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= psy8956
(333 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 110 bits (274), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 63/168 (37%), Positives = 93/168 (55%), Gaps = 11/168 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L+V +L P V L +F G + +RV R+ S G+A + F PA+A++A M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
N +I KPV I + + P R VG +F+KNL +++D + L F FG
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVG---------NIFIKNLDKSIDNKALYDTFSAFG 128
Query: 156 NIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFV 203
NI+ K+V DENG SKG+GF+ F + +AAE+AI +MNG ++ FV
Sbjct: 129 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Score = 61.2 bits (147), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 46/181 (25%), Positives = 78/181 (43%), Gaps = 19/181 (10%)
Query: 120 PVG---PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGF 175
P+G P Y ++V +L V E L F G I+ +++ RD +S G+ +
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 176 IQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVAN 235
+ F AE+A+ MN +I+ + ++ L+ + IF+ N
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPS-----------LRKSGVGNIFIKN 110
Query: 236 LPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNGHVFKS 291
L +I+N + F+ FG I S +V D K GF+ F + A A+ MNG +
Sbjct: 111 LDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND 170
Query: 292 K 292
+
Sbjct: 171 R 171
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAVSTM 284
++V +L ++ + E F+ G I S + D + +G+ + F P A A+ TM
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 285 NGHVFKSKPLKVTLSGTKPGV 305
N V K KP+++ S P +
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSL 98
>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 = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 63/168 (37%), Positives = 93/168 (55%), Gaps = 11/168 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L+V +L P V L +F G + +RV R+ S G+A + F PA+A++A M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
N +I KPV I + + P R VG +F+KNL +++D + L F FG
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVG---------NIFIKNLDKSIDNKALYDTFSAFG 123
Query: 156 NIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFV 203
NI+ K+V DENG SKG+GF+ F + +AAE+AI +MNG ++ FV
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 44/177 (24%), Positives = 76/177 (42%), Gaps = 16/177 (9%)
Query: 121 VGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFF 179
+ P Y ++V +L V E L F G I+ +++ RD +S G+ ++ F
Sbjct: 1 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
Query: 180 SYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSN 239
AE+A+ MN +I+ + ++ L+ + IF+ NL +
Sbjct: 61 QPADAERALDTMNFDVIKGKPVRIMWSQRDPS-----------LRKSGVGNIFIKNLDKS 109
Query: 240 INNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNGHVFKSK 292
I+N + F+ FG I S +V D K GF+ F + A A+ MNG + +
Sbjct: 110 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAVSTM 284
++V +L ++ + E F+ G I S + D + +G+ + F P A A+ TM
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 285 NGHVFKSKPLKVTLSGTKPGV 305
N V K KP+++ S P +
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSL 93
>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 = 78.2 bits (191), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 79/165 (47%), Gaps = 20/165 (12%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
K + V L + + +EE +S F G I K+VRD+ G+S G+GF+ + K AEKAI
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 189 IEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEEL 248
+NG +Q + VS A R ++V+ LP + E E+L
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASI-------------RDANLYVSGLPKTMTQKELEQL 108
Query: 249 FARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGH 287
F+++G I +S ++ D + +GFI F A A+ +NG
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 81/160 (50%), Gaps = 13/160 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L VN L ++ + + F G + ++ R+K +S G+ + + P +A+KA +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
NG + +K + +++ P + ++V L +T+ ++EL+ F ++G
Sbjct: 65 NGLRLQTKTIKVSYAR-----------PSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 156 NIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGR 194
II +I+ D+ G S+G GFI+F AE+AI +NG+
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAV 281
K + V LP N+ EF LF G I S LV DK GF+ +I PK A A+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 282 STMNGHVFKSKPLKVTLS 299
+T+NG ++K +KV+ +
Sbjct: 62 NTLNGLRLQTKTIKVSYA 79
>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 = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 82/165 (49%), Gaps = 20/165 (12%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
+ + V L + + ++EL+S F G + K++RD+ G S G+GF+ + + K AE+AI
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 189 IEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEEL 248
+NG +Q + VS A + + ++++ LP + + E++
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSS-------------EVIKDANLYISGLPRTMTQKDVEDM 108
Query: 249 FARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGH 287
F+RFG I +S ++ D+ G FI F A A+++ NGH
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAV 281
+ + V LP N+ E LF+ G + S+ L+ DK GF+ ++ K A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 282 STMNGHVFKSKPLKVTLS 299
+T+NG +SK +KV+ +
Sbjct: 62 NTLNGLRLQSKTIKVSYA 79
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEM 95
L+++ L ++ + + + F +FG + + RV ++ SRG A I F+ +EA++A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 96 NGHLI--GSKPVIITF 109
NGH S+P+ + F
Sbjct: 151 NGHKPPGSSEPITVKF 166
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 75.1 bits (183), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 82/165 (49%), Gaps = 20/165 (12%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
+ + V L + + ++EL+S F G + K++RD+ G S G+GF+ + + K AE+AI
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 189 IEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEEL 248
+NG +Q + VS A + + ++++ LP + + E++
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSS-------------EVIKDANLYISGLPRTMTQKDVEDM 108
Query: 249 FARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGH 287
F+RFG I +S ++ D+ G FI F A A+++ NGH
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAV 281
+ + V LP N+ E LF+ G + S+ L+ DK GF+ ++ K A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 282 STMNGHVFKSKPLKVTLS 299
+T+NG +SK +KV+ +
Sbjct: 62 NTLNGLRLQSKTIKVSYA 79
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEM 95
L+++ L ++ + + + F +FG + + RV ++ SRG A I F+ +EA++A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 96 NGHLI--GSKPVIITF 109
NGH S+P+ + F
Sbjct: 151 NGHKPPGSSEPITVXF 166
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 75.1 bits (183), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 51/172 (29%), Positives = 83/172 (48%), Gaps = 24/172 (13%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
K + V L + + ++E KS F G+I K+VRD+ G+S G+GF+ + A+KAI
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 189 IEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEEL 248
+NG +Q + VS A R ++V+ LP ++ E E+L
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASI-------------RDANLYVSGLPKTMSQKEMEQL 110
Query: 249 FARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPL 294
F+++G I +S ++ D + +GFI F A A+ +NG KPL
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPL 158
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAV 281
K + V LP N+ EF+ LF G I S LV DK GF+ + P A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 282 STMNGHVFKSKPLKVTLS 299
+T+NG ++K +KV+ +
Sbjct: 64 NTLNGLKLQTKTIKVSYA 81
>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 = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 33/71 (46%), Positives = 49/71 (69%), Gaps = 1/71 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+F+KNL +++D + L F FGNI+ K+V DENG SKG+GF+ F + +AAE+AI +MN
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 66
Query: 193 GRMIQHNSTFV 203
G ++ FV
Sbjct: 67 GMLLNDRKVFV 77
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 56/102 (54%), Gaps = 4/102 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ + NL+ S+DN+AL + F FG + +V ++N S+G+ + F T A++A +MN
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 66
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNL 138
G L+ + V + + + +R +G K++ V++KN
Sbjct: 67 GMLLNDRKVFVGRFKSRK-EREAELGARAKEFT--NVYIKNF 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHA 280
P IF+ NL +I+N + F+ FG I S +V D K GF+ F + A A
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 61
Query: 281 VSTMNGHVFKSKPLKV 296
+ MNG + + + V
Sbjct: 62 IEKMNGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 33/71 (46%), Positives = 49/71 (69%), Gaps = 1/71 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+F+KNL +++D + L F FGNI+ K+V DENG SKG+GF+ F + +AAE+AI +MN
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 72
Query: 193 GRMIQHNSTFV 203
G ++ FV
Sbjct: 73 GMLLNDRKVFV 83
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ + NL+ S+DN+AL + F FG + +V ++N S+G+ + F T A++A +MN
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 72
Query: 97 GHLIGSKPVII 107
G L+ + V +
Sbjct: 73 GMLLNDRKVFV 83
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNG 286
IF+ NL +I+N + F+ FG I S +V D K GF+ F + A A+ MNG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 287 HVFKSKPLKV 296
+ + + V
Sbjct: 74 MLLNDRKVFV 83
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 67.0 bits (162), Expect = 1e-11, Method: Composition-based stats.
