
A AL + P PI++ + K+ A +FI + K + FS+
Sbjct: 63 AQNALHNMKVLPGMHHPIQM----KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS 118
Query: 151 FGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
FG I C++ G SRG FV F A++AI ++
Sbjct: 119 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 36.2 bits (82), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFST---AE 373
+ + ++V + + S+ L+ELF ++G + V+RD + S+G FV F T A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 374 EASKALTEM 382
EA AL M
Sbjct: 62 EAQNALHNM 70
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 40/146 (27%), Positives = 70/146 (47%), Gaps = 14/146 (9%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+VG+L + + LF + G+ V + RD G+G++ + A A EL
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
+ T L +P+RI ++ + + +KNL + N+ L FS FG + V
Sbjct: 79 DGTILKSRPLRIRFA--------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 162 DSLGQSRGYGFVQFDNEESAKSAIDK 187
D G++ G GFV+F + A+ A+++
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKALER 156
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
T+ ++V NL TE+D K++F +G + + RD + FGF+ + A +
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
L+G + + A G L VKNL +S+
Sbjct: 75 KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+ L++ FS+FG + V+ D G + G GFV F+ A KAL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/153 (23%), Positives = 66/153 (43%), Gaps = 25/153 (16%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ NL I + F +G + D RG+GF++ ++ A+ A +L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNN----VYVKNLSETTTEDDLKKIFGEFGI 244
+G +L + + + RF + VKNLS + + L++ F +FG
Sbjct: 79 DGTILKSRPL----------------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGP 122
Query: 245 ITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
+ V+ D G++ GFV F A +++E
Sbjct: 123 VEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
L+V NL I+++ K LF +G + + RD RG GF+ + A A E+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 383 NGKMVVSKPLYVALA 397
+G ++ S+PL + A
Sbjct: 79 DGTILKSRPLRIRFA 93
>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 = 67.0 bits (162), Expect = 3e-11, Method: Composition-based stats.
Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 71
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 72 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
++ TD G+ RG+ FV FD+ +S K I K + +N V L KQE S +
Sbjct: 132 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 189
Query: 214 DKTR 217
R
Sbjct: 190 SSQR 193
Score = 52.8 bits (125), Expect = 5e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 75 PHKVDGRVVEPK 86
Score = 52.4 bits (124), Expect = 8e-07, Method: Composition-based stats.
Identities = 41/174 (23%), Positives = 82/174 (47%), Gaps = 15/174 (8%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDD 268
ES + + +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV +
Sbjct: 4 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 63
Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKN 328
++ ++ A K D + V + ++ RE + ++K+ ++V
Sbjct: 64 VEEVDAAMNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGG 110
Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+ + + L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 111 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
>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 = 67.0 bits (162), Expect = 3e-11, Method: Composition-based stats.
Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
++ TD G+ RG+ FV FD+ +S K I K + +N V L KQE S +
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 190
Query: 214 DKTR 217
R
Sbjct: 191 SSQR 194
Score = 52.8 bits (125), Expect = 5e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 76 PHKVDGRVVEPK 87
Score = 52.4 bits (124), Expect = 8e-07, Method: Composition-based stats.
Identities = 41/174 (23%), Positives = 82/174 (47%), Gaps = 15/174 (8%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDD 268
ES + + +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64
Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKN 328
++ ++ A K D + V + ++ RE + ++K+ ++V
Sbjct: 65 VEEVDAAMNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGG 111
Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+ + + L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 66.6 bits (161), Expect = 4e-11, Method: Composition-based stats.
Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 73
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 74 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 133
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
++ TD G+ RG+ FV FD+ +S K I K + +N V L KQE S +
Sbjct: 134 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 191
Query: 214 DKTR 217
R
Sbjct: 192 SSQR 195
Score = 52.8 bits (125), Expect = 5e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 77 PHKVDGRVVEPK 88
Score = 52.4 bits (124), Expect = 8e-07, Method: Composition-based stats.
Identities = 41/174 (23%), Positives = 82/174 (47%), Gaps = 15/174 (8%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDD 268
ES + + +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV +
Sbjct: 6 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 65
Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKN 328
++ ++ A K D + V + ++ RE + ++K+ ++V
Sbjct: 66 VEEVDAAMNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGG 112
Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+ + + L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 113 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
>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 = 65.9 bits (159), Expect = 6e-11, Method: Composition-based stats.
Identities = 52/180 (28%), Positives = 81/180 (45%), Gaps = 13/180 (7%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 65
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 66 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
++ TD G+ RG+ FV FD+ +S K I K + +N V L KQE S +
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 183
Score = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 69 PHKVDGRVVEPK 80
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 39/167 (23%), Positives = 79/167 (47%), Gaps = 15/167 (8%)
Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARS 275
+ +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV + ++ +
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
+ A K D + V + ++ RE + ++K+ ++V + + +
Sbjct: 65 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 336 DKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 64.3 bits (155), Expect = 2e-10, Method: Composition-based stats.
Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 14/154 (9%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 70
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 71 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
++ TD G+ RG+ FV FD+ +S +DK+
Sbjct: 131 VIEIMTDRGSGKKRGFAFVTFDDHDS----VDKI 160
Score = 60.8 bits (146), Expect = 2e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 72/153 (47%), Gaps = 11/153 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID-- 186
+FI L +++L F +G + C V D + +SRG+GFV + E +A++
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 187 --KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
K++G ++ K+ + +++ + ++V + E T E L+ F ++G
Sbjct: 74 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
I +M D GK + F FV FDD D + V
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 74 PHKVDGRVVEPK 85
Score = 53.1 bits (126), Expect = 5e-07, Method: Composition-based stats.
Identities = 41/174 (23%), Positives = 82/174 (47%), Gaps = 15/174 (8%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDD 268
ES + + +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV +
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 62
Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKN 328
++ ++ A K D + V + ++ RE + ++K+ ++V
Sbjct: 63 VEEVDAAMNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGG 109
Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+ + + L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 110 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 63.9 bits (154), Expect = 2e-10, Method: Composition-based stats.
Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 14/154 (9%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L D L F Q G + V RD +T+RS G+G+V Y E A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNIL 155
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
++ TD G+ RG+ FV FD+ +S +DK+
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDS----VDKI 162
Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 72/153 (47%), Gaps = 11/153 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID-- 186
+FI L +++L F +G + C V D + +SRG+GFV + E +A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 187 --KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
K++G ++ K+ + +++ + ++V + E T E L+ F ++G
Sbjct: 76 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
I +M D GK + F FV FDD D + V
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 53.1 bits (126), Expect = 4e-07, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
L++ L +D+ L+ F ++GT+T C VMRDPN SRG GFV ++T EE A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 381 --EMNGKMVVSK 390
+++G++V K
Sbjct: 76 PHKVDGRVVEPK 87
Score = 52.8 bits (125), Expect = 6e-07, Method: Composition-based stats.
Identities = 41/174 (23%), Positives = 82/174 (47%), Gaps = 15/174 (8%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDD 268
ES + + +++ LS TT++ L+ F ++G +T VMRD + K S+ FGFV +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64
Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKN 328
++ ++ A K D + V + ++ RE + ++K+ ++V
Sbjct: 65 VEEVDAAMNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGG 111
Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+ + + L++ F ++G I ++M D +G RG FV F + K + +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 63.9 bits (154), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 53/89 (59%), Gaps = 2/89 (2%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSC-KVATD-SLGQSRGYGFVQFDNEESAK 182
SG+ IFI NLD ID K L+DTFS FG IL K+ D G S+GY F+ F + +++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERES 211
+AI+ +NG L ++ + V +K + S
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKGS 91
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 51/82 (62%), Gaps = 2/82 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
+++ NLD I + L + FS FG I K+MRDP+ G S+G F+ F++ + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 382 MNGKMVVSKPLYVALAQRKEER 403
MNG+ + ++P+ V+ A +K+ +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRA 97
S+ +++G+LD +++ LYD F+ G ++ ++ RD T S GY ++N+ + + A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 98 LDELNFTPLNGKPIRIMYSYR 118
++ +N L +PI + Y+++
Sbjct: 65 IEAMNGQYLCNRPITVSYAFK 85
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
+ +++ NL E L F FG+I T +MRD D G SK + F+NF D + ++
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 277 EALNGKKFDDKEWYVGKAQKK 297
EA+NG+ ++ V A KK
Sbjct: 66 EAMNGQYLCNRPITVSYAFKK 86
>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 = 61.6 bits (148), Expect = 1e-09, Method: Composition-based stats.
Identities = 49/182 (26%), Positives = 81/182 (44%), Gaps = 20/182 (10%)
Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSVEA 278
+V + T +E DL+++F ++G + V+RD +SK FV F A + A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
L+ K + ++ K S K A E L++ + +++ +
Sbjct: 67 LHNXKVLPGXHH------------PIQXKPADSEKNNA--VEDRKLFIGXISKKCTENDI 112
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYVA 395
+ FS FG I C+++R P+G+SRG FV F+T A+ A KA + S P V
Sbjct: 113 RVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVK 172
Query: 396 LA 397
A
Sbjct: 173 FA 174
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 45/151 (29%), Positives = 66/151 (43%), Gaps = 12/151 (7%)
Query: 43 YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNY---NAAHEATRA 97
+VG + + ++ L +LF Q G V + V RD S +S G +V + AA EA A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 98 LDELNFTPLNGKPIRIMYSYRDPTIRKSGA---GNIFIKNLDKSIDNKALHDTFSTFGNI 154
L P PI+ + K+ A +FI + K + FS+FG I
Sbjct: 67 LHNXKVLPGXHHPIQ----XKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQI 122
Query: 155 LSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
C++ G SRG FV F A++AI
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 40/160 (25%), Positives = 74/160 (46%), Gaps = 11/160 (6%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD---SLGQSRGYGFVQFDNEESA 181
S A F+ + ++ K L + F +G + V D + QS+G FV F +
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF---YTR 57
Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRF---NNVYVKNLSETTTEDDLKKI 238
K+A++ N L++ +V G Q + + ++K +++ +S+ TE+D++
Sbjct: 58 KAALEAQNA--LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVX 115
Query: 239 FGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
F FG I ++R DG S+ FV F A +++A
Sbjct: 116 FSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
Score = 32.7 bits (73), Expect = 0.64, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFSTAEEAS 376
+ + +V + + S+ L+ELF ++G + V+RD + S+G FV F T + A
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 377 KALTEMNGKMVV 388
+A ++ V+
Sbjct: 62 EAQNALHNXKVL 73
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 48/79 (60%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
G ++V NLD + KLKE+FS G + ++ D +G SRG G V F + EA +A++
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 381 EMNGKMVVSKPLYVALAQR 399
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ NLD + K L + FS G ++ + D G+SRG G V F+ A AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 189 NGMLLNDKQVFV 200
NG LL D+ + V
Sbjct: 77 NGQLLFDRPMHV 88
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
+ V+V NL LK++F G++ ++ D DGKS+ G V F+ +A +++
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 279 LNGKKFDDKEWYV 291
NG+ D+ +V
Sbjct: 76 FNGQLLFDRPMHV 88
>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 = 58.9 bits (141), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASK 377
F+G NL V L + + D+L+ LFS G + S K++RD G S G GFV + TA++A +
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 378 ALTEMNGKMVVSKPLYVALAQ 398
A+ +NG + SK + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 46/80 (57%)
Query: 37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
F T+L V L + +L LF+ +G+V S ++ RD SLGYG+VNY A +A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 97 ALDELNFTPLNGKPIRIMYS 116
A++ LN L K I++ Y+
Sbjct: 77 AINTLNGLRLQSKTIKVSYA 96
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+L+ +F G + S ++RD G S +GFVN+ DA R++
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 279 LNGKKFDDKEWYVGKAQ 295
LNG + K V A+
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
N+ + L ++ L FS+ G + S K+ D + G S GYGFV + + A+ AI+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 188 LNGMLLNDKQVFV 200
LNG+ L K + V
Sbjct: 81 LNGLRLQSKTIKV 93
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT 380
+ LYV +L +I++D L+ +F FG I S ++M D G S+G GF+ FS +E A KAL
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 381 EMNGKMVVSKPLYVA 395
++NG + +P+ V
Sbjct: 87 QLNGFELAGRPMKVG 101
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 45/72 (62%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L ++ + L +F G++ S+++ D T RS GYG++ ++ + A +AL++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 102 NFTPLNGKPIRI 113
N L G+P+++
Sbjct: 89 NGFELAGRPMKV 100
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
+YV +L TED L+ IF FG I S +M D++ G+SK +GF+ F D + A +++E L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 280 NGKKFDDKEWYVGKAQKK 297
NG + + VG ++
Sbjct: 89 NGFELAGRPMKVGHVTER 106
Score = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 3/83 (3%)
Query: 122 IRKSGAG--NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNE 178
++K AG +++ +L +I L F FG I S ++ DS G+S+GYGF+ F +
Sbjct: 19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
Query: 179 ESAKSAIDKLNGMLLNDKQVFVG 201
E AK A+++LNG L + + VG
Sbjct: 79 ECAKKALEQLNGFELAGRPMKVG 101
>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 = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 47/76 (61%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
+L+VGDL+++V+D L + F +S V D+ T S GYG+V++ + +A A+D
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 101 LNFTPLNGKPIRIMYS 116
+ LNG+P+RI ++
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
NL+V +L+ ++ D+ L+ F +F + S VM D G SRG GFV+F++ ++A A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 381 EMNGKMVVSKPLYVALAQRKEE 402
M G+ + +PL + A + E
Sbjct: 62 SMQGQDLNGRPLRINWAAKLEH 83
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+F+ +L+ ++D++ L + F F + LS V D G SRGYGFV F +++ A++A+D
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 188 LNGMLLNDK 196
+ G LN +
Sbjct: 63 MQGQDLNGR 71
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
N++V +L+ ++ L+ F +F S VM D G S+ +GFV+F DDA ++++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 279 LNGKKFDDKEWYVGKAQK 296
+ G+ + + + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+ K +FG G I S ++RD G+S +GFVN+ DP+DA +++
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 279 LNGKKFDDKEWYVGKAQ 295
LNG K K V A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
NL V L +++ D+ K LF G I SCK++RD G S G GFV +S +A KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 382 MNGKMVVSKPLYVALAQ 398
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 46/77 (59%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ + LF +G + S ++ RD T +SLGYG+VNY+ ++A +A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 100 ELNFTPLNGKPIRIMYS 116
LN L K I++ Y+
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
N+ + L +++ F + G+I SCK+ D + GQS GYGFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 188 LNGMLLNDKQVFV 200
LNG+ L K + V
Sbjct: 66 LNGLKLQTKTIKV 78
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 34/92 (36%), Positives = 55/92 (59%), Gaps = 10/92 (10%)
Query: 310 QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVA 368
+S+K+T NLYV NL +I+DD+L +F ++G+I ++RD G RG FV
Sbjct: 9 ESIKDT-------NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 369 FSTAEEASKALTEMNGKMVV--SKPLYVALAQ 398
++ EEA +A++ +N + S+PL V LA+
Sbjct: 62 YNKREEAQEAISALNNVIPEGGSQPLSVRLAE 93
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
N+YV NL T T+D L IFG++G I ++RD G+ + FV ++ ++A ++ A
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 279 LN 280
LN
Sbjct: 75 LN 76
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+LYV +L ++ D QL +F + G +V + RD T R G +V YN EA A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 100 ELN 102
LN
Sbjct: 74 ALN 76
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
N+++ NL ++I + L F +G+I+ + D L G+ RG FV+++ E A+ AI