Identities = 35/86 (40%), Positives = 54/86 (62%), Gaps = 1/86 (1%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
G +Y+ ++VKNL + +D+E L+ F FG I K++ E G+SKGFGF+ F S
Sbjct: 7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSP 65
Query: 182 KAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ A KA+ EMNGR++ +V+LA+
Sbjct: 66 EEATKAVTEMNGRIVATKPLYVALAQ 91
Score = 60.8 bits (146), Expect = 9e-10, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 49/84 (58%), Gaps = 1/84 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L+V NL+ +D++ L F FGT+ +V + S+GF + F++P EA KA EMN
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 97 GHLIGSKPVIITFVELKPGQRSKP 120
G ++ +KP+ + + K ++S P
Sbjct: 77 GRIVATKPLYVALAQRKEERQSGP 100
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNG 286
++V NL I++ + F+ FGTITS+ ++ + K GF+ F P+ AT AV+ MNG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 287 HVFKSKPLKVTLSGTK 302
+ +KPL V L+ K
Sbjct: 78 RIVATKPLYVALAQRK 93
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/158 (25%), Positives = 85/158 (53%), Gaps = 13/158 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L VN L + ++ L F+ G + R+ R+ K S G+A + F + ++++A +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
NG + +K + +++ +PG S K ++V NL T+ +++L + F K+G
Sbjct: 66 NGITVRNKRLKVSYA--RPGGES---------IKDTNLYVTNLPRTITDDQLDTIFGKYG 114
Query: 156 NIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMN 192
+I++ I+RD+ G+ +G F+++ + A++AI +N
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 84/176 (47%), Gaps = 22/176 (12%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V L + + + EL + F G I +I+RD + G S G+ F+ F S +++AI +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 192 NGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEELFAR 251
NG +++ VS A + + ++V NLP I + + + +F +
Sbjct: 66 NGITVRNKRLKVSYARPGG-------------ESIKDTNLYVTNLPRTITDDQLDTIFGK 112
Query: 252 FGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGHVFK--SKPLKVTLS 299
+G+I +++ DK G F+ + + A A+S +N + + S+PL V L+
Sbjct: 113 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>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 = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 41/158 (25%), Positives = 84/158 (53%), Gaps = 13/158 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L VN L ++ L F+ G + R+ R+ K S G+A + F + ++++A +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
NG + +K + +++ +PG S K ++V NL T+ +++L + F K+G
Sbjct: 77 NGITVRNKRLKVSYA--RPGGES---------IKDTNLYVTNLPRTITDDQLDTIFGKYG 125
Query: 156 NIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMN 192
+I++ I+RD+ G+ +G F+++ + A++AI +N
Sbjct: 126 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 82/176 (46%), Gaps = 22/176 (12%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V L + + EL + F G I +I RD + G S G+ F+ F S +++AI +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 192 NGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEELFAR 251
NG +++ VS A + + ++V NLP I + + + +F +
Sbjct: 77 NGITVRNKRLKVSYARPGG-------------ESIKDTNLYVTNLPRTITDDQLDTIFGK 123
Query: 252 FGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGHVFK--SKPLKVTLS 299
+G+I +++ DK G F+ + + A A+S +N + + S+PL V L+
Sbjct: 124 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
>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 = 61.2 bits (147), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 90/188 (47%), Gaps = 11/188 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
+V+V ++ + E+ ++ F FG I + + D K KGF F+++ +AA+ A+ +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 191 MNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARK-NKIFVANLPSNINNSEFEELF 249
MN M+ + V L + AR N+I+VA++ ++++ + + +F
Sbjct: 75 MNSVMLGGRNIKVGRPS---NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 131
Query: 250 ARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
FG I S +L D K GFIE+ + + AVS+MN + L+V + T P
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 191
Query: 304 GVSITNPT 311
+T T
Sbjct: 192 MPLLTPAT 199
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 86/162 (53%), Gaps = 10/162 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
++V ++ + + F FG ++ + ++ + + +GFA + + P A+ A +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 96 NGHLIGSKPVIITFVELKPGQ--RSKPVGPE--EKQYKKDKVFVKNLVETVDEEELKSHF 151
N ++G + + + +P +++P+ + E+ ++++V ++ + + ++++KS F
Sbjct: 76 NSVMLGGRNIKVG----RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 131
Query: 152 IKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMN 192
FG I + RD GK KG+GFI++ ++++ A+ MN
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 60.8 bits (146), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 77 PHKVDGRVVEPKRAVSREDSQRPG----------AHLTVKKIFVGGIKEDTEEHHLRDYF 126
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 127 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 176
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 77/181 (42%), Gaps = 20/181 (11%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFI 176
SK P+E + + K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+
Sbjct: 3 SKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 61
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANL 236
+Y E+ MN R + + V ++ KIFV +
Sbjct: 62 ---TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGI 113
Query: 237 PSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNG 286
+ + F ++G I +++D+ G F+ F + K T+NG
Sbjct: 114 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 173
Query: 287 H 287
H
Sbjct: 174 H 174
>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 = 60.8 bits (146), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 76 PHKVDGRVVEPKRAVSREDSQRPGA----------HLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 175
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 77/181 (42%), Gaps = 20/181 (11%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFI 176
SK P+E + + K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+
Sbjct: 2 SKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANL 236
+Y E+ MN R + + V ++ KIFV +
Sbjct: 61 ---TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGI 112
Query: 237 PSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNG 286
+ + F ++G I +++D+ G F+ F + K T+NG
Sbjct: 113 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 172
Query: 287 H 287
H
Sbjct: 173 H 173
>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 = 60.8 bits (146), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 11/188 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
+V+V ++ + E+ ++ F FG I + + D K KGF F+++ +AA+ A+ +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 191 MNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARK-NKIFVANLPSNINNSEFEELF 249
MN M+ + V L + AR N+I+VA++ ++++ + + +F
Sbjct: 90 MNSVMLGGRNIKVGRPS---NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 146
Query: 250 ARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
FG I S++L D K GFIE+ + + AVS+MN + L+V + T P
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 206
Query: 304 GVSITNPT 311
+T T
Sbjct: 207 MPLLTPAT 214
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 86/162 (53%), Gaps = 10/162 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
++V ++ + + F FG ++ + ++ + + +GFA + + P A+ A +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 96 NGHLIGSKPVIITFVELKPGQ--RSKPVGPE--EKQYKKDKVFVKNLVETVDEEELKSHF 151
N ++G + + + +P +++P+ + E+ ++++V ++ + + ++++KS F
Sbjct: 91 NSVMLGGRNIKVG----RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 146
Query: 152 IKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMN 192
FG I + RD GK KG+GFI++ ++++ A+ MN
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 75 PHKVDGRVVEPKRAVSREDSQRPGA----------HLTVKKIFVGGIKEDTEEHHLRDYF 124
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 125 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 174
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 77/181 (42%), Gaps = 20/181 (11%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFI 176
SK P+E + + K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+
Sbjct: 1 SKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 59
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANL 236
+Y E+ MN R + + V ++ KIFV +
Sbjct: 60 ---TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGI 111
Query: 237 PSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNG 286
+ + F ++G I +++D+ G F+ F + K T+NG
Sbjct: 112 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 171
Query: 287 H 287
H
Sbjct: 172 H 172
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 76 PHKVDGRVVEPKRAVSREDSQRPGA----------HLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 175
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 77/181 (42%), Gaps = 20/181 (11%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFI 176
SK P+E + + K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+
Sbjct: 2 SKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANL 236
+Y E+ MN R + + V ++ KIFV +
Sbjct: 61 ---TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGI 112
Query: 237 PSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNG 286
+ + F ++G I +++D+ G F+ F + K T+NG
Sbjct: 113 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 172
Query: 287 H 287
H
Sbjct: 173 H 173
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 74 PHKVDGRVVEPKRAVSREDSQRPGA----------HLTVKKIFVGGIKEDTEEHHLRDYF 123
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 124 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 173
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 40/167 (23%), Positives = 70/167 (41%), Gaps = 19/167 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAIIE 190
K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+ +Y E+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV---TYATVEEVDAA 69
Query: 191 MNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEELFA 250
MN R + + V ++ KIFV + + + F
Sbjct: 70 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGIKEDTEEHHLRDYFE 124
Query: 251 RFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNGH 287
++G I +++D+ G F+ F + K T+NGH
Sbjct: 125 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGH 171
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAE---AKKAR 92
L + L +++L + F+++GTL D V R+ N + SRGF + + T E A AR
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 93 V-EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHF 151
+++G ++ K + +PG K+FV + E +E L+ +F
Sbjct: 69 PHKVDGRVVEPKRAVSREDSQRPGA----------HLTVKKIFVGGIKEDTEEHHLRDYF 118
Query: 152 IKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++G I ++I+ D +GK +GF F+ F + + +K +I+ + HN
Sbjct: 119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 168
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 40/167 (23%), Positives = 70/167 (41%), Gaps = 19/167 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAIIE 190
K+F+ L +E L+SHF ++G + + ++RD N K S+GFGF+ +Y E+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV---TYATVEEVDAA 64
Query: 191 MNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEELFA 250
MN R + + V ++ KIFV + + + F
Sbjct: 65 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-----KIFVGGIKEDTEEHHLRDYFE 119
Query: 251 RFGTITSSSLVSDKHIG------FIEF----IMPKHATHAVSTMNGH 287
++G I +++D+ G F+ F + K T+NGH
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGH 166
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/95 (18%), Positives = 39/95 (41%), Gaps = 10/95 (10%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHA 277
+P + K+F+ L + F ++GT+T ++ D + GF+ + +
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 278 THAVST----MNGHVFKSKPLKVTLSGTKPGVSIT 308
A++ ++G V + K +PG +T
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT 96
>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 = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 42/153 (27%), Positives = 77/153 (50%), Gaps = 23/153 (15%)
Query: 41 NLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPA---EAKKARVEMN 96
N + + DN L F K+GT+ D+++ ++ SRGF + F P+ E K + ++
Sbjct: 12 NWDTTEDN--LREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILD 69
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGN 156
G +I K I P ++Q K K+FV + V +E + F ++G
Sbjct: 70 GKVIDPKRAI----------------PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGT 113
Query: 157 IIEVKIVRDEN-GKSKGFGFIQFFSYKAAEKAI 188
II+ +++ D++ G+S+GFGF+ + S A ++
Sbjct: 114 IIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 68/140 (48%), Gaps = 22/140 (15%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L E+ L+ +F K+G + ++KI++D G+S+GFGF+ F + ++ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 191 ---MNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEE 247
++G++I + + KIFV + ++ EFEE
Sbjct: 65 QHILDGKVIDPKRAIPRDEQ------------------DKTGKIFVGGIGPDVRPKEFEE 106
Query: 248 LFARFGTITSSSLVSDKHIG 267
F+++GTI + L+ DK G
Sbjct: 107 FFSQWGTIIDAQLMLDKDTG 126
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVST 283
K+F+ L + E F ++GT+T ++ D + GF+ F P V T
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 284 MNGHVFKSK 292
H+ K
Sbjct: 65 Q--HILDGK 71
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 39/174 (22%), Positives = 77/174 (44%), Gaps = 17/174 (9%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
++V NL + + E+ LK +F G I +KI+ D+N K+ + F+++ A A+ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 193 GRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNINNSEFEELFARF 252
G+ I++N ++ A +FV +L N+++ F F
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTF-----------NLFVGDLNVNVDDETLRNAFKDF 111
Query: 253 GTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSG 300
+ S ++ D + GF+ F A +A+ +M G +PL++ +
Sbjct: 112 PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 80/162 (49%), Gaps = 16/162 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L+V NL+ ++ L F+ G + ++++ +KN+++ +A + ++ +A A +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKD---KVFVKNLVETVDEEELKSHFIK 153
G I + V I + + +Q D +FV +L VD+E L++ F
Sbjct: 63 GKQIENNIVKINW------------AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 154 FGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGR 194
F + + ++ D + G S+G+GF+ F S A+ A+ M G+
Sbjct: 111 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 152
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L V +L +VD++ L N FK F + V + + SRG+ + F + +A+ A M
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96 NGHLIGSKPVIITFV 110
G + +P+ I +
Sbjct: 150 QGQDLNGRPLRINWA 164
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
VFV +L + E++KS F FG I + ++V+D GKSKG+GF+ F++ AE AI+ M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 192 NGRMI 196
G+ +
Sbjct: 78 GGQWL 82
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEMNG 97
V +L P + + + + F FG + D RV ++ +S+G+ + F +A+ A V M G
Sbjct: 20 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 79
Query: 98 HLIGSKPVIITFVELKPGQRSKP 120
+G + + + KP S P
Sbjct: 80 QWLGGRQIRTNWATRKPPAPSGP 102
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTM 284
+FV +L I + + FA FG I+ + +V D K GF+ F A +A+ M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 285 NGHVFKSKPLKVTLSGTKP 303
G + ++ + KP
Sbjct: 78 GGQWLGGRQIRTNWATRKP 96
>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 = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
VFV +L + E++K+ F FG I + ++V+D GKSKG+GF+ FF+ AE AI +M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 192 NGRMI 196
G+ +
Sbjct: 78 GGQWL 82
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEMNG 97
V +L P + + + F FG + D RV ++ +S+G+ + F +A+ A +M G
Sbjct: 20 VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 79
Query: 98 HLIGSKPVIITFVELKP 114
+G + + + KP
Sbjct: 80 QWLGGRQIRTNWATRKP 96
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTM 284
+FV +L I + + FA FG I+ + +V D K GF+ F A +A+ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 285 NGHVFKSKPLKVTLSGTKP 303
G + ++ + KP
Sbjct: 78 GGQWLGGRQIRTNWATRKP 96
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/173 (27%), Positives = 74/173 (42%), Gaps = 30/173 (17%)
Query: 123 PEEKQY-KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
P EK Y ++ ++FV NL + EE+ K F ++G EV I RD +GFGFI+ S
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESR 68
Query: 182 KAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNIN 241
AE A E++G +++ + A + V NL ++
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFA-------------------THGAALTVKNLSPVVS 109
Query: 242 NSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTMNGHVF 289
N E+ F++FG + + +V D GF+EF A A+ F
Sbjct: 110 NELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAF 162
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 70/152 (46%), Gaps = 22/152 (14%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V NL + + F+++G +V + R+ RGF I + A+ A+ E++
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 79
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGN 156
G ++ S+P+ I F + VKNL V E L+ F +FG
Sbjct: 80 GTILKSRPLRIRFA-----------------THGAALTVKNLSPVVSNELLEQAFSQFGP 122
Query: 157 IIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+ + +V D+ G++ G GF++F + A KA+
Sbjct: 123 VEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 46/83 (55%)
Query: 227 RKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNG 286
++ ++FV NLP++I +F+ LF R+G + + D+ GFI A A + ++G
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDG 80
Query: 287 HVFKSKPLKVTLSGTKPGVSITN 309
+ KS+PL++ + +++ N
Sbjct: 81 TILKSRPLRIRFATHGAALTVKN 103
>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 = 4e-08, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 126 KQYKKD--KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKA 183
KQ ++D +++ NL ++DE+EL++ FG +I +I+RD +G S+G GF + S +
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 78