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 188 LNGML 192
LN ++
Sbjct: 75 LNNVI 79
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 57.0 bits (136), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 47/75 (62%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S+ LYVG L ++ + L +F G++ ++ + +D T RS GYG++ ++ + A RAL
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 99 DELNFTPLNGKPIRI 113
++LN L G+P+R+
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 55.5 bits (132), Expect = 1e-07, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
+ +YV +L TED L+ IF FG I + +M+D+D G+SK +GF+ F D + A R++E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 278 ALNGKKFDDKEWYVGKAQKKYE 299
LNG + + VG ++ +
Sbjct: 66 QLNGFELAGRPMRVGHVTERLD 87
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
LYV +L +I++D L+ +F FG I + +M+D + G S+G GF+ FS +E A +AL ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 383 NGKMVVSKPLYVA 395
NG + +P+ V
Sbjct: 68 NGFELAGRPMRVG 80
Score = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKS 183
SG+ +++ +L +I L F FG I + + DS G+S+GYGF+ F + E A+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 184 AIDKLNGMLLNDKQVFVG 201
A+++LNG L + + VG
Sbjct: 63 ALEQLNGFELAGRPMRVG 80
>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 = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 46/77 (59%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T+L V L ++ +L LF+ +G+V S ++ RD SLGYG+VNY A +A RA++
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 100 ELNFTPLNGKPIRIMYS 116
LN L K I++ Y+
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 48/77 (62%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
NL V L +++ D+L+ LFS G + S K++RD G S G GFV + TA++A +A+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 382 MNGKMVVSKPLYVALAQ 398
+NG + SK + V+ A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+D+L+ +F G + S ++RD G S +GFVN+ DA R++
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 279 LNGKKFDDKEWYVGKAQ 295
LNG + K V A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSA 184
G N+ + L +++ L FS+ G + S K+ D + G S GYGFV + + A+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 185 IDKLNGMLLNDKQVFV 200
I+ LNG+ L K + V
Sbjct: 63 INTLNGLRLQSKTIKV 78
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 56.6 bits (135), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 57/275 (20%), Positives = 120/275 (43%), Gaps = 31/275 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ +KNL KS + ++ F G I+ VA DSL ++ + ++F + A +AI K +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 102
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
++ ++ V E T ++ N + T+ +++ + + ++ +
Sbjct: 103 KVV-GQNEIIVSHLT-----ECT--------LWXTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
+ S+ F +++ +DA VE LNG K + Y ++
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG-----------YTLVTKVSNPL 197
Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDK-LKELFSEFGTITSCKVM--RDPNGISRGSG 365
E+S + + EG + ++NL + D+ L+E F FG+I + + + +
Sbjct: 198 EKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257
Query: 366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
F F + A +AL + N ++ ++ + V+LA +K
Sbjct: 258 FXVFENKDSAERAL-QXNRSLLGNREISVSLADKK 291
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 55/265 (20%), Positives = 113/265 (42%), Gaps = 22/265 (8%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T++ V +L S N +++Y F G ++ V V L +++ + + + A A+
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAIT 99
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNI-LSCK 158
+ + + G+ I+ + T+ + N S + + D + LS +
Sbjct: 100 KTH--KVVGQNEIIVSHLTECTL--------WXTNFPPSYTQRNIRDLLQDINVVALSIR 149
Query: 159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV---GPFLRKQERESTADK 215
+ + SR + ++ ++E A+ ++KLNG+ + + P + + +S +
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209
Query: 216 TRFNNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKS--KCFGFVNFDDPDDA 272
R + ++NLS E E+ L++ F FG I + S C F F++ D A
Sbjct: 210 GR--EIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSA 267
Query: 273 ARSVEALNGKKFDDKEWYVGKAQKK 297
R+++ N ++E V A KK
Sbjct: 268 ERALQX-NRSLLGNREISVSLADKK 291
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
++YVG LD V++ L++LF Q G VV+ + +D T + GYG+V + + +A A+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 100 ELNFTPLNGKPIRI 113
++ L GKPIR+
Sbjct: 76 IMDMIKLYGKPIRV 89
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNE 178
P ++ +++ LD+ + L + F G +++ + D + GQ +GYGFV+F +E
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
E A AI ++ + L K + V
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRV 89
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
+YV LD+ +S+ L ELF + G + + + +D G +G GFV F + E+A A+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 383 NGKMVVSKPLYV 394
+ + KP+ V
Sbjct: 78 DMIKLYGKPIRV 89
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
VYV L E +E L ++F + G + +T + +D G+ + +GFV F +DA +++ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 280 NGKKFDDKEWYVGKA 294
+ K K V KA
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
NLY+ NL S+ + +L+ + FG + S +++RD +G SRG GF + E+ +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 383 NGKMVVSKP 391
NGK + + P
Sbjct: 87 NGKFIKTPP 95
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN 177
+DPT N++I NL S+D + L + FG ++S ++ DS G SRG GF + ++
Sbjct: 23 QDPT-------NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 75
Query: 178 EESAKSAIDKLNGMLL 193
E ++ I NG +
Sbjct: 76 TEKCEAVIGHFNGKFI 91
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFV 264
++QE++ T N+Y+ NL + E +L+ + FG + ST ++RD+ G S+ GF
Sbjct: 19 KQQEQDPT-------NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFA 71
Query: 265 NFDDPDDAARSVEALNGK 282
+ + + NGK
Sbjct: 72 RMESTEKCEAVIGHFNGK 89
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNYNAAHEATRAL 98
T+LY+ +L LS+++ +L ++ GQV+S R+ RD S T R +G+ + EA
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAV--- 82
Query: 99 DELNFTPLNGKPIRIMYSYRDPT 121
NGK I+ PT
Sbjct: 83 ----IGHFNGKFIKTPPGVSAPT 101
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 44/76 (57%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+++ L+ T E LK +FG+ G I+ +++D KS+ F F+ F++P DA + + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 281 GKKFDDKEWYVGKAQK 296
GK K V +A+K
Sbjct: 70 GKSLHGKAIKVEQAKK 85
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%)
Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
G +FI L++ + K L F G I + D +SRG+ F+ F+N AK+A
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 188 LNGMLLNDKQVFV 200
+NG L+ K + V
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L++ L+ ++ LK +F + G I+ +++D SRG F+ F +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 384 GKMVVSKPLYVALAQR 399
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
NLYV L ++S ++++LFS++G I + +++ D G+SRG GF+ F EA +A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 382 MNGK--MVVSKPLYVALA 397
+NG+ + ++P+ V A
Sbjct: 63 LNGQKPLGAAEPITVKFA 80
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
N+YV L +T ++ +++++F ++G IITS ++ A G S+ GF+ FD +A +++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 279 LNGKK 283
LNG+K
Sbjct: 63 LNGQK 67
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+++ L K++ K + FS +G I++ ++ D + G SRG GF++FD A+ AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 188 LNG 190
LNG
Sbjct: 63 LNG 65
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
+LYV L +++ ++ LF+Q G++++ R+ D +T S G G++ ++ EA A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 101 LNF-TPLN-GKPIRIMYS 116
LN PL +PI + ++
Sbjct: 63 LNGQKPLGAAEPITVKFA 80
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V L+ S+D ++ LF FG I C ++R P+G S+G FV +S+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 384 GKMVV---SKPLYVALAQRKEE 402
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V L++ +EDD++++F FG I ++R DG SK FV + +A ++ AL+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 281 GKK 283
G +
Sbjct: 78 GSQ 80
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
P+ RK +F+ L+K + F FGNI C + G S+G FV++ +
Sbjct: 13 PSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHA 67
Query: 180 SAKSAIDKLNG 190
A++AI+ L+G
Sbjct: 68 EAQAAINALHG 78
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
N+++ +L + T+ DL F FG + S V D SKCFGFV+FD+PD A +++A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 279 LNGKKFDDKEWYV 291
+NG + K V
Sbjct: 102 MNGFQVGTKRLKV 114
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK 187
N+FI +L + + L TF FGN++S KV D S+ +GFV FDN +SA+ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 188 LNGMLLNDKQV 198
+NG + K++
Sbjct: 102 MNGFQVGTKRL 112
Score = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
EG NL++ +L +D L F FG + S KV D +S+ GFV+F + A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 379 LTEMNGKMVVSKPLYVAL 396
+ MNG V +K L V L
Sbjct: 99 IKAMNGFQVGTKRLKVQL 116
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
+L++ L D+ L F G V+S +V D T S +G+V+++ A A+
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 100 ELN 102
+N
Sbjct: 101 AMN 103
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 45/84 (53%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
++VGDL + + F G++ RV +D++T +S GYG+V++ +A A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKS 125
L G+ IR ++ R P KS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKS 101
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
++F+ +L I + + F+ FG I +V D + G+S+GYGFV F N+ A++AI +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 188 LNGMLLNDKQVFVGPFLRK 206
+ G L +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFST 371
K+T++ F +++V +L I+ + +K F+ FG I+ +V++D G S+G GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 372 AEEASKALTEMNGKMVVSKPLYVALAQRK 400
+A A+ +M G+ + + + A RK
Sbjct: 67 KWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA 272
D + +V+V +LS T +D+K F FG I+ V++D A GKSK +GFV+F + DA
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 273 ARSVEALNGK 282
+++ + G+
Sbjct: 71 ENAIQQMGGQ 80
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
E L+V L +D+ ++++F FGTI C V+R P+G S+G FV F T EA A+
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 380 TEMNGKMVV---SKPLYVALAQRKEE 402
++ + S L V A ++E
Sbjct: 71 NTLHSSRTLPGASSSLVVKFADTEKE 96
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
++V L + T++D++K+F FG I V+R DG SK FV F +A ++ L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 280 NGKK 283
+ +
Sbjct: 74 HSSR 77
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ L K ++ + F FG I C V G S+G FV+F A++AI+ L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 189 N 189
+
Sbjct: 74 H 74
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+VG L N+ L +F++ GQ+ V V +D T+RS G+G+V + +A A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 102 NFTPLNGKPIRI 113
N ++G+ IR+
Sbjct: 75 NGKSVDGRQIRV 86
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
++V LS T E L+++F ++G I+ V++D + +S+ FGFV F++ DDA ++ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 280 NGKKFDDKEWYVGKAQK 296
NGK D ++ V +A K
Sbjct: 75 NGKSVDGRQIRVDQAGK 91
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
L+V L ++ L+++FS++G I+ V++D SRG GFV F ++A A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
NGK V + + V A + + R+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKS 183
S G +F+ L + ++L FS +G I V D Q SRG+GFV F+N + AK
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 184 AIDKLNGMLLNDKQVFV 200
A+ +NG ++ +Q+ V
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 62/271 (22%), Positives = 109/271 (40%), Gaps = 35/271 (12%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
I I+ L + N+ +HD S + + C V + +G FV N E A++AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST 248
+ L ++++ V Q + + A + V NL + T+ +++ FG +
Sbjct: 78 HQSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERC 125
Query: 249 -AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK 307
V + G+SK +GF + D AAR+ L GK + YV
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------H 170
Query: 308 FEQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
+ + + T L V L +D D L S + T C++ +G +G
Sbjct: 171 WTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAV 230
Query: 367 VAFSTAEEASKALTEMNGKMVVSKPLYVALA 397
+ + TAE A +A + +G + L V+
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 67/163 (41%), Gaps = 6/163 (3%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +L S+ Q +L G + + T +S GYG+ Y A RA +L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 102 NFTPLNGKPIRIMYS---YRDPTIRKSGAGNIFIKNLDKSI-DNKALHDTFSTFGNILSC 157
PL + + + ++ P + S + + L D AL S + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 158 KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
++A GQ +G+ ++++ E A+ A + +G+ L + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 62/271 (22%), Positives = 109/271 (40%), Gaps = 35/271 (12%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
I I+ L + N+ +HD S + + C V + +G FV N E A++AI+
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 75
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST 248
+ L ++++ V Q + + A + V NL + T+ +++ FG +
Sbjct: 76 HQSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERC 123
Query: 249 -AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK 307
V + G+SK +GF + D AAR+ L GK + YV
Sbjct: 124 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------H 168
Query: 308 FEQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
+ + + T L V L +D D L S + T C++ +G +G
Sbjct: 169 WTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAV 228
Query: 367 VAFSTAEEASKALTEMNGKMVVSKPLYVALA 397
+ + TAE A +A + +G + L V+
Sbjct: 229 LEYETAEMAEEAQQQADGLSLGGSHLRVSFC 259
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 67/163 (41%), Gaps = 6/163 (3%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +L S+ Q +L G + + T +S GYG+ Y A RA +L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 102 NFTPLNGKPIRIMYS---YRDPTIRKSGAGNIFIKNLDKSI-DNKALHDTFSTFGNILSC 157
PL + + + ++ P + S + + L D AL S + C
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 213
Query: 158 KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
++A GQ +G+ ++++ E A+ A + +G+ L + V
Sbjct: 214 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 62/271 (22%), Positives = 109/271 (40%), Gaps = 35/271 (12%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
I I+ L + N+ +HD S + + C V + +G FV N E A++AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST 248
+ L ++++ V Q + + A + V NL + T+ +++ FG +
Sbjct: 78 HQSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERC 125
Query: 249 -AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK 307
V + G+SK +GF + D AAR+ L GK + YV
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------H 170
Query: 308 FEQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
+ + + T L V L +D D L S + T C++ +G +G
Sbjct: 171 WTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAV 230
Query: 367 VAFSTAEEASKALTEMNGKMVVSKPLYVALA 397
+ + TAE A +A + +G + L V+
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 42.4 bits (98), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 67/163 (41%), Gaps = 6/163 (3%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +L S+ Q +L G + + T +S GYG+ Y A RA +L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 102 NFTPLNGKPIRIMYS---YRDPTIRKSGAGNIFIKNLDKSI-DNKALHDTFSTFGNILSC 157
PL + + + ++ P + S + + L D AL S + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 158 KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
++A GQ +G+ ++++ E A+ A + +G+ L + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
NL V + ++ + +L++LF +G I S K++ D SRG GFV F + A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 382 MNGKMVVSKPLYVALAQRKEER 403
+NG +++K L VALA +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+ + + ++D L F +G I S K+ D QSRGYGFV+F + SA+ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYV 223
LNG + +K++ V +R A N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
V +L V + +V++ QL LF + G + SV++ D TR+S GYG+V + + A +A
Sbjct: 41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100
Query: 98 LDELN-FTPLNGK 109
+ LN F LN +
Sbjct: 101 IAGLNGFNILNKR 113
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSV 276
N+ V + T E L+++F +G I S ++ D + + S+ +GFV F A +++
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 277 EALNGKKFDDKEWYVGKAQKKYER 300
LNG +K V A ++R
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQR 125
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 89/186 (47%), Gaps = 30/186 (16%)
Query: 29 GGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLST 77
G +G AR+ LYVG++ + + + D FN QM V++V++ +D +
Sbjct: 1 GPLGSARR-----LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN- 54
Query: 78 RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKS--GAGNIFIKNL 135
+ ++ + + E T+A+ + G+ ++I R P + GA +FI L
Sbjct: 55 -----FAFLEFRSVDETTQAM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHKLFIGGL 104
Query: 136 DKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLN 194
+++ + + ++FG + + + DS G S+GY F ++ + AI LNGM L
Sbjct: 105 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 164
Query: 195 DKQVFV 200
DK++ V
Sbjct: 165 DKKLLV 170
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 14/175 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFST---FGNILSCK---VATDSLGQSRGYGFVQFDNEES 180
A +++ N+ I +A+ D F+ G + V + Q + + F++F
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF----- 60
Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
++D+ + D +F G L+ + + +++ L +D +K++
Sbjct: 61 --RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLT 118
Query: 241 EFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
FG + + +++D A G SK + F + D + +++ LNG + DK+ V +A
Sbjct: 119 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
L++ L + ++DD++KEL + FG + + +++D G+S+G F + +A+ +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 383 NGKMVVSKPLYVALA 397
NG + K L V A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 4/80 (5%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEASKAL 379
L++KNL+ S +++ LK +FS+ G I SC + + N +S G GFV + E+A KAL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 380 TEMNGKMVVSKPLYVALAQR 399
++ G V L V +++R
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS----LGQSRGYGFVQFDNEES 180
SG+ +FIKNL+ S + L FS G I SC ++ + S G+GFV++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 181 AKSAIDKLNG 190
A+ A+ +L G
Sbjct: 63 AQKALKQLQG 72
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK----SKCFGFVNFDDPDDAAR 274
+ +++KNL+ +TTE+ LK +F + G I S + + + S FGFV + P+ A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 275 SVEALNGKKFD 285
+++ L G D
Sbjct: 66 ALKQLQGHTVD 76
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 44/83 (53%), Gaps = 3/83 (3%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR---RSLGYGYVNYNAAHEAT 95
S+ L++ +L+ S + L +F+++G + S + + + S+G+G+V Y +A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 96 RALDELNFTPLNGKPIRIMYSYR 118
+AL +L ++G + + S R
Sbjct: 65 KALKQLQGHTVDGHKLEVRISER 87
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L V NLD +SD ++ELF+EFGT+ V D +G S G+ V F +A KA+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 384 GKMVVSKPLYVAL 396
G + +P+ + L
Sbjct: 91 GVPLDGRPMNIQL 103
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +LD V+D+ + +LF + G + V D S R SLG V++ +A +A+ +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQY 89
Query: 102 NFTPLNGKPIRI 113
N PL+G+P+ I
Sbjct: 90 NGVPLDGRPMNI 101
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+ V NL ++ D++++F EFG + AV D G+S V+F+ DA ++++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 281 GKKFD 285
G D
Sbjct: 91 GVPLD 95
Score = 36.2 bits (82), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ + NLD + + + + F+ FG + V D G+S G V F+ + A A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 190 GMLLN 194
G+ L+
Sbjct: 91 GVPLD 95
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
L+V L+ S++ + LF FG I C V+R P+G S+G FV FS+ EA A+ +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 383 NGKMVV---SKPLYVALAQRKEE 402
+G + S L V A +E
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
++V L++ +E+D+ ++F FG+I V+R DG SK FV F +A ++ AL
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 280 NGKK 283
+G +
Sbjct: 77 HGSQ 80
Score = 36.6 bits (83), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ L+K + + F FG I C V G S+G FV+F + A++AI L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 189 NG 190
+G
Sbjct: 77 HG 78
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
S++VG++ + QL D+F+++G VVS R+ D T + GYG+ Y A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 101 LNFTPLNGKPIRI 113
LN +G+ +R+
Sbjct: 70 LNGREFSGRALRV 82
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
+V+V N+ TE+ LK IF E G + S ++ D + GK K +GF + D + A ++
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELK 305
LNG++F + V A + +E ELK
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKE-ELK 95
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
++F+ N+ + L D FS G ++S ++ D G+ +GYGF ++ ++E+A SA+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 188 LNG 190
LNG
Sbjct: 70 LNG 72
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
+++V N+ ++++LK++FSE G + S +++ D G +G GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 382 MNGKMVVSKPLYV---ALAQRKEERRA 405
+NG+ + L V A + KEE ++
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELKS 96
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 46/184 (25%), Positives = 88/184 (47%), Gaps = 30/184 (16%)
Query: 31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLSTRR 79
+G AR+ LYVG++ + + + D FN QM V++V++ +D +
Sbjct: 1 LGSARR-----LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--- 52
Query: 80 SLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKS--GAGNIFIKNLDK 137
+ ++ + + E T+A+ + G+ ++I R P + GA +FI L
Sbjct: 53 ---FAFLEFRSVDETTQAM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHKLFIGGLPN 104
Query: 138 SIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK 196
+++ + + ++FG + + + DS G S+GY F ++ + AI LNGM L DK
Sbjct: 105 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 164
Query: 197 QVFV 200
++ V
Sbjct: 165 KLLV 168
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 14/175 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFST---FGNILSCK---VATDSLGQSRGYGFVQFDNEES 180
A +++ N+ I +A+ D F+ G + V + Q + + F++F
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF----- 58
Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
++D+ + D +F G L+ + + +++ L +D +K++
Sbjct: 59 --RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLT 116
Query: 241 EFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
FG + + +++D A G SK + F + D + +++ LNG + DK+ V +A
Sbjct: 117 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
L++ L + ++DD++KEL + FG + + +++D G+S+G F + +A+ +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 383 NGKMVVSKPLYVALA 397
NG + K L V A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 5/104 (4%)
Query: 298 YEREMELKGKFEQSLKETA----DKFE-GLNLYVKNLDDSISDDKLKELFSEFGTITSCK 352
Y R L K++ L ++ + E G L V NLD +SD ++ELF+EFGT+
Sbjct: 60 YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119
Query: 353 VMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL 396
V D +G S G+ V F +A KA+ + G + +P+ + L
Sbjct: 120 VDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
L V +LD V+D+ + +LF + G + V D S R SLG V++ +A +A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKA 145
Query: 98 LDELNFTPLNGKPIRI 113
+ + PL+G+P+ I
Sbjct: 146 MKQYKGVPLDGRPMDI 161
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+ V NL ++ D++++F EFG + AV D G+S V+F+ DA ++++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 281 GKKFDDK 287
G D +
Sbjct: 151 GVPLDGR 157
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 32/67 (47%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ + NLD + + + + F+ FG + V D G+S G V F+ A A+ +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 190 GMLLNDK 196
G+ L+ +
Sbjct: 151 GVPLDGR 157
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
NL V L ++D +L LF G I +C++MRD G S G FV F++ ++ +A+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 382 MNGKMVVSKPLYVALAQ 398
+NG V +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+T+L V L + D +LY LF +G + + R+ RD T S GY +V++ + ++ RA+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 99 DELNFTPLNGKPIRIMYS 116
LN + K +++ Y+
Sbjct: 63 KVLNGITVRNKRLKVSYA 80
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+ + L + + ++ L+ F G I +C++ D G S GY FV F +E ++ AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 188 LNGMLLNDKQVFV 200
LNG+ + +K++ V
Sbjct: 65 LNGITVRNKRLKV 77
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
N+ V L + T+ +L +F G I + +MRD G S + FV+F D+ R+++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 279 LNGKKFDDKEWYVGKAQ 295
LNG +K V A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 40/73 (54%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L V NLD +SD ++ELF+EFGT+ V D +G S G+ V F +A KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 384 GKMVVSKPLYVAL 396
G + +P + L
Sbjct: 92 GVPLDGRPXNIQL 104
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +LD V+D+ + +LF + G + V D S R SLG V++ +A +A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAXKQY 90
Query: 102 NFTPLNGKPIRI 113
N PL+G+P I
Sbjct: 91 NGVPLDGRPXNI 102
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+ V NL ++ D++++F EFG + AV D G+S V+F+ DA ++ + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 281 GKKFD 285
G D
Sbjct: 92 GVPLD 96
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ + NLD + + + + F+ FG + V D G+S G V F+ + A A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 190 GMLLN 194
G+ L+
Sbjct: 92 GVPLD 96
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 42/76 (55%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
G L V NLD +SD ++ELF+EFGT+ V D +G S G+ V F +A KA+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 381 EMNGKMVVSKPLYVAL 396
+ G + +P+ + L
Sbjct: 95 QYKGVPLDGRPMDIQL 110
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +LD V+D+ + +LF + G + V D S R SLG V++ +A +A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQY 96
Query: 102 NFTPLNGKPIRI 113
PL+G+P+ I
Sbjct: 97 KGVPLDGRPMDI 108
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
+ V NL ++ D++++F EFG + AV D G+S V+F+ DA ++++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 280 NGKKFDDK 287
G D +
Sbjct: 97 KGVPLDGR 104
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+ + NLD + + + + F+ FG + V D G+S G V F+ A A+ +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 189 NGMLLNDK 196
G+ L+ +
Sbjct: 97 KGVPLDGR 104
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 42/76 (55%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
G L V NLD +SD ++ELF+EFGT+ V D +G S G+ V F +A KA+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 381 EMNGKMVVSKPLYVAL 396
+ G + +P+ + L
Sbjct: 95 QYKGVPLDGRPMDIQL 110
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L V +LD V+D+ + +LF + G + V D S R SLG V++ +A +A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQY 96
Query: 102 NFTPLNGKPIRI 113
PL+G+P+ I
Sbjct: 97 KGVPLDGRPMDI 108
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
+ V NL ++ D++++F EFG + AV D G+S V+F+ DA ++++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 280 NGKKFDDK 287
G D +
Sbjct: 97 KGVPLDGR 104
Score = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+ + NLD + + + + F+ FG + V D G+S G V F+ A A+ +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 189 NGMLLNDK 196
G+ L+ +
Sbjct: 97 KGVPLDGR 104
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L V+D L+ F G + +++ D T + G+ +V + A +A A+D +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 102 NFTPLNGKPIRI 113
N + L G+ IR+
Sbjct: 75 NESELFGRTIRV 86
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ L + +D+K LH F FG+I ++ D + RG+ FV+F+ E A +AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 189 N 189
N
Sbjct: 75 N 75
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
LYV L + + D L F FG IT ++ D RG FV F AE+A+ A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 383 NGKMVVSKPLYVALAQ 398
N + + + V LA+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 32.7 bits (73), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
+YV L+E + L F FG IT + D + K + F FV F+ +DAA +++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 280 N 280
N
Sbjct: 75 N 75
>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 = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
+FI L K L D FS FG ++ C + D + G+SRG+GFV F ES +D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 187 --KLNGMLLNDKQ 197
KLNG +++ K+
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE- 381
+++ L + LK+ FS+FG + C + DP G SRG GFV F +E K + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 382 ---MNGKMVVSK 390
+NGK++ K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE-- 277
+++ LS TT+ DLK F +FG ++ T + G+S+ FGFV F + + + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 278 --ALNGKKFDDK 287
LNGK D K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
+++G L L D F++ G+VV + D T RS G+G+V + + + +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 102 NFTPLNGKPI 111
LNGK I
Sbjct: 62 EHK-LNGKVI 70
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
+ V NLSE T E DL+++F FG I+ + +D G+SK F F++F +DAAR++ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 280 NGKKFD 285
+G +D
Sbjct: 78 SGFGYD 83
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNE 178
P R I + NL + L + F FG+I +A D + GQS+G+ F+ F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 179 ESAKSAIDKLNG 190
E A AI ++G
Sbjct: 68 EDAARAIAGVSG 79
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNG 384
V NL + + L+ELF FG+I+ + +D G S+G F++F E+A++A+ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Score = 32.3 bits (72), Expect = 0.86, Method: Composition-based stats.
Identities = 13/60 (21%), Positives = 34/60 (56%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+ ++ V +L ++ L +LF G + + + +D +T +S G+ +++++ +A RA+
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-K 187
+F+ +D +D + F+ +G++ K+ TD G S+GYGFV F N+ + ++ +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 188 LNGMLLNDKQVFVGPFLRKQ 207
+N + K++ +GP +RKQ
Sbjct: 71 IN---FHGKKLKLGPAIRKQ 87
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 33/57 (57%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
++V +D + + +++ F+ +G++ K++ D G+S+G GFV+F + K +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
N V+V + E +++ F +G + ++ D G SK +GFV+F + D + VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 279 ---LNGKKF 284
+GKK
Sbjct: 70 QINFHGKKL 78
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F+ +D +D + F+ +G++ K+ TD G S+GYGFV F N+ + ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 190 GMLLNDKQVFVGPFLRKQ 207
+ + K++ +GP +RKQ
Sbjct: 70 QINFHGKKLKLGPAIRKQ 87
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 33/56 (58%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
++V +D + + +++ F+ +G++ K++ D G+S+G GFV+F + K +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
N V+V + E +++ F +G + ++ D G SK +GFV+F + D + VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 279 ---LNGKKF 284
+GKK
Sbjct: 70 QINFHGKKL 78
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 46/79 (58%), Gaps = 4/79 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-KL 188
+F+ +D +D + F+ +G++ K+ TD G S+GYGFV F N+ + ++ ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 72
Query: 189 NGMLLNDKQVFVGPFLRKQ 207
N + K++ +GP +RKQ
Sbjct: 73 N---FHGKKLKLGPAIRKQ 88
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 33/56 (58%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
++V +D + + +++ F+ +G++ K++ D G+S+G GFV+F + K +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 68
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
N V+V + E +++ F +G + ++ D G SK +GFV+F + D + VE+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 279 ---LNGKKF 284
+GKK
Sbjct: 71 QINFHGKKL 79
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 53/89 (59%), Gaps = 11/89 (12%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V+NL ++++++ L++ FS+FG + K ++D F+ F + A KA+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 384 GKMVVSKPLYVALA----QRKEERRARLQ 408
GK + + + + A Q+++ER+A+ Q
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQ 95
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 7/65 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V+NL+ T TE+ L+K F +FG + ++D + F++FD+ D A +++E +N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 281 GKKFD 285
GK +
Sbjct: 67 GKDLE 71
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 10/76 (13%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F++NL ++ + L FS FG + K D Y F+ FD + A A++++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 190 GMLL---NDKQVFVGP 202
G L N + VF P
Sbjct: 67 GKDLEGENIEIVFAKP 82
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 8/75 (10%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V +L +V + L F+Q G++ V+ +D Y +++++ A +A++E+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 102 NFTPLNGKPIRIMYS 116
N L G+ I I+++
Sbjct: 66 NGKDLEGENIEIVFA 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 49.3 bits (116), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L V+D L+ F G + +++ D T + G+ +V + A +A A+D +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 102 NFTPLNGKPIRI 113
N + L G+ IR+
Sbjct: 126 NESELFGRTIRV 137
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ L + +D+K LH F FG+I ++ D + RG+ FV+F+ E A +AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 189 N 189
N
Sbjct: 126 N 126
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
LYV L + + D L F FG IT ++ D RG FV F AE+A+ A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 383 NGKMVVSKPLYVALA 397
N + + + V LA
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
+YV L+E + L F FG IT + D + K + F FV F+ +DAA +++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 280 N 280
N
Sbjct: 126 N 126
>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 = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
EG NL++ +L D L ++F FG + S KV D +S+ GFV++ A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRA 405
+ MNG + K L V L + K + ++
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
N+++ +L + + DL ++F FG + S V D SKCFGFV++D+P A ++++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 279 LNGKKFDDKEWYV 291
+NG + K V
Sbjct: 87 MNGFQIGMKRLKV 99
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
N+FI +L + ++ L F FGN++S KV D S+ +GFV +DN SA++AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 188 LNGMLLNDKQVFV 200
+NG + K++ V
Sbjct: 87 MNGFQIGMKRLKV 99
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++ L D L +F G VVS +V D T S +G+V+Y+ A A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSG 126
N + K +++ R KSG
Sbjct: 88 NGFQIGMKRLKVQLK-RSKNDSKSG 111
>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
pdb|3NTW|C Chain C, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
Length = 65
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 566 QRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 622
R LGE LYP V ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 6 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62
>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein:
An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding
Protein
Length = 61
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 566 QRTLLGENLYPLVDQLEHDNAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 622
R LGE LYP V ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
SGA IF++NL K L D F+ G++L + ++ G+S+G G V+F++ E A+ A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERA 64
Query: 185 IDKLNGMLLNDKQVFV 200
+NGM L+ +++ V
Sbjct: 65 CRMMNGMKLSGREIDV 80
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V+NL T LK F E G + A ++ +GKSK G V F+ P+ A R+ +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVL-YADIKMENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 281 GKKFDDKE 288
G K +E
Sbjct: 70 GMKLSGRE 77
Score = 35.8 bits (81), Expect = 0.070, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
++V+NL + LK+ F+E G + + + NG S+G G V F + E A +A MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 384 G 384
G
Sbjct: 70 G 70
>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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L Y +F+Q GQ++ + V R L R G +V + AT
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS+FG I V R RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 50/99 (50%), Gaps = 7/99 (7%)
Query: 215 KTRFNN-VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
+TR N+ +Y+ NL+E +D+LKK IF +FG I V R + + FV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEV 62
Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
A ++ ++ G F DK + A+ + ++KG F
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVE 277
+ VYV NL + T +DL +IF ++G + +M+D D KSK F+ F D D A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 278 ALNGKKF 284
A+N K+
Sbjct: 77 AINNKQL 83
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 41/63 (65%), Gaps = 3/63 (4%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY---NAAHEATR 96
+++YV +L S+ ++ LY +F++ G+VV V + +D TR+S G ++ + ++A TR
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 97 ALD 99
A++
Sbjct: 77 AIN 79
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKALTEM 382
+YV NL S++++ L +FS++G + +M+D + S+G F+ F + A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 383 NGKMVVSKPLYVALA 397
N K + + + ++A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 88/189 (46%), Gaps = 37/189 (19%)
Query: 42 LYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLSTRRSLGYGYVNYNA 90
LYVG++ + + + D FN QM V++V++ +D + + ++ + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 91 AHEATRAL--DELNFTPLNGKPIRIMYSYR-------DPTIRKSG---------AGNIFI 132
E T+A+ D + F + K IR + Y+ +P++ G A +FI
Sbjct: 61 VDETTQAMAFDGIIFQGQSLK-IRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 133 KNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGM 191
L +++ + + ++FG + + + DS G S+GY F ++ + AI LNGM
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 192 LLNDKQVFV 200
L DK++ V
Sbjct: 180 QLGDKKLLV 188
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 41/191 (21%), Positives = 82/191 (42%), Gaps = 20/191 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFG---EFGIITSTA---VMRDADGKSKCFGFVNFDDPDDAAR 274
+YV N+ TE+ + F G +T V+ + K F F+ F D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 275 SVEALNGKKFDDKEWYVGKAQK-------KYEREMELKGKFEQSLKETADKFEGLNLYVK 327
++ A +G F + + + + + G + ++A K L++
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK-----LFIG 120
Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKM 386
L + ++DD++KEL + FG + + +++D G+S+G F + +A+ +NG
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180
Query: 387 VVSKPLYVALA 397
+ K L V A
Sbjct: 181 LGDKKLLVQRA 191
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L Y +F+Q GQ++ + V R L R G +V + AT
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS+FG I V R RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQ 398
M G KP+ + A+
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF +FG I V R + + FV F + A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATN 66
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
++ ++ G F DK + A+ + ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
+T +K++ ++V N+ + DL+++FG+FG I ++ + G SK FGFV F++
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSA 80
Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKK 297
DA R+ E L+G + ++ V A +
Sbjct: 81 DADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 315 TADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEE 374
T +K + L+V N+ D L+++F +FG I +++ + G S+G GFV F + +
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 375 ASKALTEMNGKMVVSKPLYV 394
A +A +++G +V + + V
Sbjct: 82 ADRAREKLHGTVVEGRKIEV 101
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
T KS + + N+ + L F FG IL ++ + G S+G+GFV F+N
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 181 AKSAIDKLNGMLLNDKQVFV 200
A A +KL+G ++ +++ V
Sbjct: 82 ADRAREKLHGTVVEGRKIEV 101
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
SG+ IF++NL K L D F+ G++L + ++ G+S+G G V+F++ E A+ A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERA 61
Query: 185 IDKLNGMLLNDKQVFV 200
+NGM L+ +++ V
Sbjct: 62 CRMMNGMKLSGREIDV 77
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
+ ++V+NL T LK F E G + A ++ +GKSK G V F+ P+ A R+
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVL-YADIKMENGKSKGCGVVKFESPEVAERACRM 64
Query: 279 LNGKKFDDKE 288
+NG K +E
Sbjct: 65 MNGMKLSGRE 74
Score = 35.8 bits (81), Expect = 0.084, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
++V+NL + LK+ F+E G + + + NG S+G G V F + E A +A MN
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 66
Query: 384 G 384
G
Sbjct: 67 G 67
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
+ AD+T V+V NL E+ L ++F + G +T + +D +GK K FGFV F P
Sbjct: 12 QEEADRT----VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 270 DDAARSVEALNG 281
+ + ++ LNG
Sbjct: 68 ESVSYAIALLNG 79
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA 372
+E AD+ ++V NL+ + ++ L ELF + G +T + +D G + GFV F
Sbjct: 12 QEEADR----TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 373 EEASKALTEMNGKMVVSKPLYVA 395
E S A+ +NG + +P+ V+
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
A++ +++VG+L+ V + LY+LF Q G + V +C+D + +G+V +
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHPES 69
Query: 94 ATRALDELNFTPLNGKPIRI 113
+ A+ LN L G+PI +
Sbjct: 70 VSYAIALLNGIRLYGRPINV 89
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F+ NL+ + + L++ F G + + D G+ + +GFV F + ES AI LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 190 GMLLNDKQVFV-GP 202
G+ L + + V GP
Sbjct: 79 GIRLYGRPINVSGP 92
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDAARSVE 277
+ +Y++ L TT+ DL K+ +G I ST A++ K K +GFV+FD P A ++V
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 278 ALN 280
AL
Sbjct: 66 ALK 68
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S+ LY+ L D L L G++VS + D +T + GYG+V++++ A +A+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 99 DELN 102
L
Sbjct: 65 TALK 68
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKS 183
SG+ ++I+ L ++ L +G I+S K D + + +GYGFV FD+ +A+
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 184 AIDKLN 189
A+ L
Sbjct: 63 AVTALK 68
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L V+D L+ F G + +++ D T + G+ +V + A +A A+D +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 102 NFTPLNGKPIRI 113
N + L G+ IR+
Sbjct: 65 NESELFGRTIRV 76
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ L + +D+K LH F FG+I ++ D + RG+ FV+F+ E A +AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 189 N 189
N
Sbjct: 65 N 65
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
LYV L + + D L F FG IT ++ D RG FV F AE+A+ A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 383 NGKMVVSKPLYVALA 397
N + + + V LA
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 33.1 bits (74), Expect = 0.47, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
+YV L+E + L F FG IT + D + K + F FV F+ +DAA +++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 280 N 280
N
Sbjct: 65 N 65
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
++YVG+L S Q+ +LF+Q G+V +V++ D T++ G+G+V + A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 101 LNFTPLNGKPIRI 113
L+ T G+ IR+
Sbjct: 62 LDNTDFMGRTIRV 74
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
NI++ NL S ++ + + FS FG + + K+ D + +G+GFV+ EES AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 188 LNGMLLNDKQVFVGPFLRKQE 208
L D F+G +R E
Sbjct: 62 L------DNTDFMGRTIRVTE 76
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGIS-RGSGFVAFSTAEEASKALTE 381
N+YV NL S + +++KELFS+FG + + K++ D +G GFV E S+A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 382 MNGKMVVSKPLYVALAQRKE 401
++ + + + V A K+
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
Score = 36.2 bits (82), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKS-KCFGFVNFDDPDDAARSVEA 278
N+YV NL + T + +K++F +FG + + ++ D + K K FGFV + + + ++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 279 LNGKKFDDKEWYVGKAQKK 297
L+ F + V +A K
Sbjct: 62 LDNTDFMGRTIRVTEANPK 80
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L V+D L+ F G + +++ D T + G+ +V + A +A A+D +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 102 NFTPLNGKPIRI 113
N + L G+ IR+
Sbjct: 68 NESELFGRTIRV 79
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ L + +D+K LH F FG+I ++ D + RG+ FV+F+ E A +AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 189 N 189
N
Sbjct: 68 N 68
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
LYV L + + D L F FG IT ++ D RG FV F AE+A+ A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 383 NGKMVVSKPLYVALAQ 398
N + + + V LA+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
+YV L+E + L F FG IT + D + K + F FV F+ +DAA +++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 280 N 280
N
Sbjct: 68 N 68
>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 = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
LYVG L V+D L+ F G + +++ D T + G+ +V + A +A A+D +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 102 NFTPLNGKPIRI 113
N + L G+ IR+
Sbjct: 70 NESELFGRTIRV 81
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ L + +D+K LH F FG+I ++ D + RG+ FV+F+ E A +AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 189 N 189
N
Sbjct: 70 N 70
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
LYV L + + D L F FG IT ++ D RG FV F AE+A+ A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 383 NGKMVVSKPLYVALAQ 398
N + + + V LA+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 33.1 bits (74), Expect = 0.51, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
+YV L+E + L F FG IT + D + K + F FV F+ +DAA +++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 280 N 280
N
Sbjct: 70 N 70
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 48/96 (50%), Gaps = 4/96 (4%)
Query: 29 GGVGDARQFVSTS----LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
G G + Q TS ++VGDL + + F G++ RV +D++T +S GYG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 85 YVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
+V++ +A A+ + L G+ IR ++ R P
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
++F+ +L I + + F+ FG I +V D + G+S+GYGFV F N+ A++AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 188 LNGMLLNDKQV 198
+ G L +Q+
Sbjct: 77 MGGQWLGGRQI 87
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 50/89 (56%), Gaps = 4/89 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFST 371
K+T++ F +++V +L I+ + +K F+ FG I+ +V++D G S+G GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 372 AEEASKALTEMNGKMVVSKPLYVALAQRK 400
+A A+ M G+ + + + A RK
Sbjct: 67 KLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA 272
D + +V+V +LS T +D+K F FG I+ V++D A GKSK +GFV+F + DA
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 273 ARSVEALNGKKFDDKEWYVGKAQKK 297
++ + G+ ++ A +K
Sbjct: 71 ENAIVHMGGQWLGGRQIRTNWATRK 95
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L Y +F+Q GQ++ + V R L R G +V + AT
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS+FG I V R RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQ 398
M G KP+ + A+
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF +FG I V R + + FV F + A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAK 88
>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 = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
AG F+ L K L D F+ FG ++ C + D + G+SRG+GF+ F + S + +
Sbjct: 11 AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 186 D----KLNGMLLNDKQ 197
D +L+G +++ K+
Sbjct: 71 DQKEHRLDGRVIDPKK 86
Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMN 383
+V L S LK+ F++FG + C + DPN G SRG GF+ F A K L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 384 GKM 386
++
Sbjct: 75 HRL 77
Score = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 43 YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
+VG L + L D F + G+VV + D +T RS G+G++ + A + LD+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Score = 36.6 bits (83), Expect = 0.048, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALN 280
+V LS T++ DLK F +FG + + D + G+S+ FGF+ F D A SVE
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD----AASVE--- 67
Query: 281 GKKFDDKE 288
K D KE
Sbjct: 68 -KVLDQKE 74
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
++V+NLS T++E+DL+K+F +G ++ D+ K K F FV F P+ A ++ +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 280 NGKKFDDKEWYV 291
+G+ F + +V
Sbjct: 71 DGQVFQGRMLHV 82
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
L+V+NL + S++ L++LFS +G ++ D +G FV F E A KA E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 383 NGKMVVSKPLYVALAQRKEE 402
+G++ + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQS-RGYGFVQFDNEESAKSAIDKL 188
+F++NL + + L FS +G + DSL + +G+ FV F E A A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 189 NGMLLNDKQVFVGPFLRKQE 208
+G + + + V P K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V +L + ++ L LF+ G + + D T++ G+ +V + A +A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGA 127
+ G+ + ++ S TI+K +
Sbjct: 71 DGQVFQGRMLHVLPS----TIKKEAS 92
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSV 276
++ V NL+ T+ D L+++F ++G + + RD K S+ F FV F D DA ++
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 277 EALNGKKFDDKEWYVGKAQ 295
+A++G D +E V A+
Sbjct: 107 DAMDGAVLDGRELRVQMAR 125
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
TSL V +L + L +F + G+V V + RD T+ S G+ +V ++ +A A+D
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 100 ELNFTPLNGKPIRI 113
++ L+G+ +R+
Sbjct: 108 AMDGAVLDGRELRV 121
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 306 GKFEQSLKETADKFEGL-NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRG 363
G+ S EG+ +L V NL S D L+ +F ++G + + RD SRG
Sbjct: 31 GRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 90
Query: 364 SGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
FV F +A A+ M+G ++ + L V +A+
Sbjct: 91 FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 1/86 (1%)
Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
SY P G ++ + NL L F +G + + D +SRG+ FV+
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
F ++ A+ A+D ++G +L+ +++ V
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRV 121
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 47/85 (55%), Gaps = 6/85 (7%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSC---KVMRDPNGISRGSGFVAFSTAEEASKAL 379
+L+V +L + D L E F + SC KV+ D G+S+G GFV F+ E +AL
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 380 TEMNGKM-VVSKPLYVALAQRKEER 403
TE G + + SKP+ +++A K R
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKASR 93
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 129 NIFIKNLDKSIDNKALHDTF-STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
++F+ +L +D+ L++ F + + KV D G S+GYGFV+F +E K A+ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 188 LNGML-LNDKQVFVGPFLRKQER 209
G + L K V + + K R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 13/80 (16%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQM------GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
SL+VGDL V+D LY+ F ++ G+VV + T S GYG+V + E
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ------TGVSKGYGFVKFTDELEQ 64
Query: 95 TRALDEL-NFTPLNGKPIRI 113
RAL E L KP+R+
Sbjct: 65 KRALTECQGAVGLGSKPVRL 84
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
V LS TTE DL+++F ++G I +++ D + S+ F FV F++ DDA + E NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 282 KKFDDKEWYV 291
+ D + V
Sbjct: 111 MELDGRRIRV 120
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 142 KALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
+ L + FS +G I + D + SRG+ FV F+N + AK A ++ NGM L+ +++ V
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+ L V L L + L ++F++ G + V + D +RRS G+ +V + +A A
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 99 DELNFTPLNGKPIRIMYS 116
+ N L+G+ IR+ +S
Sbjct: 106 ERANGMELDGRRIRVDFS 123
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKAL 379
GL+LY D L+E+FS++G I ++ D SRG FV F ++A +A
Sbjct: 53 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 380 TEMNG 384
NG
Sbjct: 106 ERANG 110
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
VYV NL + +L++ FG +G + S V R+ G F FV F+DP DAA +V L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 281 GK 282
G+
Sbjct: 132 GR 133
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
+YV NL ++ + +L+ F +G + S V R+P G + FV F +A+ A+ E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 384 GKMVVSKPLYVALAQ 398
G+ + + V L+
Sbjct: 132 GRTLCGCRVRVELSN 146
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
+ +YVG+L + N ++L F G + SV V R+ G+ +V + +A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 98 LDELNFTPLNGKPIRIMYS 116
+ EL+ L G +R+ S
Sbjct: 127 VRELDGRTLCGCRVRVELS 145
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+++ NL + + L F +G + S VA + G + FV+F++ A A+ +L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 190 GMLLNDKQVFV 200
G L +V V
Sbjct: 132 GRTLCGCRVRV 142
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V+ + + +L E+F FG + K++ G FV F AE A+KA+ E++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 384 GKMVVSKPLYVALAQRKEER 403
GK ++PL V ++ +R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V+ E +L +IFG FG + ++ F FV F++ + AA+++E ++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 86
Query: 281 GKKFDDK 287
GK F ++
Sbjct: 87 GKSFANQ 93
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F++ + L++ F FG + K+ G+ FV+F+ ESA AI++++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 190 G 190
G
Sbjct: 87 G 87
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
VYV NL + +L++ FG +G + S V R+ G F FV F+DP DAA +V L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 281 GK 282
G+
Sbjct: 132 GR 133
Score = 35.8 bits (81), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
+YV NL ++ + +L+ F +G + S V R+P G + FV F +A+ A+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRDLD 131
Query: 384 GKMVVSKPLYVALAQ 398
G+ + + V L+
Sbjct: 132 GRTLCGCRVRVELSN 146
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
+ +YVG+L + N ++L F G + SV V R+ G+ +V + +A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 98 LDELNFTPLNGKPIRIMYS 116
+ +L+ L G +R+ S
Sbjct: 127 VRDLDGRTLCGCRVRVELS 145
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+++ NL + + L F +G + S VA + G + FV+F++ A A+ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 190 GMLLNDKQVFV 200
G L +V V
Sbjct: 132 GRTLCGCRVRV 142
>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 = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 77/169 (45%), Gaps = 14/169 (8%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
N+FI NL+ + L S V G +R +G+V F++ E + A++ L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRF-NNVYVKNLSETTTEDDLKKIFGEFGIITS 247
G+ +VF ++ + + K R + KNLS TED+LK++F + I
Sbjct: 74 TGL-----KVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR- 127
Query: 248 TAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE---WYVGK 293
+ DGKSK ++ F DA +++E G + D + +Y G+
Sbjct: 128 ---LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
N+++ NL+ + +LK E AV+ G ++ FG+V+F+ +D +++E L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLK 339
G K E + K KG+ + ++ L KNL +I++D+LK
Sbjct: 74 TGLKVFGNEIKLEKP----------KGRDSKKVRAAR------TLLAKNLSFNITEDELK 117
Query: 340 ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV 387
E+F + I + +G S+G ++ F + +A K L E G +
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
NL++ NL+ + S +LK SE V+ G +R G+V F +AE+ KAL E
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-E 72
Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
+ G V + + + ++ ++ R
Sbjct: 73 LTGLKVFGNEIKLEKPKGRDSKKVR 97
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 5/64 (7%)
Query: 204 LRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFG 262
L +++RE K +F +++ LS TTE+ L+ + ++G +T VMRD A +S+ FG
Sbjct: 17 LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 263 FVNF 266
FV F
Sbjct: 73 FVTF 76
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT- 380
L++ L +++ L+ + ++G +T C VMRDP + SRG GFV FS+ E A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 381 ---EMNGKMVVSK 390
++G++V K
Sbjct: 89 RPHSIDGRVVEPK 101
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
L++G L + L + + Q G++ V RD +++RS G+G+V +++ E A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 32.3 bits (72), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDN 177