Query: 184 AEKAIIEMNGRMIQ 197
E I NG+ I+
Sbjct: 79 CEAVIGHFNGKFIK 92
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L+++NL S+D Q L N K FG + R+ R+ + SRG + + + N
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 97 GHLIGSKPVI 106
G I + P +
Sbjct: 88 GKFIKTPPGV 97
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHATHAVSTMN 285
++++NLP +++ E E + FG + S+ ++ D + +GF + + N
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 286 GHVFKSKP 293
G K+ P
Sbjct: 88 GKFIKTPP 95
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 72/143 (50%), Gaps = 14/143 (9%)
Query: 55 FKKFGTLRDVRVARNKND---ESRGFAIIVFNTPAEAKKARVEMNGHLIGSK--PVIITF 109
F+++G + ++ V R+++ +S+G + F T +KA +E L K P +
Sbjct: 36 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT----RKAALEAQNALHNMKVLPGMHHP 91
Query: 110 VELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK 169
+++KP K E++ K+F+ + + E +++ F FG I E +I+R +G
Sbjct: 92 IQMKPADSEKNNAVEDR-----KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGL 146
Query: 170 SKGFGFIQFFSYKAAEKAIIEMN 192
S+G F+ F + A+ AI M+
Sbjct: 147 SRGCAFVTFTTRAMAQTAIKAMH 169
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENG---KSKGFGFIQFF 179
P++ K+FV + T E++L+ F ++G + E+ ++RD + +SKG F+ F+
Sbjct: 8 PDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFY 67
Query: 180 SYKAAEKA 187
+ KAA +A
Sbjct: 68 TRKAALEA 75
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 72/143 (50%), Gaps = 14/143 (9%)
Query: 55 FKKFGTLRDVRVARNKND---ESRGFAIIVFNTPAEAKKARVEMNGHLIGSK--PVIITF 109
F+++G + ++ V R+++ +S+G + F T +KA +E L K P +
Sbjct: 24 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT----RKAALEAQNALHNMKVLPGMHHP 79
Query: 110 VELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK 169
+++KP K E++ K+F+ + + E +++ F FG I E +I+R +G
Sbjct: 80 IQMKPADSEKNNAVEDR-----KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGL 134
Query: 170 SKGFGFIQFFSYKAAEKAIIEMN 192
S+G F+ F + A+ AI M+
Sbjct: 135 SRGCAFVTFTTRAMAQTAIKAMH 157
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENG---KSKGFGFIQFFSYKAAEKA 187
K+FV + T E++L+ F ++G + E+ ++RD + +SKG F+ F++ KAA +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>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 = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 91/194 (46%), Gaps = 23/194 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI-- 188
+V+V ++ + E+ ++ F FG I + D K KGF F+++ +AA+ A+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 189 ---IEMNGRMIQ-HNSTFVSLAEIXXXXXXXXXXXXXLLQPARK-NKIFVANLPSNINNS 243
+ + GR I+ + + A+ L + AR N+I+VA++ ++++
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQ---------PIIDQLAEEARAFNRIYVASVHQDLSDD 124
Query: 244 EFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVT 297
+ + +F FG I S +L D K GFIE+ + + AVS+ N + L+V
Sbjct: 125 DIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVG 184
Query: 298 LSGTKPGVSITNPT 311
+ T P +T T
Sbjct: 185 KAVTPPXPLLTPAT 198
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 33/162 (20%), Positives = 82/162 (50%), Gaps = 10/162 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
++V ++ + + F FG ++ + + + + +GFA + + P A+ A +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 96 NGHLIGSKPVIITFVELKPGQ--RSKPVGPE--EKQYKKDKVFVKNLVETVDEEELKSHF 151
N +G + + + +P +++P+ + E+ ++++V ++ + + ++++KS F
Sbjct: 75 NSVXLGGRNIKVG----RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 130
Query: 152 IKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMN 192
FG I + RD GK KG+GFI++ ++++ A+ N
Sbjct: 131 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 65/142 (45%), Gaps = 25/142 (17%)
Query: 123 PEEKQY-KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
P EK + ++ ++FV NL + EEE++ F K+G EV I +D KGFGFI+ +
Sbjct: 14 PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETR 68
Query: 182 KAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNKIFVANLPSNIN 241
AE A +E++ ++ V A + V NLP ++
Sbjct: 69 TLAEIAKVELDNMPLRGKQLRVRFA-------------------CHSASLTVRNLPQYVS 109
Query: 242 NSEFEELFARFGTITSSSLVSD 263
N EE F+ FG + + ++ D
Sbjct: 110 NELLEEAFSVFGQVERAVVIVD 131
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 66/152 (43%), Gaps = 22/152 (14%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V NL P + + + F+K+G +V + ++K GF I T A+ A+VE++
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVELD 79
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGN 156
+ K + + F + V+NL + V E L+ F FG
Sbjct: 80 NMPLRGKQLRVRFA-----------------CHSASLTVRNLPQYVSNELLEEAFSVFGQ 122
Query: 157 IIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+ ++ D+ G+ G G ++F AA KA+
Sbjct: 123 VERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%)
Query: 226 ARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMN 285
+++++FV NLP +I E +LF ++G + DK GFI A A ++
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 286 GHVFKSKPLKVTLSGTKPGVSITN 309
+ K L+V + +++ N
Sbjct: 80 NMPLRGKQLRVRFACHSASLTVRN 103
>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 = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/139 (25%), Positives = 68/139 (48%), Gaps = 14/139 (10%)
Query: 55 FKKFGTLRDVRVARNKND---ESRGFAIIVFNTPAEAKKARVEMNGHLIGSK--PVIITF 109
F+++G + ++ V R+++ +S+G + F T +KA +E L K P
Sbjct: 24 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT----RKAALEAQNALHNXKVLPGXHHP 79
Query: 110 VELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK 169
++ KP K E++ K+F+ + + E +++ F FG I E +I+R +G
Sbjct: 80 IQXKPADSEKNNAVEDR-----KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGL 134
Query: 170 SKGFGFIQFFSYKAAEKAI 188
S+G F+ F + A+ AI
Sbjct: 135 SRGCAFVTFTTRAXAQTAI 153
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 2/76 (2%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEV-KIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+F+ NL +DE+ L F FG I++ KI+RD + G SKG+ FI F S+ A++ AI
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 191 MNGRMIQHNSTFVSLA 206
MNG+ + + VS A
Sbjct: 68 MNGQYLCNRPITVSYA 83
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGT-LRDVRVARNKND-ESRGFAIIVFNTPAEAKKARVE 94
+ + NL+P +D + L + F FG L+ ++ R+ + S+G+A I F + + A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 95 MNGHLIGSKPVIITFVELKPGQRSKP 120
MNG + ++P+ +++ K + S P
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKGSGP 93
Score = 31.6 bits (70), Expect = 0.59, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV-------SDKHIGFIEFIMPKHATHAVST 283
IF+ NL I+ + F+ FG I + + + K FI F + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 284 MNGHVFKSKPLKVTLSGTK 302
MNG ++P+ V+ + K
Sbjct: 68 MNGQYLCNRPITVSYAFKK 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V + TVDE +L+ F ++G I VKIV D E +S+G+GF++F S +A++AI +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 192 NGRMIQHNSTFVSLA 206
NG I + V+LA
Sbjct: 105 NGFNILNKRLKVALA 119
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 9/85 (10%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAVSTM 284
+ V +P+ ++ + +LF R+G I S +V D+ GF++F A A++ +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 285 NGHVFKSKPLKVTLSGT---KPGVS 306
NG +K LKV L+ + +PG++
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIA 129
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L VN + +VD L F+++G + V++ ++ +SRG+ + F + + A++A +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 96 NG 97
NG
Sbjct: 105 NG 106
>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 = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHAT 278
P R N + V LP N+ E LF+ G + S+ L+ DK GF+ ++ K A
Sbjct: 2 PGRTN-LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 279 HAVSTMNGHVFKSKPLKVTLS 299
A++T+NG +SK +KV+ +
Sbjct: 61 RAINTLNGLRLQSKTIKVSYA 81
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
+ + V L + + ++EL+S F G + K++RD+ G S G+GF+ + + K AE+AI
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 189 IEMNGRMIQHNSTFVSLAE 207
+NG +Q + VS A
Sbjct: 64 NTLNGLRLQSKTIKVSYAR 82
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
K+FV L +E+ L+ F K+G I EV +V+D E +S+GFGF+ F + A+ A++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 191 MNGRMI 196
MNG+ +
Sbjct: 74 MNGKSV 79
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEM 95
L V L + Q+L F K+G + +V V +++ + SRGF + F +AK A + M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 96 NGHLIGSKPVIITFVELKPGQRSKP 120
NG + + + + RS P
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSGP 99
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAV 281
+ K+FV L + N E++F+++G I+ +V D+ GF+ F A A+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 282 STMNGHVFKSKPLKVTLSG 300
MNG + ++V +G
Sbjct: 72 MAMNGKSVDGRQIRVDQAG 90
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 38/58 (65%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+ VFV + +DE E++S F ++G++ EVKI+ D G SKG+GF+ F++ +K +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Score = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEF 271
N +FV + ++ +E FAR+G++ +++D K GF+ F
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 37/56 (66%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
VFV + +DE E++S F ++G++ EVKI+ D G SKG+GF+ F++ +K +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 68
Score = 32.0 bits (71), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEF 271
N +FV + ++ +E FAR+G++ +++D K GF+ F
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 9/54 (16%), Positives = 30/54 (55%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKK 90
+ V ++ +D + + F ++G++++V++ ++ S+G+ + F + +K
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 66
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 37/56 (66%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
VFV + +DE E++S F ++G++ EVKI+ D G SKG+GF+ F++ +K +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEF 271
N +FV + ++ +E FAR+G++ +++D K GF+ F
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 9/54 (16%), Positives = 30/54 (55%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKK 90
+ V ++ +D + + F ++G++++V++ ++ S+G+ + F + +K
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 1/84 (1%)
Query: 124 EEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYK 182
E ++ + V L + ++EL+S F G + K++RD+ G S G+GF+ + + K
Sbjct: 13 ENLYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK 72
Query: 183 AAEKAIIEMNGRMIQHNSTFVSLA 206
AE+AI +NG +Q + VS A
Sbjct: 73 DAERAINTLNGLRLQSKTIKVSYA 96
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAVSTM 284
+ V LP N E LF+ G + S+ L+ DK GF+ ++ K A A++T+
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 285 NGHVFKSKPLKVTLS 299
NG +SK +KV+ +
Sbjct: 82 NGLRLQSKTIKVSYA 96
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+F+ L +E+ LK+ F K G I EV +++D KS+GF FI F + A+ A +M
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 192 NGRMIQHNSTFVSLAE 207
NG+ + + V A+
Sbjct: 69 NGKSLHGKAIKVEQAK 84
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L + L + + L F K G + +V + +++ +SRGFA I F PA+AK A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 97 GHLIGSKPVIITFVE---LKPGQRSKP 120
G + K + + + + G R +P
Sbjct: 70 GKSLHGKAIKVEQAKKPSFQSGGRRRP 96
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 5/72 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDK-----HIGFIEFIMPKHATHAVSTM 284
K+F+ L N + +F + G I+ L+ D+ FI F P A +A M
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 285 NGHVFKSKPLKV 296
NG K +KV
Sbjct: 69 NGKSLHGKAIKV 80
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAV 281
K + V LP N+ EF+ LF G I S LV DK GF+ + P A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 282 STMNGHVFKSKPLKVTLS 299
+T+NG ++K +KV+ +
Sbjct: 64 NTLNGLKLQTKTIKVSYA 81
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI 188
K + V L + + ++E KS F G+I K+VRD+ G+S G+GF+ + A+KAI
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 189 IEMNGRMIQHNSTFVSLA 206
+NG +Q + VS A
Sbjct: 64 NTLNGLKLQTKTIKVSYA 81
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFIQFFSYKAAEKAIIE 190
K FV L +++LK +F KFG +++ I D N G+S+GFGFI F + EK + +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 191 ----MNGRMIQ 197
++GR+I
Sbjct: 73 KEHRLDGRVID 83
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKK 90
V L + L + F KFG + D + + N SRGF I+F A +K
Sbjct: 16 VGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSY 181
P + K ++V NL T+ +++L + F K+G+I++ I+RD+ G+ +G F+++
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 65
Query: 182 KAAEKAIIEMN 192
+ A++AI +N
Sbjct: 66 EEAQEAISALN 76
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTM 284
++V NLP I + + + +F ++G+I +++ DK G F+ + + A A+S +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 285 NGHVFK--SKPLKVTLS 299
N + + S+PL V L+
Sbjct: 76 NNVIPEGGSQPLSVRLA 92
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L+V NL ++ + L F K+G++ + R+K RG A + +N EA++A +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 96 NGHLI--GSKPVIITFVE 111
N + GS+P+ + E
Sbjct: 76 NNVIPEGGSQPLSVRLAE 93
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 192 N-----GRMIQHN 199
N GR I+ N
Sbjct: 75 NESELFGRTIRVN 87
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + + ++ RGFA + F +A A M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 96 N 96
N
Sbjct: 75 N 75
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 14/91 (15%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAV 281
K ++V L +++ F FG IT + D KH GF +EF + + A A+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 282 STMN-----GHVFK---SKPLKVTLSGTKPG 304
MN G + +KP+++ SG G
Sbjct: 72 DNMNESELFGRTIRVNLAKPMRIKESGPSSG 102
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+++V +L + E+ L+ F FG I ++++ D E G+SKG+GFI F + A+KA+ +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 191 MNG 193
+NG
Sbjct: 88 LNG 90
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVST 283
+++V +L NI +F FG I S L+ D K GFI F + A A+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 284 MNGHVFKSKPLKV 296
+NG +P+KV
Sbjct: 88 LNGFELAGRPMKV 100
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L+V +L ++ L F+ FG + +++ + + S+G+ I F+ AKKA ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 96 NGHLIGSKPVIITFV 110
NG + +P+ + V
Sbjct: 89 NGFELAGRPMKVGHV 103
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 192 N-----GRMIQHN 199
N GR I+ N
Sbjct: 126 NESELFGRTIRVN 138
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + + ++ RGFA + F +A A M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96 N 96
N
Sbjct: 126 N 126
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAV 281
K ++V L +++ F FG IT + D KH GF +EF + + A A+
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 282 STMNGHVFKSKPLKVTLS 299
MN + ++V L+
Sbjct: 123 DNMNESELFGRTIRVNLA 140
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S GP + +FVK L E EE LK F + +IV D E G SKGFGF+
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFV 59
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F S + A+ A M I N + A
Sbjct: 60 DFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM- 95
L V L + L F G++R V + S+GF + FN+ +AK A+ M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 96 NGHLIGSKPVIITFVELKP 114
+G + G+K +T KP
Sbjct: 76 DGEIDGNK---VTLDWAKP 91
>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 = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHATHAVS 282
K+K+F++ LP + E EE+ GT+ LV++ K + ++E+ A+ AV
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
M+G K +KV +S + P
Sbjct: 77 KMDGMTIKENIIKVAISNSGP 97
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 42/71 (59%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+K K+F+ L + +EEL+ G + ++++V + GK KG ++++ + A +A+
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75
Query: 189 IEMNGRMIQHN 199
++M+G I+ N
Sbjct: 76 MKMDGMTIKEN 86
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 35/64 (54%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L ++ L S + L K GT++D+R+ N+ + +G A + + ++A +A ++M+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 97 GHLI 100
G I
Sbjct: 80 GMTI 83
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+F+ +L + + +L S F+ FGN+I K+ D + SK FGF+ F + +A+ AI M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 192 NGRMI 196
NG +
Sbjct: 103 NGFQV 107
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTM 284
+F+ +LP +++ F FG + S+ + DK GF+ F P A A+ M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 285 NGHVFKSKPLKVTL 298
NG +K LKV L
Sbjct: 103 NGFQVGTKRLKVQL 116
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEM 95
L + +L + L + F FG + +V +K S+ F + F+ P A+ A M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 96 NGHLIGSK 103
NG +G+K
Sbjct: 103 NGFQVGTK 110
>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 = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 192 N-----GRMIQHN 199
N GR I+ N
Sbjct: 70 NESELFGRTIRVN 82
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES-RGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + E RGFA + F +A A M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 96 N 96
N
Sbjct: 70 N 70
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAV 281
K ++V L +++ F FG IT + D KH GF +EF + + A A+
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 282 STMNGHVFKSKPLKVTLS 299
MN + ++V L+
Sbjct: 67 DNMNESELFGRTIRVNLA 84
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+FV L + E++++ F FGNI E I+R +G SKG F+++ S+ A+ AI +
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 192 NG 193
+G
Sbjct: 77 HG 78
Score = 28.5 bits (62), Expect = 5.9, Method: Composition-based stats.
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 17/90 (18%)
Query: 222 LLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLV-----SDKHIGFIEFIMPKH 276
L QP K+FV L + + LF FG I +++ + K F+++
Sbjct: 9 LRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAE 68
Query: 277 ATHAVSTMNGHVFKSKPLKVTLSGTKPGVS 306
A A++ ++G S T PG S
Sbjct: 69 AQAAINALHG------------SQTMPGAS 86
Score = 28.1 bits (61), Expect = 7.0, Method: Composition-based stats.