+FI L ++L + + +G + C V D + SRG+GFV F +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V N+ + DL+++FG+FG I ++ + G SK FGFV F++ DA R+ E L+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 281 GKKFDDKEWYVGKAQKK 297
G + ++ V A +
Sbjct: 77 GTVVEGRKIEVNNATAR 93
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V N+ D L+++F +FG I +++ + G S+G GFV F + +A +A +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 384 GKMVVSKPLYV 394
G +V + + V
Sbjct: 77 GTVVEGRKIEV 87
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ + N+ + L F FG IL ++ + G S+G+GFV F+N A A +KL+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 190 GMLLNDKQVFV 200
G ++ +++ V
Sbjct: 77 GTVVEGRKIEV 87
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
V LS TTE DL+++F ++G I +++ D + S+ F FV F++ DDA + E NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 282 KKFDDKEWYV 291
+ D + V
Sbjct: 77 MELDGRRIRV 86
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 142 KALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
+ L + FS +G I + D + SRG+ FV F+N + AK A ++ NGM L+ +++ V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+ L V L L + L ++F++ G + V + D +RRS G+ +V + +A A
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 99 DELNFTPLNGKPIRIMYS 116
+ N L+G+ IR+ +S
Sbjct: 72 ERANGMELDGRRIRVDFS 89
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKAL 379
GL+LY D L+E+FS++G I ++ D SRG FV F ++A +A
Sbjct: 19 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 380 TEMNG 384
NG
Sbjct: 72 ERANG 76
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDA----ARS 275
+++ LS TT++ L++ FG+FG + VMRD +S+ FGFV F D A+S
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 276 VEALNGKKFDDKEWYVGKAQKK 297
L+ K D K + +AQ K
Sbjct: 88 RHELDSKTIDPKVAFPRRAQPK 109
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
G +++ L + + L+E F +FG + C VMRDP SRG GFV F K L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 380 T----EMNGKMVVSKPLYVALAQRK 400
E++ K + K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 35.4 bits (80), Expect = 0.091, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
+++G L L + F Q G+V V RD T+RS G+G+V +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKS 183
S +FI L + L + F FG + C V D L + SRG+GFV F ++ +
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ----A 78
Query: 184 AIDKL 188
+DK+
Sbjct: 79 GVDKV 83
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
V LS TTE DL+++F ++G I +++ D + S+ F FV F++ DDA + E NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 282 KKFDDKEWYV 291
+ D + V
Sbjct: 80 MELDGRRIRV 89
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 142 KALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
+ L + FS +G I + D + SRG+ FV F+N + AK A ++ NGM L+ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Query: 201 -GP 202
GP
Sbjct: 90 SGP 92
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
L V L L + L ++F++ G + V + D +RRS G+ +V + +A A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 100 ELNFTPLNGKPIRI 113
N L+G+ IR+
Sbjct: 76 RANGMELDGRRIRV 89
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKAL 379
GL+LY D L+E+FS++G I ++ D SRG FV F ++A +A
Sbjct: 22 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 380 TEMNGKMVVSKPLYVA 395
NG + + + V+
Sbjct: 75 ERANGMELDGRRIRVS 90
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
++ ++ G F DK + A+ + ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 68
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 69 RSMQGFPFYDK 79
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V+ + + +L E+F FG + K++ G FV F AE A+KA+ E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 384 GKMVVSKPLYVALAQ 398
GK ++PL V ++
Sbjct: 60 GKSFANQPLEVVYSK 74
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V+ E +L +IFG FG + ++ F FV F++ + AA+++E ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 59
Query: 281 GKKFDDK 287
GK F ++
Sbjct: 60 GKSFANQ 66
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F++ + L++ F FG + K+ G+ FV+F+ ESA AI++++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 190 G 190
G
Sbjct: 60 G 60
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
V LS TTE DL+++F ++G I +++ D + S+ F FV F++ DDA + E NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 282 KKFDDKEWYV 291
+ D + V
Sbjct: 80 MELDGRRIRV 89
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+ L V L L + L ++F++ G + V + D +RRS G+ +V + +A A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 99 DELNFTPLNGKPIRIMYS 116
+ N L+G+ IR+ +S
Sbjct: 75 ERANGMELDGRRIRVDFS 92
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 142 KALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
+ L + FS +G I + D + SRG+ FV F+N + AK A ++ NGM L+ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKAL 379
GL+LY D L+E+FS++G I ++ D SRG FV F ++A +A
Sbjct: 22 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 380 TEMNG 384
NG
Sbjct: 75 ERANG 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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 69
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 70 RSMQGFPFYDK 80
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAK 88
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 66
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 64
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSDI 90
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 66
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 67 RSMQGFPFYDK 77
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 64
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAK 85
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 68
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 69 RSMQGFPFYDK 79
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAK 87
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 69
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 70 RSMQGFPFYDK 80
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKG 306
++ ++ G F DK + A+ + ++KG
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG 99
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +++ + +L Y LF+Q G VV + + + R G +V + +T
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMR---GQAFVIFKELGSSTN 64
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL +L P GKP+RI Y+ D I
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAKTDSDI 90
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 12/82 (14%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGT---ITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
+Y+ N++D I ++LK LFS+FG I + K M+ RG FV F ++
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQAFVIFKELGSST 63
Query: 377 KALTEMNGKMVVSKPLYVALAQ 398
AL ++ G KP+ + A+
Sbjct: 64 NALRQLQGFPFYGKPMRIQYAK 85
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQ 398
M G KP+ + A+
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 68
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 69 RSMQGFPFYDK 79
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAK 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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 65
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ + A+ + A+++
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 63
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSDI 89
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ SL + RG FV F SA +A+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SL-KMRGQAFVIFKEVSSATNAL 65
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 66 RSMQGFPFYDK 76
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 63
Query: 275 SVEALNGKKFDDKEWYVGKAQ 295
++ ++ G F DK + A+
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAK 84
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V+NL +++++ L++ FSEFG + K ++D FV F A KA+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 384 GKMVVSKPLYVALAQRKEERRA 405
GK + + + + LA+ +++R+
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 7/62 (11%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V+NL+ T TE+ L+K F EFG + ++D + FV+F+D A ++++ +N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 281 GK 282
GK
Sbjct: 71 GK 72
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F++NL ++ + L +FS FG + K D Y FV F++ +A A+D++N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 190 G 190
G
Sbjct: 71 G 71
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V +L +V + L F++ G++ V+ +D Y +V++ A +A+DE+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 102 N 102
N
Sbjct: 70 N 70
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +LYVG+L + Q+Y+LF++ G + + + D + + G+ +V Y + +A A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 99 DELNFTPLNGKPIR 112
+N T L+ + IR
Sbjct: 99 RYINGTRLDDRIIR 112
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 6/86 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC-FGFVNFDDPDDAARSVEAL 279
+YV NLS TTE+ + ++F + G I + D K+ C F FV + DA ++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 280 NGKKFDDK----EWYVG-KAQKKYER 300
NG + DD+ +W G K ++Y R
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQYGR 127
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSR-GYGFVQFDNEESAKSAIDKL 188
+++ NL + +++ FS G+I + D + ++ G+ FV++ + A++A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 189 NGMLLNDK 196
NG L+D+
Sbjct: 102 NGTRLDDR 109
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 77/171 (45%), Gaps = 14/171 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
A N+F+ NL+ + L S V +G +R +G+V F++ E + A++
Sbjct: 7 AFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE 66
Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTR-FNNVYVKNLSETTTEDDLKKIFGEFGII 245
L G+ +VF ++ + + K R + KNL T+D+LK++F + I
Sbjct: 67 -LTGL-----KVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEI 120
Query: 246 TSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE---WYVGK 293
+ DGKSK ++ F DA ++ E G + D + +Y G+
Sbjct: 121 R----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGE 167
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 76/169 (44%), Gaps = 23/169 (13%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
N++V NL+ + +LK + AV+ G ++ FG+V+F+ +D +++E
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELT 68
Query: 280 NGKKFDDKEWYVGKAQKKYEREMEL-KGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
K F + E++L K K + S KE + L KNL ++ D+L
Sbjct: 69 GLKVFGN--------------EIKLEKPKGKDSKKER----DARTLLAKNLPYKVTQDEL 110
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV 387
KE+F + I + +G S+G ++ F T +A K E G +
Sbjct: 111 KEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
NL+V NL+ + S +LK S+ V+ G++R G+V F +AE+ KAL E
Sbjct: 8 FNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKAL-E 66
Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
+ G V + + + K+ ++ R
Sbjct: 67 LTGLKVFGNEIKLEKPKGKDSKKER 91
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
G +F+ LD S + L FS +G ++ C + D + QSRG+GFV+F + + +
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
L+VG LD S L F+Q G+VV + +D +T +S G+G+V +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA----ARS 275
++V L +TT++ L+ F ++G + +M+D +S+ FGFV F DP+ A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 276 VEALNGKKFDDK 287
L+G+ D K
Sbjct: 79 PHTLDGRNIDPK 90
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE- 381
L+V LD S + + L+ FS++G + C +M+D SRG GFV F L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 382 ---MNGKMVVSKPL 392
++G+ + KP
Sbjct: 79 PHTLDGRNIDPKPC 92
>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 = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 63
Query: 380 TEMNGKMVVSKPLYVALAQ 398
M G KP+ + A+
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 61
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSDI 87
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ + RG FV F SA +A+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 64 RSMQGFPFYDK 74
Score = 36.2 bits (82), Expect = 0.064, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
+ +Y+ NL+E +D+LKK IF FG I V R + + FV F + A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61
Query: 275 SVEALNGKKFDDK 287
++ ++ G F DK
Sbjct: 62 ALRSMQGFPFYDK 74
>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 = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 64
Query: 380 TEMNGKMVVSKPLYVALAQ 398
M G KP+ + A+
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 62
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL + P KP+RI Y+ D I
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSDI 88
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ + RG FV F SA +A+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 64
Query: 186 DKLNGMLLNDK 196
+ G DK
Sbjct: 65 RSMQGFPFYDK 75
Score = 36.2 bits (82), Expect = 0.053, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 216 TRFNN-VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
TR N+ +Y+ NL+E +D+LKK IF FG I V R + + FV F +
Sbjct: 1 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVS 58
Query: 271 DAARSVEALNGKKFDDK 287
A ++ ++ G F DK
Sbjct: 59 SATNALRSMQGFPFYDK 75
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++VK LSE TTE+ LK+ F G + + V G SK FGFV+F+ +DA + EA+
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 281 GKKFD 285
+ D
Sbjct: 76 DGEID 80
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
P R + +F+K L + + L ++F G++ + V G S+G+GFV F++EE
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 180 SAKSAIDKLNGMLLNDKQV 198
AK+A + + ++ +V
Sbjct: 66 DAKAAKEAMEDGEIDGNKV 84
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
L+VK L + +++ LKE F G++ + V G S+G GFV F++ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 212 TADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
++ + N +Y+ NLS T DDL+++FG+ + + V+ + + FV++ D +
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----GYAFVDYPDQNW 56
Query: 272 AARSVEALNGK 282
A R++E L+GK
Sbjct: 57 AIRAIETLSGK 67
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 320 EGLN-LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
G+N LY+ NL +++ D L++LF + + +V+ + G FV + A +A
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-----LKSGYAFVDYPDQNWAIRA 60
Query: 379 LTEMNGKM 386
+ ++GK+
Sbjct: 61 IETLSGKV 68
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 44/79 (55%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
++VGDL + + + F G++ RV +D++T +S GYG+V++ +A A+ ++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 102 NFTPLNGKPIRIMYSYRDP 120
L G+ IR ++ R P
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
++F+ +L I A+ F+ FG I +V D + G+S+GYGFV F N+ A++AI +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 188 LNGMLLNDKQV 198
+ G L +Q+
Sbjct: 68 MGGQWLGGRQI 78
Score = 36.2 bits (82), Expect = 0.057, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 345 FGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
FG I+ +V++D G S+G GFV+F +A A+ +M G+ + + + A RK
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Score = 35.8 bits (81), Expect = 0.079, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
+V+V +LS T + F FG I+ V++D A GKSK +GFV+F + DA +++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 279 LNGKKFDDKEWYVGKAQKK 297
+ G+ ++ A +K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
TSL V +L + L +F + G+V V + RD T+ S G+ +V ++ +A A+D
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 100 ELNFTPLNGKPIRI 113
++ L+G+ +R+
Sbjct: 131 AMDGAVLDGRELRV 144
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
V NL+ T+ D L+++F ++G + + RD K S+ F FV F D DA +++A++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 282 KKFDDKEWYVGKAQ 295
D +E V A+
Sbjct: 135 AVLDGRELRVQMAR 148
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 320 EGL-NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASK 377
EG+ +L V NL S D L+ +F ++G + + RD SRG FV F +A
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 378 ALTEMNGKMVVSKPLYVALAQ 398
A+ M+G ++ + L V +A+
Sbjct: 128 AMDAMDGAVLDGRELRVQMAR 148
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSA 184
G ++ + NL L F +G + + D +SRG+ FV+F ++ A+ A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 185 IDKLNGMLLNDKQVFV 200
+D ++G +L+ +++ V
Sbjct: 129 MDAMDGAVLDGRELRV 144
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+FI NL+ ++ K+ + FS +G + C V +GY FVQ+ NE A++A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGE 82
Query: 189 NGMLL 193
NG +L
Sbjct: 83 NGRVL 87
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDA----ARS 275
+++ LS TT++ L++ FG+FG + VMRD +S+ FGFV F D A+S
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 276 VEALNGKKFDDK 287
L+ K D K
Sbjct: 63 RHELDSKTIDPK 74
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
+++ L + + L+E F +FG + C VMRDP SRG GFV F K L +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Score = 36.2 bits (82), Expect = 0.064, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
+++G L L + F Q G+V V RD T+RS G+G+V +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
+FI L + L + F FG + C V D L + SRG+GFV F ++ + +DK+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ----AGVDKV 58
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKS-KCFGFVNFDDPDDAARSVEALNG 281
V NL+ T+ D L+++F ++G + + R+ K+ + F FV F D DA + A++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 282 KKFDDKEWYV 291
+ D +E V
Sbjct: 78 AELDGRELRV 87
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +LYVG+L + Q+Y+LF++ G + + + D + + G+ +V Y + +A A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAM 76
Query: 99 DELNFTPLNGKPIR 112
+N T L+ + IR
Sbjct: 77 RYINGTRLDDRIIR 90
Score = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
+E+E K+ +YV NLS TTE+ + ++F + G I + D + F FV +
Sbjct: 9 EEQEKLLKKS--CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEY 66
Query: 267 DDPDDAARSVEALNGKKFDDK----EWYVG 292
DA ++ +NG + DD+ +W G
Sbjct: 67 YSRADAENAMRYINGTRLDDRIIRTDWDAG 96
Score = 34.3 bits (77), Expect = 0.20, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 37/67 (55%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+++ NL + +++ FS G+I + D + + G+ FV++ + A++A+ +N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 190 GMLLNDK 196
G L+D+
Sbjct: 81 GTRLDDR 87
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LYV NL +++++ ELFS+ G I + D + G FV + + +A A+ +N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 384 G 384
G
Sbjct: 81 G 81
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
VYV NL + +L++ F +G + + + R+ G F FV F+DP DA +V L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 281 GK 282
GK
Sbjct: 59 GK 60
Score = 35.8 bits (81), Expect = 0.067, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
+ +YV NL +L+ FS +G + + + R+P G + FV F +A A+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRG 56
Query: 382 MNGKMVVSKPLYVALAQRKEERRARL 407
++GK++ + V L+ RR+R
Sbjct: 57 LDGKVICGSRVRVELST-GMPRRSRF 81
Score = 29.6 bits (65), Expect = 5.6, Method: Composition-based stats.
Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 10/90 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+++ NL L FS +G + + +A + G+ FV+F++ A+ A+ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGLD 58
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFN 219
G +V G +R + ++RF+
Sbjct: 59 G------KVICGSRVRVELSTGMPRRSRFD 82
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKV-MRDPNGISRGSGFVAFSTAEEASKALTEM 382
LY+KNL +++ L LF+ F + R G RG F+ F E A +AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 383 NGKMVVSKPLYVALAQRKEER 403
NG + K L + + K++R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAV-MRDADGKSKCFGFVNFDDPDDAARSVEAL 279
+Y+KNLS TE DL +F F + R G+ + F+ F + + A +++ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 280 NGKKFDDKEWYVGKAQKKYER 300
NG K K + + K +R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTF----GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
+++KNL + + L F+ F G + ++ T G+ RG F+ F N+E A A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 186 DKLNGMLLNDKQVFVGPFLRKQERES 211
+NG L K + + K++R S
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
L++ L + ++DD++KEL + FG + + +++D G+S+G F + +A+ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 383 NGKMVVSKPLYV 394
NG + K L V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAI 185
A +FI L +++ + + ++FG + + + DS G S+GY F ++ + AI
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 186 DKLNGMLLNDKQVFV 200
LNGM L DK++ V
Sbjct: 61 AGLNGMQLGDKKLLV 75
Score = 35.8 bits (81), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
+ +++ L +D +K++ FG + + +++D A G SK + F + D + +++
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 278 ALNGKKFDDKEWYVGKA 294
LNG + DK+ V +A
Sbjct: 62 GLNGMQLGDKKLLVQRA 78
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L++G L +ND Q+ +L G + + + +D +T S GY + Y + +A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 102 NFTPLNGKPIRI 113
N L K + +
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 324 LYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
LYV+NL S S++ +++ F+ G + K +RD FV FS E+A +A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 382 MNGKMVVSKPLYVALAQ 398
+NGK++ P+ V LA+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+YV+NL +T+E+ ++K EF I AV R K + + FV+F + +DA +++ALN
Sbjct: 18 LYVRNLMLSTSEEMIEK---EFNNIKPGAVERVK--KIRDYAFVHFSNREDAVEAMKALN 72
Query: 281 GKKFD 285
GK D
Sbjct: 73 GKVLD 77
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 26 ANNGGVGDARQFVSTS-LYVGDLDLSVNDSQLYDLFNQM--GQVVSVRVCRDLSTRRSLG 82
++G GD S LYV +L LS ++ + FN + G V V+ RD
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------- 52
Query: 83 YGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
Y +V+++ +A A+ LN L+G PI +
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 83
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
++++NL S + + F+ NI A + + + R Y FV F N E A A+ LN
Sbjct: 18 LYVRNLMLSTSEEMIEKEFN---NIKPG--AVERVKKIRDYAFVHFSNREDAVEAMKALN 72
Query: 190 GMLLNDKQVFV 200
G +L+ + V
Sbjct: 73 GKVLDGSPIEV 83
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 1/91 (1%)
Query: 111 IRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK-VATDSLGQSRG 169
+++ + DP + +F+ ++ L F +G I V + G+ RG
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 170 YGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
Y F+++++E SA +G ++ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTA-VMRDADGKSKCFGFVNFDDPDDAARSV 276
F ++V ++ TTE L++ F +G I V GK + + F+ ++ D +
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 277 EALNGKKFDDK 287
+ +GKK D +
Sbjct: 162 KHADGKKIDGR 172
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIIT--STAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
V++ L+ T+D + +IF +G I V R SK + +V F++PD+A ++++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 279 LNGKKFDDKE 288
++G + D +E
Sbjct: 67 MDGGQIDGQE 76
Score = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTIT--SCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
+++ L +++ D + E+FS +G I V R +S+G +V F +EA KAL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 382 MNGKMV 387
M+G +
Sbjct: 67 MDGGQI 72
Score = 36.2 bits (82), Expect = 0.064, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ--SRGYGFVQFDNEESAKSAIDK 187
+ I L +++ + + FST+G I + + + S+GY +V+F+N + A+ A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 188 LNGMLLNDKQV 198
++G ++ +++
Sbjct: 67 MDGGQIDGQEI 77
Score = 32.3 bits (72), Expect = 0.83, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR-----SLGYGYVNYNAAHEA 94
T +++G L +V + ++F+ G++ + D+ R S GY YV + EA
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMI----DMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 95 TRALDELNFTPLNGKPI 111
+AL ++ ++G+ I
Sbjct: 61 EKALKHMDGGQIDGQEI 77
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAAR 274
T F ++V L TT+ L+K F FG I V+ D GKS+ +GFV D A R
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 275 SVE----ALNGKKFDDKEWYVG 292
+ + ++G+K + Y+G
Sbjct: 75 ACKDPNPIIDGRKANVNLAYLG 96
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
IF+ L + +L F FG+I V TD G+SRGYGFV + +A+ A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 189 NGML 192
N ++
Sbjct: 80 NPII 83
Score = 35.8 bits (81), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T ++VG L D+ L F G + V D T +S GYG+V A RA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 100 ELN 102
+ N
Sbjct: 78 DPN 80
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
++V L +D L++ F FG I V+ D G SRG GFV + A +A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 383 N 383
N
Sbjct: 80 N 80
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
E L + NL S +++ L+E+F + T KV ++ NG S+G F+ F++ E+A +AL
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 380 TEMNGKMVVSKPLYVAL 396
N + + + + + L
Sbjct: 71 NSCNKREIEGRAIRLEL 87
Score = 35.8 bits (81), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+ + NLS + TE+ L+++F + I V ++ +GKSK + F+ F +DA ++ + N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 281 GKKFDDK 287
++ + +
Sbjct: 75 KREIEGR 81
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 130 IFIKNLDKSIDNKALHDTF--STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
+ + NL S + L + F +TF KV + G+S+GY F++F + E AK A++
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATF-----IKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 188 LN 189
N
Sbjct: 73 CN 74
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +L + +L S + L ++F + ++V ++ +S GY ++ + + +A AL
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQN-QNGKSKGYAFIEFASFEDAKEAL 70
Query: 99 DELNFTPLNGKPIRI 113
+ N + G+ IR+
Sbjct: 71 NSCNKREIEGRAIRL 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
IF+ N+ + ++ L F G ++ C V D Y FV + E AK+AI +LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 190 GMLLNDKQVFVGPFLRKQER 209
G + K++ V + Q++
Sbjct: 65 GKEVKGKRINVELSTKGQKK 84
Score = 34.3 bits (77), Expect = 0.25, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V N+S T +L+ +F G + V++D + FV+ + DA ++ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 281 GKKFDDKEWYV---GKAQKK 297
GK+ K V K QKK
Sbjct: 65 GKEVKGKRINVELSTKGQKK 84
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
++VG++ + +L LF + G+V+ V +D Y +V+ +A A+ +L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSG 126
N + GK I + S + +KSG
Sbjct: 64 NGKEVKGKRINVELSTKGQ--KKSG 86
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 307 KFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
+FE + +++ K +Y + ++D +++ FS FG I +V + +G F
Sbjct: 13 RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSF 65
Query: 367 VAFSTAEEASKALTEMNGKMV 387
V FST E A+ A+ +NG +
Sbjct: 66 VRFSTHESAAHAIVSVNGTTI 86
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
++ + + ++ + TFS FG I+ +V + +GY FV+F ESA AI +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 190 G 190
G
Sbjct: 83 G 83
Score = 32.3 bits (72), Expect = 0.90, Method: Composition-based stats.
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
++Y G + + D + F+ GQ++ +RV + GY +V ++ A A+
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80
Query: 101 LNFTPLNGKPIRIMYSYRDPTI 122
+N T + G ++ + P +
Sbjct: 81 VNGTTIEGHVVKCYWGKESPDM 102
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 66
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL P KP RI Y+ D I
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSDI 92
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--XRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQ 398
G KP + A+
Sbjct: 69 RSXQGFPFYDKPXRIQYAK 87
Score = 37.0 bits (84), Expect = 0.038, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ + RG FV F SA +A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 68
Query: 186 DKLNGMLLNDK 196
G DK
Sbjct: 69 RSXQGFPFYDK 79
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 215 KTRFNN-VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
+TR N+ +Y+ NL+E +D+LKK IF FG I V R + + FV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEV 61
Query: 270 DDAARSVEALNGKKFDDK 287
A ++ + G F DK
Sbjct: 62 SSATNALRSXQGFPFYDK 79
>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 = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 67
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL P KP RI Y+ D I
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSDI 93
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--XRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQ 398
G KP + A+
Sbjct: 70 RSXQGFPFYDKPXRIQYAK 88
Score = 37.0 bits (84), Expect = 0.038, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ + RG FV F SA +A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 69
Query: 186 DKLNGMLLNDK 196
G DK
Sbjct: 70 RSXQGFPFYDK 80
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 215 KTRFNN-VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
+TR N+ +Y+ NL+E +D+LKK IF FG I V R + + FV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEV 62
Query: 270 DDAARSVEALNGKKFDDK 287
A ++ + G F DK
Sbjct: 63 SSATNALRSXQGFPFYDK 80
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 41 SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++Y+ +L+ + +L + +F++ GQ++ + V R L R G +V + AT
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 64
Query: 97 ALDELNFTPLNGKPIRIMYSYRDPTI 122
AL P KP RI Y+ D I
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSDI 90
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I D+LK+ +FS FG I V R RG FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--XRGQAFVIFKEVSSATNAL 66
Query: 380 TEMNGKMVVSKPLYVALAQ 398
G KP + A+
Sbjct: 67 RSXQGFPFYDKPXRIQYAK 85
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
I+I NL++ I K+LH FS FG IL V+ + RG FV F SA +A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 66
Query: 186 DKLNGMLLNDK 196
G DK
Sbjct: 67 RSXQGFPFYDK 77
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 215 KTRFNN-VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
+TR N+ +Y+ NL+E +D+LKK IF FG I V R + + FV F +
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEV 59
Query: 270 DDAARSVEALNGKKFDDK 287
A ++ + G F DK
Sbjct: 60 SSATNALRSXQGFPFYDK 77
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
++I+NL I + ++D F +G I +V ++RG +V +++ AK+A+D L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 190 GMLLNDKQVFV 200
G ++++ + V
Sbjct: 69 GFNVSNRYLVV 79
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LY++NL I+ +++ ++F ++G I +V P +RG+ +V + +A A+ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 384 GKMVVSKPLYV 394
G V ++ L V
Sbjct: 69 GFNVSNRYLVV 79
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
V+ LY+ +L + ++YD+F + G + +RV TR G YV Y +A A
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 63
Query: 98 LDELNFTPLNGKPIRIMY 115
+D L+ ++ + + ++Y
Sbjct: 64 VDHLSGFNVSNRYLVVLY 81
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 56/105 (53%), Gaps = 7/105 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+Y++NL T +++ IFG++G I V + ++ +V ++D DA +V+ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 281 GKKFDDKEWYV--GKAQKKYEREMELKGKFEQSLKETADKFEGLN 323
G ++ V A + +++ M+ K K E+ LK +K+ G+N
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQK-MDTKKK-EEQLKLLKEKY-GIN 110
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 37/72 (51%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+FI L S + L + G + ++ T+ G+ +G +V+++NE A A+ K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 190 GMLLNDKQVFVG 201
GM + + + V
Sbjct: 80 GMTIKENIIKVA 91
Score = 36.6 bits (83), Expect = 0.042, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 42/79 (53%)
Query: 319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
E L++ L S + ++L+E+ GT+ +++ + G +G +V + +AS+A
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQA 74
Query: 379 LTEMNGKMVVSKPLYVALA 397
+ +M+G + + VA++
Sbjct: 75 VMKMDGMTIKENIIKVAIS 93
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD--SLGQSRGYGFVQFDNEES 180
+K I ++N+ + + + + FSTFG + + ++ G RG+GFV F ++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 181 AKSAIDKL 188
AK A + L
Sbjct: 71 AKKAFNAL 78
Score = 36.6 bits (83), Expect = 0.050, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGIS--RGSGFVAFSTAEEASKALTE 381
+ V+N+ + +++ELFS FG + + ++ + G RG GFV F T ++A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 382 M 382
+
Sbjct: 78 L 78
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD--ADGKSKCFGFVNFDDPDDA 272
K + + V+N+ + +++++F FG + + + + G + FGFV+F DA
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 273 ARSVEAL 279
++ AL
Sbjct: 72 KKAFNAL 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
++V N+S T T +L+ F E+G + +++D + FV+ + +DA ++ L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 281 GKKFDDKEWYV 291
+F K +V
Sbjct: 66 NTEFQGKRMHV 76
Score = 35.4 bits (80), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V N+ + ++ +L+ F E+G + C +++D FV AE+A +A+ ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 384 GKMVVSKPLYVALA 397
K ++V L+
Sbjct: 66 NTEFQGKRMHVQLS 79
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 8/65 (12%)
Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
+FI NL+ + K+ + FS +G I+ C V +G+ FVQ+ NE +A++A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 70
Query: 189 NGMLL 193
+G ++
Sbjct: 71 DGRMI 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 33/157 (21%), Positives = 71/157 (45%), Gaps = 16/157 (10%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ +KNL KS + ++ F G I+ VA DSL ++ + ++F + A +AI K +
Sbjct: 7 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
++ ++ V E T +++ N + T+ +++ + + ++ +
Sbjct: 66 KVV-GQNEIIVSHLT-----ECT--------LWMTNFPPSYTQRNIRDLLQDINVVALSI 111
Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFD 285
+ S+ F +++ +DA VE LNG K +
Sbjct: 112 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 148
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 29/153 (18%), Positives = 68/153 (44%), Gaps = 13/153 (8%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
T++ V +L S N +++Y F G ++ V V L +++ + + + A A+
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAIT 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNI-LSCK 158
+ + + G+ I+ + T+ ++ N S + + D + LS +
Sbjct: 63 KTH--KVVGQNEIIVSHLTECTL--------WMTNFPPSYTQRNIRDLLQDINVVALSIR 112
Query: 159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGM 191
+ + SR + ++ ++E A+ ++KLNG+
Sbjct: 113 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL 145
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 56 LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
LY +F+Q GQ++ + + L R G +V + A+ AL + P KP++I Y
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMR---GQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAY 83
Query: 116 SYRDPTI 122
S D I
Sbjct: 84 SKSDSDI 90
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDD----KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
+Y+ NL++ I + L +FS+FG I ++ RG FV F AS AL
Sbjct: 9 IYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEIGSASNAL 66
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
M G KP+ +A ++ + A+++
Sbjct: 67 RTMQGFPFYDKPMQIAYSKSDSDIVAKIK 95
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 6/98 (6%)
Query: 221 VYVKNLS----ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSV 276
+Y+ NL+ + + L IF +FG I ++ + + FV F + A+ ++
Sbjct: 9 IYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQA--FVIFKEIGSASNAL 66
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKE 314
+ G F DK + ++ + ++KG F++ K+
Sbjct: 67 RTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKK 104
>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 = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 6 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
Score = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V + + ++D F + G++ ++ + D T GY V Y EA A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NFTPLNGKPIRIMYSY 117
N L G+PI + + +
Sbjct: 70 NGQDLMGQPISVDWCF 85
Score = 36.6 bits (83), Expect = 0.051, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ + + + +HD F+ +G I + + D G +GY V+++ + A++A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 189 NGMLLNDKQVFV 200
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 32.3 bits (72), Expect = 0.81, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 280 NGK 282
NG+
Sbjct: 70 NGQ 72
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
+ + L++ + ++ + LK LF EFG I V++D G+ +G F+ + E A KA
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 379 LTEMN 383
+ ++
Sbjct: 72 QSALH 76
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 122 IRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEES 180
++ A +FI + +++D K L F FG I V D G +G F+ + ES
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 181 AKSAIDKLN 189
A A L+
Sbjct: 68 ALKAQSALH 76
Score = 32.7 bits (73), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
+++ + E DLK +F EFG I V++D G K F+ + + + A ++ A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 279 LNGKK 283
L+ +K
Sbjct: 75 LHEQK 79
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 6 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
Score = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V + + ++D F + G++ ++ + D T GY V Y EA A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NFTPLNGKPIRIMYSY-RDP 120
N L G+PI + + + R P
Sbjct: 70 NGQDLMGQPISVDWCFVRGP 89
Score = 36.2 bits (82), Expect = 0.061, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ + + + +HD F+ +G I + + D G +GY V+++ + A++A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 189 NGMLLNDKQVFV 200
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 32.3 bits (72), Expect = 0.96, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 280 NGK 282
NG+
Sbjct: 70 NGQ 72
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVE 277
N ++V + E +L++ F +FG++T ++ DA+ + + FGF+ F+D ++V
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 278 A----LNGKKFDDK 287
+ GKK + K
Sbjct: 71 MHFHDIMGKKVEVK 84
Score = 32.7 bits (73), Expect = 0.71, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
++VG + + +++L + F + G V V + D +R G+G++ + +A++ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 102 NFTPLNGKPIRI 113
+F + GK + +
Sbjct: 72 HFHDIMGKKVEV 83
Score = 32.3 bits (72), Expect = 0.83, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQS-RGYGFVQFDNEESAKSAID 186
IF+ + + L + F FG + + D+ Q RG+GF+ F++E+S A++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Score = 30.0 bits (66), Expect = 4.4, Method: Composition-based stats.
Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGIS-RGSGFVAFSTAEEASKALTEM 382
++V + + + +L+E F +FG +T ++ D RG GF+ F + +A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
+ ++ K + V A+ ++ + +
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSS 94
>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 = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 6 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
L+V + + ++D F + G++ ++ + D T GY V Y EA A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NFTPLNGKPIRIMYSY-RDP 120
N L G+PI + + + R P
Sbjct: 70 NGQDLMGQPISVDWCFVRGP 89
Score = 36.2 bits (82), Expect = 0.064, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ + + + +HD F+ +G I + + D G +GY V+++ + A++A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 189 NGMLLNDKQVFV 200
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 280 NGK 282
NG+
Sbjct: 70 NGQ 72
>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 = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 8 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 67
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 68 MEGLNGQDLMGQPISV 83
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
G R L+V + + ++D F + G++ ++ + D T GY V Y
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 92 HEATRALDELNFTPLNGKPIRIMYSY-RDP 120
EA A++ LN L G+PI + + + R P
Sbjct: 62 KEAQAAMEGLNGQDLMGQPISVDWCFVRGP 91
Score = 36.2 bits (82), Expect = 0.066, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
+F+ + + + +HD F+ +G I + + D G +GY V+++ + A++A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 189 NGMLLNDKQVFV 200
NG L + + V
Sbjct: 72 NGQDLMGQPISV 83
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 280 NGK 282
NG+
Sbjct: 72 NGQ 74
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +Y+G + + Q+ DL + +G V+++++ D T RS GY ++ + + A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 99 DELNFTPLNGKPIRIMYS 116
LN L + ++ YS
Sbjct: 64 RNLNGYQLGSRFLKCGYS 81
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
+++ ++ + + D S G +++ K+ D G+S+GY F++F + ES+ SA+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 189 NGMLLNDKQVFVG 201
NG L + + G
Sbjct: 67 NGYQLGSRFLKCG 79
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
+Y+ ++ +++++ +L S G + + K+M DP G S+G F+ F E ++ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 383 NGKMVVSKPL 392
NG + S+ L
Sbjct: 67 NGYQLGSRFL 76
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
VY+ ++ TE+ + + G + + +M D G+SK + F+ F D + +A +V L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 280 NGKKFDDKEWYVG 292
NG + + G
Sbjct: 67 NGYQLGSRFLKCG 79
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V ++ + +D+++E F ++G I + + D G S+G V + T ++A A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 379 LTEMNGKMVVSKPLYV 394
+NG ++ + + V
Sbjct: 85 KEALNGAEIMGQTIQV 100
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 119 DPTIRKSGAGNI-FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFD 176
+P ++S G I F+ ++ + + + F +G I + + D G S+GY V+++
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 177 NEESAKSAIDKLNG 190
+ A +A + LNG
Sbjct: 77 THKQALAAKEALNG 90
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
++V ++ E ED++++ F ++G I + + D G SK + V ++ A + EAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 280 NGKK 283
NG +
Sbjct: 89 NGAE 92
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 19/86 (22%), Positives = 38/86 (44%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
G R L+V + + ++ + F G++ ++ + D T S GY V Y
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 92 HEATRALDELNFTPLNGKPIRIMYSY 117
+A A + LN + G+ I++ + +
Sbjct: 79 KQALAAKEALNGAEIMGQTIQVDWCF 104
>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 = 37.7 bits (86), Expect = 0.021, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 81 MEGLNGQDLMGQPISV 96
Score = 37.0 bits (84), Expect = 0.038, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 39/86 (45%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
G R L+V + + ++D F + G++ ++ + D T GY V Y
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 92 HEATRALDELNFTPLNGKPIRIMYSY 117
EA A++ LN L G+PI + + +
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISVDWCF 100
Score = 35.8 bits (81), Expect = 0.081, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 119 DPTIRKSGAGNI-FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFD 176
+P ++S G I F+ + + + +HD F+ +G I + + D G +GY V+++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 177 NEESAKSAIDKLNGMLLNDKQVFV 200
+ A++A++ LNG L + + V
Sbjct: 73 TYKEAQAAMEGLNGQDLMGQPISV 96
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 280 NGK 282
NG+
Sbjct: 85 NGQ 87
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
++ SL++GDL+ ++++ + F MG+ V+SV++ R+ T GY +V + A +
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
Query: 97 ALDELNFTPLNG 108
L ++N PL G
Sbjct: 68 CLHKINGKPLPG 79
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDSL-GQSRGYGFVQFDNEESAKSA 184
A ++++ +L+ +D + F+T G ++S K+ + L G GY FV+F + +A+
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 185 IDKLNG 190
+ K+NG
Sbjct: 69 LHKING 74
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +Y+G + + Q+ DL + +G V+++++ D T RS GY ++ + + A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 99 DELNFTPLNGKPIRIMYS 116
LN L + ++ YS
Sbjct: 62 RNLNGYQLGSRFLKCGYS 79
Score = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 144 LHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
+ D S G +++ K+ D G+S+GY F++F + ES+ SA+ LNG L + + G
Sbjct: 19 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 77
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
+Y+ ++ +++++ +L S G + + K+M DP G S+G F+ F E ++ A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 383 NGKMVVSKPL 392
NG + S+ L
Sbjct: 65 NGYQLGSRFL 74
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
VY+ ++ TE+ + + G + + +M D G+SK + F+ F D + +A +V L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 280 NGKKFDDK 287
NG + +
Sbjct: 65 NGYQLGSR 72
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGI-ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
N V ++ L + TEDD++ G+ +MR+ + G+S+ F FV F DA R +
Sbjct: 2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM 61
Query: 277 EA 278
EA
Sbjct: 62 EA 63
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFST---AE 373
+ + ++V + + S+ L+ELF ++G + V+RD + S+G FV F T A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 374 EASKALTEM 382
EA AL M
Sbjct: 62 EAQNALHNM 70
Score = 36.2 bits (82), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNY---NAAHE 93
+ ++VG + + ++ L +LF Q G V + V RD S +S G +V + AA E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 94 ATRALDELNFTPLNGKPIRI 113
A AL + P PI++
Sbjct: 63 AQNALHNMKVLPGMHHPIQM 82
Score = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSVE 277
++V + T +E DL+++F ++G + V+RD +SK FV F A +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 278 ALNGKK 283
AL+ K
Sbjct: 66 ALHNMK 71
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTA---------VMRDADGKSKCFGFVNFDDPDD 271
+YV+ L+++ T DDL F + G++ + GK K V+++DP
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 272 AARSVEALNGKKFDDKEWYVGKAQKK 297
A +VE +GK F + V A+KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP---------NGISRGSGFVAFSTAEE 374
+YV+ L+DS++ D L + F + G + K P G +G V++
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 375 ASKALTEMNGKMVVSKPLYVALAQRK 400
A A+ +GK L V+LA++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>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 = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V ++ + +D+++E F ++G I + + D G S+G V + T ++A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
+NG ++ + + V K +R +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVK 158
Score = 32.3 bits (72), Expect = 0.92, Method: Composition-based stats.
Identities = 24/102 (23%), Positives = 51/102 (50%), Gaps = 3/102 (2%)
Query: 119 DPTIRKSGAGNI-FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFD 176
+P ++S G I F+ ++ + + + F +G I + + D G S+GY V+++
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 177 NEESAKSAIDKLNGMLLNDKQVFVG-PFLRKQERESTADKTR 217
+ A +A + LNG + + + V F++ +R ++K R
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
++V ++ E ED++++ F ++G I + + D G SK + V ++ A + EAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 280 NGKK 283
NG +
Sbjct: 135 NGAE 138
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 19/86 (22%), Positives = 38/86 (44%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
G R L+V + + ++ + F G++ ++ + D T S GY V Y
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 92 HEATRALDELNFTPLNGKPIRIMYSY 117
+A A + LN + G+ I++ + +
Sbjct: 125 KQALAAKEALNGAEIMGQTIQVDWCF 150
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
+ + L+V + + + LK LF EFG I V++D G+ +G F+ + + A KA
Sbjct: 14 DAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Query: 379 LTEMN 383
+ ++
Sbjct: 74 QSALH 78
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
++V + E DLK +F EFG I V++D G K F+ + D A ++ A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 279 LNGKK 283
L+ +K
Sbjct: 77 LHEQK 81
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
+F+ + + +D + L F FG I V D L G +G F+ + +SA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 188 LN 189
L+
Sbjct: 77 LH 78
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEE 374
+D EG ++++NL ++ L E+ +FG + +V+ P+ S+G F F T E
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 375 ASKAL------TEMNGKMVVSKPLYVALAQRKEE 402
A K L E G + + L V LA ++E
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
+FI+NL + +AL + FG++ +V S+G F QF +E+A+ +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>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 = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
EG L+V + + +++ + + F+E+G I + + D G +G V + T +EA A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 379 LTEMNGKMVVSKPLYV 394
+ +NG+ ++ +P+ V
Sbjct: 82 MEGLNGQDLMGQPISV 97
Score = 36.6 bits (83), Expect = 0.046, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
G R L+V + + ++D F + G++ ++ + D T GY V Y
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 92 HEATRALDELNFTPLNGKPIRIMYSY-RDP 120
EA A++ LN L G+PI + + + R P
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 119 DPTIRKSGAGNI-FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFD 176
+P ++S G I F+ + + + +HD F+ +G I + + D G +GY V+++
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 177 NEESAKSAIDKLNGMLLNDKQVFV 200
+ A++A++ LNG L + + V
Sbjct: 74 TYKEAQAAMEGLNGQDLMGQPISV 97
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
++V + E TE+D+ F E+G I + + D G K + V ++ +A ++E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 280 NGK 282
NG+
Sbjct: 86 NGQ 88
>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 = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
S +Y+G + + Q+ DL + +G V+++++ D T RS GY ++ + + A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 99 DELNFTPLNGKPIRIMYS 116
LN L + ++ YS
Sbjct: 63 RNLNGYQLGSRFLKCGYS 80
Score = 36.6 bits (83), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 144 LHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
+ D S G +++ K+ D G+S+GY F++F + ES+ SA+ LNG L + + G
Sbjct: 20 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 78
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
+Y+ ++ +++++ +L S G + + K+M DP G S+G F+ F E ++ A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 383 NGKMVVSKPL 392
NG + S+ L
Sbjct: 66 NGYQLGSRFL 75
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
VY+ ++ TE+ + + G + + +M D G+SK + F+ F D + +A +V L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 280 NGKKFDDK 287
NG + +
Sbjct: 66 NGYQLGSR 73
>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A) Binding
Protein From Saccharomyces Cerevisiae
Length = 92
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 564 EQQRTLLGENLYPLVDQL--EHDNAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 621
++QR LGE LY V + A K+TGM+L++ EV LLES E + EA
Sbjct: 18 QKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAA 77
Query: 622 LRNVAQQQ 629
+ ++Q
Sbjct: 78 YESFKKEQ 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 212 TADKTRF-NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
T+ K R + KNLS TED+LK++F + I + DGKSK ++ F
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEA 64
Query: 271 DAARSVEALNGKKFDDKE---WYVGK 293
DA +++E G + D + +Y G+
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGE 90
Score = 32.7 bits (73), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L KNL +I++D+LKE+F + I + +G S+G ++ F + +A K L E
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 384 GKMV 387
G +
Sbjct: 75 GAEI 78
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.0 bits (84), Expect = 0.035, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LY++NL I+ +++ ++F ++G I +V P +RG+ +V + +A A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 384 GKMVVSKPLYV 394
G V ++ L V
Sbjct: 73 GFNVCNRYLVV 83
Score = 35.8 bits (81), Expect = 0.076, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
V+ LY+ +L + ++YD+F + G + +RV TR G YV Y +A A
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 67
Query: 98 LDELN 102
D L+
Sbjct: 68 CDHLS 72
Score = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
++I+NL I + ++D F +G I +V ++RG +V +++ AK+A D L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNACDHLS 72
Query: 190 GMLLNDKQVFV 200
G + ++ + V
Sbjct: 73 GFNVCNRYLVV 83
Score = 30.0 bits (66), Expect = 4.4, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+Y++NL T +++ IFG++G I V + + +V ++D DA + + L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGT--AYVVYEDIFDAKNACDHLS 72
Query: 281 G 281
G
Sbjct: 73 G 73
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.6 bits (83), Expect = 0.041, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
+++ V L TTE DLK+ F FG + V +D G SK FGFV F + + V+
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET---QVK 72
Query: 278 ALNGKKFDDKEW 289
++ + D W
Sbjct: 73 VMSQRHMIDGRW 84
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 144 LHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEES 180
L + FSTFG +L +V D G S+G+GFV+F E+
Sbjct: 32 LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
+L V L ++ LKE FS FG + +V +D G S+G GFV F+ E K +++
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 24 GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
G + + GV A Q S + +G L + L + F+ G+V+ V+V +DL T S G+
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLG-LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGF 59
Query: 84 GYVNYNAAHEATRALDE 100
G+V + + + +
Sbjct: 60 GFVRFTEYETQVKVMSQ 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.6 bits (83), Expect = 0.045, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
++V LS TT +D+K F +FG + +M D + + FGFV F+ D + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
Score = 32.7 bits (73), Expect = 0.68, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
++VG L ++ + F Q G+V + D +T R G+G+V + + + + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE-SEDIVEKVCEI 60
Query: 102 NFTPLNGKPI 111
+F +N K +
Sbjct: 61 HFHEINNKMV 70
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 36.2 bits (82), Expect = 0.052, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSK----CFGFVNFDDPDDAARSV 276
+YV NL D++ +F ++G I RD D K++ F FV F+DP DA +V
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 277 EALNGKKFD 285
+G +D
Sbjct: 79 YGRDGYDYD 87
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.2 bits (82), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
+FI NL K++ + L FS +G+I+ + +GF+QFDN +S + AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 221 VYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
+++ NL + +++DL +IF +G I + FGF+ FD+P ++E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.2 bits (82), Expect = 0.060, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
SG +FI NL + + + F +G +L C + + YGFV +++ +A+ A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 185 IDKLN 189
I L+
Sbjct: 59 IRNLH 63
>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 = 35.8 bits (81), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+ I+NL I + ++D F +G I +V ++RG +V +++ AK+A D L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNACDHLS 78
Query: 190 GMLLNDKQVFV 200
G + ++ + V
Sbjct: 79 GFNVCNRYLVV 89
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
V+ L + +L + ++YD+F + G + +RV TR G YV Y +A A
Sbjct: 17 VNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 73
Query: 98 LDELNFTPLNGKPIRIMY 115
D L+ + + + ++Y
Sbjct: 74 CDHLSGFNVCNRYLVVLY 91
>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 = 35.8 bits (81), Expect = 0.073, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LY++NL I+ +++ ++F ++G I +V P +RG+ +V + +A A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 384 GKMVVSKPLYV 394