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 55 FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNG 97
F+ FG + + + R + S+G A + +++ AEA+ A ++G
Sbjct: 36 FEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALHG 78
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 192 N-----GRMIQHN 199
N GR I+ N
Sbjct: 68 NESELFGRTIRVN 80
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES-RGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + E RGFA + F +A A M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 96 N 96
N
Sbjct: 68 N 68
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAV 281
K ++V L +++ F FG IT + D KH GF +EF + + A A+
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 282 STMNGHVFKSKPLKVTLS 299
MN + ++V L+
Sbjct: 65 DNMNESELFGRTIRVNLA 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L +T+ ++E++ F ++G II +I+ D+ G S+G GFI+F AE+AI +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 192 NGR 194
NG+
Sbjct: 64 NGQ 66
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 10/70 (14%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTM 284
++V+ LP ++ E E+LF+++G I +S ++ D + +GFI F A A+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 285 NGHVFKSKPL 294
NG KPL
Sbjct: 64 NGQ----KPL 69
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 7/62 (11%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+FV+NL TV EE L+ F +FG + VK ++D + F+ F AA KA+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 193 GR 194
G+
Sbjct: 71 GK 72
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
K+FV L + L+ +F FG+I E ++ D + GKS+G+GF+ AAE+A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 191 MN 192
N
Sbjct: 79 PN 80
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG 267
KIFV LP + ++ + F FG I + +++D+ G
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTG 56
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
VFV N+ EE+LK F + G ++ ++V D E GK KG+GF ++ + A A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 192 NGR 194
NGR
Sbjct: 71 NGR 73
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAVSTM 284
+FV N+P + +++F+ G + S LV D+ GF E+ + A A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 285 NGHVFKSKPLKV 296
NG F + L+V
Sbjct: 71 NGREFSGRALRV 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 192 N-----GRMIQHN 199
N GR I+ N
Sbjct: 65 NESELFGRTIRVN 77
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + E RGFA + F +A A M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 96 N 96
N
Sbjct: 65 N 65
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGF--IEFIMPKHATHAV 281
K ++V L +++ F FG IT + D KH GF +EF + + A A+
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 282 STMNGHVFKSKPLKVTLS 299
MN + ++V L+
Sbjct: 62 DNMNESELFGRTIRVNLA 79
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFIQFFS 180
GP + + V NL E E +L+ F FG+I + + +D+ G+SKGF FI F
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66
Query: 181 YKAAEKAIIEMNGRMIQH 198
+ A +AI ++G H
Sbjct: 67 REDAARAIAGVSGFGYDH 84
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTM 284
I V NL + ++ +ELF FG+I+ L DK G FI F + A A++ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 285 NG 286
+G
Sbjct: 78 SG 79
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/189 (21%), Positives = 79/189 (41%), Gaps = 30/189 (15%)
Query: 132 KVFVKNLVETVDEEELKSHF---IKFGN--------IIEVKIVRDENGKSKGFGFIQFFS 180
+++V N+ + EE + F ++ G ++ V+I +D+N F F++F S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-----FAFLEFRS 60
Query: 181 YKAAEKAIIEMNGRMIQHNST-------FVSLAEIXXXXXXXXXXXXXLLQPARKNKIFV 233
+A+ +G + Q S + L + + P +K+F+
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 234 ANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGH 287
LP+ +N+ + +EL FG + + +LV D G F E++ A++ +NG
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 288 VFKSKPLKV 296
K L V
Sbjct: 180 QLGDKKLLV 188
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L ++++++K FG + +V+D G SKG+ F ++ ++AI
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 191 MNGRMIQHNSTFVSLAEI 208
+NG + V A +
Sbjct: 176 LNGMQLGDKKLLVQRASV 193
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
VFV NL V EE L F++ G + +V I +D GK K FGF+ F ++ AI +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 193 G 193
G
Sbjct: 79 G 79
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHAT 278
Q +FV NL + + ELF + G +T ++ D K GF+ F P+ +
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71
Query: 279 HAVSTMNGHVFKSKPLKVT 297
+A++ +NG +P+ V+
Sbjct: 72 YAIALLNGIRLYGRPINVS 90
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 32/70 (45%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGH 98
V NLE V + L F + G L V + +++ + + F + F P A +NG
Sbjct: 21 VGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGI 80
Query: 99 LIGSKPVIIT 108
+ +P+ ++
Sbjct: 81 RLYGRPINVS 90
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 135 VKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAIIEMNG 193
V NL + L+ F K+G + +V I RD K S+GF F++F + AE A+ M+G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 194 RMIQHNSTFVSLAE 207
++ V +A
Sbjct: 112 AVLDGRELRVQMAR 125
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL L F+K+G + DV + R++ ESRGFA + F+ +A+ A M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 96 NGHLIGSKPVIITFVE 111
+G ++ + + +
Sbjct: 110 DGAVLDGRELRVQMAR 125
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVST 283
++FV NL + + E+LF+ +G ++ D K F+ F+ P+HA A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 284 MNGHVFKSKPLKVTLSGTKPGVSITNPT 311
++G VF+ + L V S K S + P+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQSGPS 97
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
++FV+NL T EE+L+ F +G + E+ D K KGF F+ F + A KA E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 191 MNGRMIQ 197
++G++ Q
Sbjct: 70 VDGQVFQ 76
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 7/65 (10%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+FV+NL TV EE L+ F +FG + VK ++D + FI F A KA+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 193 GRMIQ 197
G+ ++
Sbjct: 67 GKDLE 71
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVFK 290
+FV NL + + E+ F++FG + + D FI F A A+ MNG +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--YAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 291 SKPLKVTLSGTKPGVSITNPTKAPKKPA 318
+ +++ + KP KA ++ A
Sbjct: 72 GENIEIVFA--KPPDQKRKERKAQRQAA 97
>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 = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/44 (45%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 154 FGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMI 196
FG I + ++V+D GKSKG+GF+ FF+ AE AI +M G+ +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 73
Score = 32.0 bits (71), Expect = 0.51, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEMNG 97
V +L P + A+ F FG + D RV ++ +S+G+ + F +A+ A +M G
Sbjct: 11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70
Query: 98 HLIGSKPVIITFVELKP 114
+G + + + KP
Sbjct: 71 QWLGGRQIRTNWATRKP 87
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
++V +L + E+ L+ F FG I + +++D + G+SKG+GFI F + A +A+ ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 192 NG 193
NG
Sbjct: 68 NG 69
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTM 284
++V +L NI +F FG I + L+ D K GFI F + A A+ +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 285 NGHVFKSKPLKV 296
NG +P++V
Sbjct: 68 NGFELAGRPMRV 79
Score = 32.0 bits (71), Expect = 0.46, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPAEAKKARVEM 95
L+V +L ++ L F+ FG + ++ + ++ + S+G+ I F+ A++A ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 96 NGHLIGSKPVIITFV 110
NG + +P+ + V
Sbjct: 68 NGFELAGRPMRVGHV 82
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 135 VKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAIIEMNG 193
V NL + L+ F K+G + +V I RD K S+GF F++F + AE A+ M+G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 194 RMIQHNSTFVSLA 206
++ V +A
Sbjct: 135 AVLDGRELRVQMA 147
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL L F+K+G + DV + R++ ESRGFA + F+ +A+ A M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 96 NGHLIGSKPVII 107
+G ++ + + +
Sbjct: 133 DGAVLDGRELRV 144
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAI 188
+K+FV + E EL+ +F KFG + EV ++ D E + +GFGFI F ++ ++A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVS 282
NKIFV +P N +E E F +FG +T ++ D + GFI F + AV+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 283 TMNGHVFKSKPLKV 296
M+ H K ++V
Sbjct: 71 -MHFHDIMGKKVEV 83
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTM 284
+F+ +LP + + ++F FG + S+ + DK GF+ + P A A+ +M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 285 NGHVFKSKPLKVTLSGTK 302
NG K LKV L +K
Sbjct: 88 NGFQIGMKRLKVQLKRSK 105
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+F+ +L + +++L F+ FGN++ K+ D + SK FGF+ + + +A+ AI M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 192 NGRMI 196
NG I
Sbjct: 88 NGFQI 92
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+FV+NL + LK F + G+++ I + ENGKSKG G ++F S + AE+A MN
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMN 66
Query: 193 G 193
G
Sbjct: 67 G 67
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ + NL + EE L+ F K +K+ +++NGKSKG+ FI+F S++ A++A+ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 193 GRMIQHNSTFVSL 205
R I+ + + L
Sbjct: 75 KREIEGRAIRLEL 87
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 8/88 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L ++NL S + L F+K T ++V +N+N +S+G+A I F + +AK+A N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK-ATF--IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 97 GHLIGSKPVIITFVELKPGQRSKP-VGP 123
I + + + EL+ G R P GP
Sbjct: 75 KREIEGRAIRL---ELQ-GPRGSPNSGP 98
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKA 187
K + V L E++LK +F FG ++ V++ +D + G SKGFGF++F Y+ K
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 188 I 188
+
Sbjct: 74 M 74
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 66/139 (47%), Gaps = 21/139 (15%)
Query: 63 DVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVG 122
DVR N R F + F + + +KA +E+ G + + + KP G
Sbjct: 47 DVRTGTN-----RKFGYVDFESAEDLEKA-LELTGLKVFGNEIKL----------EKPKG 90
Query: 123 PEEKQYKKDKVFV-KNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
+ K+ + + + KNL + E+ELK F + +E+++V ++GKSKG +I+F S
Sbjct: 91 RDSKKVRAARTLLAKNLSFNITEDELKEVF---EDALEIRLV-SQDGKSKGIAYIEFKSE 146
Query: 182 KAAEKAIIEMNGRMIQHNS 200
AEK + E G I S
Sbjct: 147 ADAEKNLEEKQGAEIDGRS 165
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
++FV+NL + LK F + G+++ I + ENGKSKG G ++F S + AE+A M
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 192 NG 193
NG
Sbjct: 69 NG 70
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 7/79 (8%)
Query: 124 EEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYK 182
E++Q++K +F+ L EE L++++ ++G + + ++RD K S+GFGF+ F S
Sbjct: 23 EKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80
Query: 183 AAEKAII----EMNGRMIQ 197
+ A+ ++GR+++
Sbjct: 81 EVDAAMAARPHSIDGRVVE 99
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
++ ++FV NL + EEE++ F K+G EV I +D KGFGFI+ + AE A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAK 68
Query: 189 IEMN 192
+E++
Sbjct: 69 VELD 72
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%)
Query: 226 ARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMN 285
+++++FV NLP +I E +LF ++G + DK GFI A A ++
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 286 GHVFKSKPLKVTLS 299
+ K L+V +
Sbjct: 73 NMPLRGKQLRVRFA 86
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V NL P + + + F+K+G +V + ++K GF I T A+ A+VE++
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVELD 72
Query: 97 GHLIGSKPVIITFV 110
+ K + + F
Sbjct: 73 NMPLRGKQLRVRFA 86
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 36/62 (58%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+FV L + EE++ F FG I E ++R +G SKG F++F S+ A+ AI +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 192 NG 193
+G
Sbjct: 77 HG 78
Score = 28.9 bits (63), Expect = 4.3, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 30/61 (49%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V L + ++ F+ FG + + V R + S+G A + F++ EA+ A ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 97 G 97
G
Sbjct: 78 G 78
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 31/91 (34%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKK-FGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V +L P VD+ L F K + + R +V ++ S+G+ + F E K+A E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 96 NGHL-IGSKPVIITFVELKPGQRSKPV--GP 123
G + +GSKPV ++ V + R KPV GP
Sbjct: 72 QGAVGLGSKPVRLS-VAIPKASRVKPVESGP 101
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIK-FGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV +L VD+ L F+K + + K+V D+ G SKG+GF++F ++A+ E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 192 NG 193
G
Sbjct: 72 QG 73
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
VFV NL V ++LK F G ++ I+ D++GKS+G G + F A +AI N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 193 GRMIQHNSTFVSLAE 207
G+++ V + E
Sbjct: 78 GQLLFDRPMHVKMDE 92
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 223 LQPAR-KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKH 276
LQ R + +FVANL + + +E+F+ G + + ++ DK IG + F
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIE 68
Query: 277 ATHAVSTMNGHVFKSKPLKVTL 298
A A+S NG + +P+ V +
Sbjct: 69 AVQAISMFNGQLLFDRPMHVKM 90
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 9/95 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V NL+ V + L F G + + +K+ +SRG + F EA +A N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVG----PEEKQ 127
G L+ +P + +K +R+ P G PE Q
Sbjct: 78 GQLLFDRP-----MHVKMDERALPKGDFFPPERPQ 107
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 125 EKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAA 184
E + + ++ V N+ + +L+ F +FG I++V+I+ +E G SKGFGF+ F + A
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADA 82
Query: 185 EKAIIEMNGRMIQ 197
++A +++G +++
Sbjct: 83 DRAREKLHGTVVE 95
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
LHV+N+ + L F +FG + DV + N+ S+GF + F A+A +AR +++
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 90
Query: 97 GHLIGSKPV 105
G ++ + +
Sbjct: 91 GTVVEGRKI 99
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLV----SDKHIGFIEFIMPKHATH 279
QP R + V+N+P + + ++F +FG I ++ K GF+ F A
Sbjct: 28 QPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84
Query: 280 AVSTMNGHVFKSKPLKV 296
A ++G V + + ++V
Sbjct: 85 AREKLHGTVVEGRKIEV 101
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQF 178
K+FV L + +E L+S+F ++G +++ I++D+ +S+GFGF++F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV +L VD+E L++ F F + + ++ D + G S+G+GF+ F S A+ A+ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 192 NGR 194
G+
Sbjct: 64 QGQ 66
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L V +L +VD++ L N FK F + V + + SRG+ + F + +A+ A M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96 NGHLIGSKPVIITF 109
G + +P+ I +
Sbjct: 64 QGQDLNGRPLRINW 77
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV------SDKHIGFIEFIMPKHATHAVSTM 284
+FV +L N+++ F F + S ++ S + GF+ F A +A+ +M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 285 NGHVFKSKPLKV 296
G +PL++
Sbjct: 64 QGQDLNGRPLRI 75
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
++ V N+ + +L+ F +FG I++V+I+ +E G SKGFGF+ F + A++A ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKL 75
Query: 192 NGRMIQ 197
+G +++
Sbjct: 76 HGTVVE 81
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
LHV+N+ + L F +FG + DV + N+ S+GF + F A+A +AR +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 97 GHLIGSKPV 105
G ++ + +
Sbjct: 77 GTVVEGRKI 85
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLV----SDKHIGFIEFIMPKHATHAVSTMN 285
++ V+N+P + + ++F +FG I ++ K GF+ F A A ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 286 GHVFKSKPLKV 296
G V + + ++V
Sbjct: 77 GTVVEGRKIEV 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK----SKGFGFIQFFSYKAAEKAI 188
+F+KNL + EE LK F K G I I + +N S GFGF+++ + A+KA+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 189 IEMNGRMIQHNSTFVSLAE 207
++ G + + V ++E
Sbjct: 68 KQLQGHTVDGHKLEVRISE 86
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE----SRGFAIIVFNTPAEAKKAR 92
L + NL S + L F K G ++ +++ KN S GF + + P +A+KA
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93 VEMNGHLI 100
++ GH +
Sbjct: 68 KQLQGHTV 75
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 11/84 (13%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKH---------IGFIEFIMPKHATHAV 281
+F+ NL + + +F++ G I S ++ K+ GF+E+ P+ A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 282 STMNGHVFKSKPLKVTLS--GTKP 303
+ GH L+V +S TKP
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKP 91
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 225 PARKN--KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH---IGFIEFIMPKHATH 279
PA N +I+V NLP +I + E++F ++G I L + + F+EF P+ A
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 76
Query: 280 AVSTMNGHVFKSKPLKV 296
AV +G+ + L+V
Sbjct: 77 AVYGRDGYDYDGYRLRV 93
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
++V NL P + + + + F K+G +RD+ + + FA + F P +A+ A +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGRD 82
Query: 97 GH 98
G+
Sbjct: 83 GY 84
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 77/183 (42%), Gaps = 38/183 (20%)
Query: 132 KVFVKNLVETVDEEELKSHF---IKFGN--------IIEVKIVRDENGKSKGFGFIQFFS 180
+++V N+ + EE + F ++ G ++ V+I +D+N F F++F S
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-----FAFLEFRS 62
Query: 181 YKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQP-ARKNKIFVANLPSN 239
+A+ +G + Q S + QP +K+F+ LP+
Sbjct: 63 VDETTQAM-AFDGIIFQGQSLKIRRPHDY--------------QPLPGAHKLFIGGLPNY 107
Query: 240 INNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTMNGHVFKSKP 293
+N+ + +EL FG + + +LV D G F E++ A++ +NG K
Sbjct: 108 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 167
Query: 294 LKV 296
L V
Sbjct: 168 LLV 170
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L ++++++K FG + +V+D G SKG+ F ++ ++AI
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 191 MNGRMIQHNSTFVSLA 206
+NG + V A
Sbjct: 158 LNGMQLGDKKLLVQRA 173
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQ 177
++V NLV + E++K F +FG + VK++ D E K KGFGF++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE 49
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTM 284
I+V NL + + + +ELF++FG + + L+ D K GF+E + + + A++ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 285 NGHVFKSKPLKVT 297
+ F + ++VT
Sbjct: 63 DNTDFMGRTIRVT 75
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVS 282
+K+F+ LP+ +N+ + +EL FG + + +LV D G F E++ A++
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 283 TMNGHVFKSKPLKV 296
+NG K L V
Sbjct: 155 GLNGMQLGDKKLLV 168
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L ++++++K FG + +V+D G SKG+ F ++ ++AI