G V ++ L V
Sbjct: 79 GFNVCNRYLVV 89
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
V+ LY+ +L + ++YD+F + G + +RV TR G YV Y +A A
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 73
Query: 98 LDELN 102
D L+
Sbjct: 74 CDHLS 78
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
++I+NL I + ++D F +G I +V ++RG +V +++ AK+A D L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNACDHLS 78
Query: 190 GMLLNDKQVFV 200
G + ++ + V
Sbjct: 79 GFNVCNRYLVV 89
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 7/105 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
+Y++NL T +++ IFG++G I V + + +V ++D DA + + L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGT--AYVVYEDIFDAKNACDHLS 78
Query: 281 GKKFDDKEWYV--GKAQKKYEREMELKGKFEQSLKETADKFEGLN 323
G ++ V A + +++ M+ K K EQ LK +K+ G+N
Sbjct: 79 GFNVCNRYLVVLYYNANRAFQK-MDTKKKEEQ-LKLLKEKY-GIN 120
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 35.4 bits (80), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 75/183 (40%), Gaps = 29/183 (15%)
Query: 221 VYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
+ V NL+ E T L +FG +G + ++ + K V D + A ++ L
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 92
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSL-------------KETADKFEGL---- 322
NG K K + K ++ +G+ +Q L K + F+ +
Sbjct: 93 NGHKLHGKPIRI-TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 323 -NLYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
L++ N+ S+S++ LK LFS G + K + R + + EEA +AL
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 207
Query: 381 EMN 383
+++
Sbjct: 208 DLH 210
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
L V NL+ + ++ L LF +G + K++ + + + V + +A A++ +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 92
Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
NG + KP+ + L++ + + R
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPR 116
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
+FI NL K++ + L FS +G+I+ + +GF+QFDN +S + AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
Score = 29.3 bits (64), Expect = 7.6, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
N+ +KN+S+ +DL +IF +G I + FGF+ FD+P ++E
Sbjct: 29 NLPLKNVSK----EDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK-VATDSLGQSRGYGFVQF 175
+ DP + +F+ ++ L F +G I V + G+ RGY F+++
Sbjct: 92 HNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Query: 176 DNEESAKSAIDKLNGMLLNDKQVFV 200
++E SA +G ++ ++V V
Sbjct: 152 EHERDMHSAYKHADGKKIDGRRVLV 176
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDD 268
+ A F ++V ++ TTE L++ F +G I V GK + + F+ ++
Sbjct: 94 DPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153
Query: 269 PDDAARSVEALNGKKFDDK 287
D + + +GKK D +
Sbjct: 154 ERDMHSAYKHADGKKIDGR 172
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
+FI NL K++ + L FS +G+I+ + +GF+QFDN +S + AI+
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 63
Score = 28.9 bits (63), Expect = 8.8, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
N+ +KN+S+ +DL +IF +G I + FGF+ FD+P ++E
Sbjct: 17 NLPLKNVSK----EDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 63
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
+FI NL K++ + L FS +G+I+ + +GF+QFDN +S + AI+
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 55
Score = 28.9 bits (63), Expect = 9.0, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
N+ +KN+S+ +DL +IF +G I + FGF+ FD+P ++E
Sbjct: 9 NLPLKNVSK----EDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 55
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
+ +++ L + L D F+ +G+V VR+ D ++RRS G YV + A+
Sbjct: 25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
Query: 99 DELNFTPLNGKPIRIMYS 116
L L G PI + S
Sbjct: 85 G-LTGQRLLGVPIIVQAS 101
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 6/103 (5%)
Query: 107 NGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFG--NILSCKVATDSL 164
N K I+Y+Y R++ +++ + ++ L + G +++ K A +
Sbjct: 38 NNKTPAILYTYSGLRNRRAA---VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 165 -GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRK 206
GQS+GY V +E S ++ L G +LN ++V V P R+
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
>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 = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPF 203
L FS FGNI+ S+ R FV ++ ESA A+ +LNG + Q+ V
Sbjct: 54 LRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN-I 107
Query: 204 LRKQ 207
RKQ
Sbjct: 108 ARKQ 111
>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 = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
+ L+VG+L + + ++ LF + G+ V + +D G+G++ A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 69
Query: 100 ELNFTPLNGKPIRIMYS 116
EL+ PL GK +R+ ++
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
Score = 32.3 bits (72), Expect = 0.82, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
L+V NL I+++++++LF ++G + +D +G GF+ T A A E++
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 384 GKMVVSKPLYVALA 397
+ K L V A
Sbjct: 73 NMPLRGKQLRVRFA 86
Score = 29.3 bits (64), Expect = 6.7, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
+F+ NL I + + F +G K + + +G+GF++ + A+ A +L+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYG-----KAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 190 GMLLNDKQVFV 200
M L KQ+ V
Sbjct: 73 NMPLRGKQLRV 83
Score = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFD 267
T+ + ++V NL TE++++K+F ++G + +D K FGF+ +
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLE 59
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LYV NL +++ + +LFS+ G SCK++ + + FV F +A+ AL MN
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN 76
Query: 384 GKMVVSKPLYVALAQRKEERRA 405
G+ ++ K + V A +++
Sbjct: 77 GRKILGKEVKVNWATTPSSQKS 98
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
+LYVG+L V + + LF+Q+G S ++ + ++ Y +V + +A AL
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 101 LNFTPLNGKPIRIMYSYRDPTIRKSG 126
+N + GK +++ ++ P+ +KSG
Sbjct: 75 MNGRKILGKEVKVNWA-TTPSSQKSG 99
Score = 28.9 bits (63), Expect = 9.8, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
D + +YV NLS TE + ++F + G S ++ + + FV F + DAA
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAA 69
Query: 274 RSVEALNGKKFDDKE 288
++ A+NG+K KE
Sbjct: 70 AALAAMNGRKILGKE 84
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPF 203
L FS FGNI+ S+ R FV ++ ESA A+ +LNG + Q+ V
Sbjct: 30 LRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN-I 83
Query: 204 LRKQ 207
RKQ
Sbjct: 84 ARKQ 87
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 52/112 (46%), Gaps = 14/112 (12%)
Query: 300 REMELKGKFEQSLKETADKFEG-------LNLYVKNLDDSISDDKLKELFSEFGTITS-- 350
RE+E KG+ + ET F +YVKNL + + LK +F + +S
Sbjct: 18 RELE-KGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSET 76
Query: 351 CKVMRD----PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
++M D G +G F+ + A+KAL E NG ++ KP+ V A+
Sbjct: 77 QRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 221 VYVKNLSETTTEDDLKKIFGEF 242
+YVKNL++ E DLK IFG +
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRY 69
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 75/183 (40%), Gaps = 29/183 (15%)
Query: 221 VYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
+ V NL+ E T L +FG +G + ++ + K V D + A ++ L
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 61
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSL-------------KETADKFEGL---- 322
NG K K + K ++ +G+ +Q L K + F+ +
Sbjct: 62 NGHKLHGKPIRI-TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 323 -NLYVKNLDDSISDDKLKELFSEF-GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
L++ N+ S+S++ LK LFS G + K + R + + EEA +AL
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 176
Query: 381 EMN 383
+++
Sbjct: 177 DLH 179
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
L V NL+ + ++ L LF +G + K++ + + + V + +A A++ +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 61
Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
NG + KP+ + L++ + + R
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPR 85
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-GKSKCFGFVNFDDP 269
N ++V+ L E T + + F + GII + + D + GK K V+FDDP
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 270 DDAARSVEALNGKKF 284
A +++ +GK+F
Sbjct: 74 PSAKAAIDWFDGKEF 88
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCK--------VATD-SLGQSRGYGFVQFDNEES 180
IF++ L +++ +++ D F G I + K + TD G+ +G V FD+ S
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 181 AKSAIDKLNG 190
AK+AID +G
Sbjct: 76 AKAAIDWFDG 85
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-GKSKCFGFV 264
D + N ++V+ L E T + + F + GII + + D + GK K V
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 265 NFDDPDDAARSVEALNGKKF 284
+FDDP A +++ +GK+F
Sbjct: 63 SFDDPPSAKAAIDWFDGKEF 82
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP---------NGISRGSGFVAFSTAEE 374
++V+ L ++++ + + + F + G I + K P G +G V+F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 375 ASKALTEMNGKMVVSKPLYVALAQRK 400
A A+ +GK P+ V+ A R+
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRR 95
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCK--------VATD-SLGQSRGYGFVQFDNEES 180
IF++ L +++ +++ D F G I + K + TD G+ +G V FD+ S
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 181 AKSAIDKLNG 190
AK+AID +G
Sbjct: 70 AKAAIDWFDG 79
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNYNAAH 92
+++V L +V + D F Q+G + + + + D T + G V+++
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 93 EATRALDELNFTPLNGKPIRIMYSYR 118
A A+D + +G PI++ ++ R
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFATR 94
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.51, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
LYV L D+I++ L+ F +FG I + V++ + F+ F+T + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSF 69
Query: 384 GKMVVS 389
K++V+
Sbjct: 70 NKLIVN 75
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
S DKT +YV L +T TE DL+ F +FG I + V++ + +C F+ F
Sbjct: 6 SGEDKT-ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQC-AFIQFATRQ 59
Query: 271 DAARSVEA------LNGKKFDDK 287
A + E +NG++ + K
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVK 82
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAK 182
++ A +I++ N+D + L F G++ + D G +G+ +++F ++ES +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 183 SAIDKLNGMLLNDKQVFVGP 202
+++ L+ L +Q+ V P
Sbjct: 63 TSL-ALDESLFRGRQIKVIP 81
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 29 GGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
G DAR S+YVG++D +L F+ G V V + D + G+ Y+ +
Sbjct: 1 GXEADAR-----SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 55
Query: 89 NAAHEATRALDELNFTPLNGKPIRIM 114
+ E+ R L+ + G+ I+++
Sbjct: 56 -SDKESVRTSLALDESLFRGRQIKVI 80
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAK 182
++ A +I++ N+D + L F G++ + D G +G+ +++F ++ES +
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 183 SAIDKLNGMLLNDKQVFVGP 202
+++ L+ L +Q+ V P
Sbjct: 62 TSL-ALDESLFRGRQIKVIP 80
Score = 29.3 bits (64), Expect = 6.3, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
DAR S+YVG++D +L F+ G V V + D + G+ Y+ + +
Sbjct: 3 ADAR-----SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SD 56
Query: 92 HEATRALDELNFTPLNGKPIRIM 114
E+ R L+ + G+ I+++
Sbjct: 57 KESVRTSLALDESLFRGRQIKVI 79
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 32.7 bits (73), Expect = 0.60, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 235 LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWY 290
+ KIF +FG IT+ + DGK+K + F+ + P A +V+ +G K D + +
Sbjct: 24 IHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMR-DPNGISRGSGFVAFSTAEEASKALTEM 382
+ V+N+ ++S D++ + F + I ++ + G+ G VAF + +EA+ A+ ++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 383 NGKMVVSKPLYVALAQ 398
N + + S+ + + L
Sbjct: 78 NDRPIGSRKVKLVLGS 93
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK 187
IF+ L + + + F FG + S ++ D+ + RG+ F+ F EE K ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK 187
IF+ L + + + F FG + S ++ D+ + RG+ F+ F EE K ++K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 235 LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWY 290
+ KIF +FG IT+ + DGK+K + F+ + P A +V+ +G K D + +
Sbjct: 38 IHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
NL++ NL+ + S +LK SE V+ G +R G+V F +AE+ KAL E
Sbjct: 18 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-E 76
Query: 382 MNGKMV 387
+ G V
Sbjct: 77 LTGLKV 82
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
N+++ NL+ + +LK E AV+ G ++ FG+V+F+ +D +++E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78
Query: 280 NGKKF 284
K F
Sbjct: 79 GLKVF 83
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
SG+ I I+ L + N+ +HD S + + C V + +G FV N E A++A
Sbjct: 3 SGSSGILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAA 56
Query: 185 IDKLNGMLLNDKQVFV 200
I+ + L ++++ V
Sbjct: 57 INTFHQSRLRERELSV 72
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMR-DPNGISRGSGFVAFSTAEEASKALTEM 382
+ V+N+ ++S D++ + F + I ++ + G+ G VAF + +EA+ A+ ++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 383 NGKMVVSK 390
N + + S+
Sbjct: 78 NDRPIGSR 85
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
++Y+K + D +KE + G + + ++ R + +GS FV F + E A K E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK-FVET 71
Query: 383 NGKMVVSKPLYVA-----LAQRKEERR 404
G+ L + A++ EER+
Sbjct: 72 PGQKYKETDLLILFKDDYFAKKNEERK 98
>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 = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH--EATRAL 98
S+YVG++D L F+ G + + + D + GY Y+ + + +A A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 99 DELNFTPLNGKPIRIM 114
DE F G+ I+++
Sbjct: 98 DETVF---RGRTIKVL 110
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
++++ N+D + L FS+ G+I + D G +GY +++F S +A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 156 SCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERE 210
+ V D+ GQ G VQF NE+ A+ + ++L+ LN ++ FV + RE
Sbjct: 45 AVHVLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFVHVVTLEDMRE 98
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 132 IKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG 190
I+N+ + + L +G + SC +V TDS V + +++ A+ A+DKLNG
Sbjct: 20 IRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQALDKLNG 76
Query: 191 MLLND 195
L +
Sbjct: 77 FQLEN 81
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 142 KALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
KAL FS G +++ + D + G+++G+ FV+ + AK I +G L+ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86
Query: 201 GPFLRKQERESTAD 214
++ ER ++ D
Sbjct: 87 LYTMKDVERYNSDD 100
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 253 DADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
+A GK+K F FV +DA + +++ +GK+ D K K ER
Sbjct: 48 EATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVER 95
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 29.6 bits (65), Expect = 5.4, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 299 EREMELKGKFEQSLKETADKFEG----LNLYVKNLDDSISDDKLKELFSEFGTITSCKVM 354
E + +++ + L E D+++ ++Y+K + D +KE + G + + +
Sbjct: 84 EDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXR 143
Query: 355 RDPNGISRGSGFVAFSTAEEASK 377
R + +GS FV F + E A K
Sbjct: 144 RTLHKAFKGSIFVVFDSIESAKK 166
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 29.6 bits (65), Expect = 5.4, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 299 EREMELKGKFEQSLKETADKFEG----LNLYVKNLDDSISDDKLKELFSEFGTITSCKVM 354
E + +++ + L E D+++ ++Y+K + D +KE + G + + +
Sbjct: 85 EDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXR 144
Query: 355 RDPNGISRGSGFVAFSTAEEASK 377
R + +GS FV F + E A K
Sbjct: 145 RTLHKAFKGSIFVVFDSIESAKK 167
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 29.6 bits (65), Expect = 5.5, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNIL---SCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
+F+ L ID + +F FG ++ K + S +GY F+ F E S ++ ID
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 29.6 bits (65), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK 377
++Y+K + D +KE + G + + ++ R + +GS FV F + E A K
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 165
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
0.316 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,929,570
Number of Sequences: 62578
Number of extensions: 690993
Number of successful extensions: 3225
Number of sequences better than 100.0: 249
Number of HSP's better than 100.0 without gapping: 167
Number of HSP's successfully gapped in prelim test: 82
Number of HSP's that attempted gapping in prelim test: 2235
Number of HSP's gapped (non-prelim): 740
length of query: 650
length of database: 14,973,337
effective HSP length: 105
effective length of query: 545
effective length of database: 8,402,647
effective search space: 4579442615
effective search space used: 4579442615
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)