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 191 MNGRMIQHNSTFVSLA 206
+NG + V A
Sbjct: 156 LNGMQLGDKKLLVQRA 171
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
++FV P ++ SE E+F FG + +++ F+EF + A A+ ++G
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHGKS 89
Query: 289 FKSKPLKVTLS 299
F ++PL+V S
Sbjct: 90 FANQPLEVVYS 100
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 124 EEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKA 183
+E + ++FV+ V E EL F FG + EVKI+ GF F++F ++
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAES 77
Query: 184 AEKAIIEMNGR 194
A KAI E++G+
Sbjct: 78 AAKAIEEVHGK 88
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 76/192 (39%), Gaps = 32/192 (16%)
Query: 112 LKPGQRSKPVGPEEKQYK-KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS 170
L P + K + E+Q++ + K+ ++ L V +E+ + E+K + K
Sbjct: 1 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVD--KY 54
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNK 230
KG F+ + + AE AI + ++ V L QP
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------------QPT-DAL 95
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV------SDKHIGFIEFIMPKHATHAVSTM 284
+ VANLP ++ +FEEL FG++ LV K GF E++ A A S +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 285 NGHVFKSKPLKV 296
G + L V
Sbjct: 156 LGKPLGPRTLYV 167
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+FV N+ +EL+S F + G +IE +V+D + F+ A+ AI ++
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQL 63
Query: 192 NGRMIQHNSTFVSLA 206
NG+ ++ V L+
Sbjct: 64 NGKEVKGKRINVELS 78
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 34/57 (59%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
K+FV L + +E+++ F FG I E ++R +G SKG F++F ++ A+ AI
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Score = 31.2 bits (69), Expect = 0.92, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 55 FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKA 91
F+ FGT+ + V R + S+G A + F T AEA+ A
Sbjct: 33 FEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAA 69
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 230 KIFVANLPSN-INNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
++F+ NL + + S+ E +F+++G + S+ K F+++ +HA AV NG V
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRV 86
Query: 289 FKSKPLKVTLSG 300
+ L + ++G
Sbjct: 87 LAGQTLDINMAG 98
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 132 KVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIE 190
+VF+ NL V + ++++ F K+G + + KG+ F+Q+ + + A A++
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLG 81
Query: 191 MNGRMIQHNSTFVSLA 206
NGR++ + +++A
Sbjct: 82 ENGRVLAGQTLDINMA 97
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 76/192 (39%), Gaps = 32/192 (16%)
Query: 112 LKPGQRSKPVGPEEKQYK-KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS 170
L P + K + E+Q++ + K+ ++ L V +E+ + E+K + K
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVD--KY 56
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNK 230
KG F+ + + AE AI + ++ V L QP
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------------QPT-DAL 97
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV------SDKHIGFIEFIMPKHATHAVSTM 284
+ VANLP ++ +FEEL FG++ LV K GF E++ A A S +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 285 NGHVFKSKPLKV 296
G + L V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 76/192 (39%), Gaps = 32/192 (16%)
Query: 112 LKPGQRSKPVGPEEKQYK-KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS 170
L P + K + E+Q++ + K+ ++ L V +E+ + E+K + K
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVD--KY 56
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXXXXXXXLLQPARKNK 230
KG F+ + + AE AI + ++ V L QP
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------------QPT-DAL 97
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV------SDKHIGFIEFIMPKHATHAVSTM 284
+ VANLP ++ +FEEL FG++ LV K GF E++ A A S +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 285 NGHVFKSKPLKV 296
G + L V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L +E L+ +F +FG + E ++RD +S+GFGF+ F +K + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
++FV P ++ SE E+F FG + +++ F+EF + A A+ ++G
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHGKS 62
Query: 289 FKSKPLKVTLS 299
F ++PL+V S
Sbjct: 63 FANQPLEVVYS 73
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
++FV+ V E EL F FG + EVKI+ GF F++F ++A KAI E+
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEV 58
Query: 192 NGR 194
+G+
Sbjct: 59 HGK 61
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L +E L+ +F +FG + E ++RD +S+GFGF+ F +K + +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENG---KSKGFGFIQFFSYKAAEKA 187
K+FV + T E++L+ F ++G + E+ ++RD + +SKG F+ F++ KAA +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 119 KPVGPEEK-QYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFI 176
+P+ EEK + K V+V N+ ++L++HF G+I + I+ D+ +G KG+ +I
Sbjct: 24 QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83
Query: 177 QFFSYKAAEKAI 188
+F + + A+
Sbjct: 84 EFAERNSVDAAV 95
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI--- 188
V+V L E V E L F++ G ++ + +D G+ +G+GF++F S + A+ AI
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 189 --IEMNGRMIQHN 199
I++ G+ I+ N
Sbjct: 78 DMIKLYGKPIRVN 90
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDK------HIGFIEFIMPKHATHAVSTM 284
++V L ++ ELF + G + ++ + D+ GF+EF+ + A +A+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 285 NGHVFKSKPLKV 296
+ KP++V
Sbjct: 78 DMIKLYGKPIRV 89
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 3/83 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLR--DVRVARNKNDESRGFAIIVFNTPAEAKKARVE 94
+H+ L +V ++ F +G ++ D+ V R S+G+A + F P EA+KA
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 95 MNGHLIGSKPVIITFVELKPGQR 117
M+G I + + T V L P R
Sbjct: 67 MDGGQIDGQEITATAV-LAPWPR 88
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFGNI--IEVKIVRDENGKSKGFGFIQFFSYKAAEK 186
K KV + L V ++ + F +G I I++ + R SKG+ +++F + AEK
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 187 AIIEMNGRMI 196
A+ M+G I
Sbjct: 63 ALKHMDGGQI 72
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVS 282
+K+F+ LP+ +N+ + +EL FG + + +LV D G F E++ A++
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 283 TMNGHVFKSKPLKV 296
+NG K L V
Sbjct: 62 GLNGMQLGDKKLLV 75
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L ++++++K FG + +V+D G SKG+ F ++ ++AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 191 MNGRMIQHNSTFVSLAEI 208
+NG + V A +
Sbjct: 63 LNGMQLGDKKLLVQRASV 80
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 118 SKPVGPEEKQYKKDKVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFI 176
S G + + +VF+ NL V + ++++ F K+G I+ + KGF F+
Sbjct: 3 SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFV 55
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
Q+ + + A A+ +GRMI ++LA
Sbjct: 56 QYVNERNARAAVAGEDGRMIAGQVLDINLA 85
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFS 180
G K + K+FV + +DE++LK F +FG I E+ +++D G KG F+ + +
Sbjct: 7 GVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCA 66
Query: 181 YKAAEKA 187
+A KA
Sbjct: 67 RDSALKA 73
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF 268
K+FV +P ++ + + LF FG I +++ D+ G
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGL 55
>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 = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE- 190
+F+ L +++LK +F KFG +++ + D G+S+GFGF+ F ++ +K + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 191 ---MNGRMI 196
+NG++I
Sbjct: 62 EHKLNGKVI 70
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENG-KSKGFGFIQFFSYKAAEKAI 188
K V+V NL ++ +L F K+G +++V I++D++ KSKG FI F +A+
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 189 IEMNGRMI 196
+N + +
Sbjct: 76 RAINNKQL 83
Score = 34.7 bits (78), Expect = 0.085, Method: Composition-based stats.
Identities = 16/78 (20%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAV 281
K+ ++V+NLP ++ N++ +F+++G + +++ DK + FI F+ A +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 282 STMNGHVFKSKPLKVTLS 299
+N + +K +++
Sbjct: 76 RAINNKQLFGRVIKASIA 93
Score = 28.1 bits (61), Expect = 6.8, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVF 82
++V+NL S+ N L F K+G + V + ++K+ +S+G A I+F
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 38/139 (27%), Positives = 65/139 (46%), Gaps = 21/139 (15%)
Query: 63 DVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVG 122
DVR+ +R F + F + + +KA +E+ G + + + KP G
Sbjct: 41 DVRIGM-----TRKFGYVDFESAEDLEKA-LELTGLKVFGNEIKL----------EKPKG 84
Query: 123 PEEKQYKKDKVFV-KNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
+ K+ + + + KNL V ++ELK F + E+++V ++GKSKG +I+F +
Sbjct: 85 KDSKKERDARTLLAKNLPYKVTQDELKEVF---EDAAEIRLVS-KDGKSKGIAYIEFKTE 140
Query: 182 KAAEKAIIEMNGRMIQHNS 200
AEK E G I S
Sbjct: 141 ADAEKTFEEKQGTEIDGRS 159
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 35/152 (23%), Positives = 57/152 (37%), Gaps = 24/152 (15%)
Query: 157 IIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIXXXXXXXX 216
+++V+I G ++ FG++ F S + EKA +E+ G + N + L +
Sbjct: 39 VVDVRI-----GMTRKFGYVDFESAEDLEKA-LELTGLKVFGNE--IKLEKPKGKDSKKE 90
Query: 217 XXXXXLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVS----DKHIGFIEFI 272
LL NLP + E +E+F I LVS K I +IEF
Sbjct: 91 RDARTLL---------AKNLPYKVTQDELKEVFEDAAEI---RLVSKDGKSKGIAYIEFK 138
Query: 273 MPKHATHAVSTMNGHVFKSKPLKVTLSGTKPG 304
A G + + + +G G
Sbjct: 139 TEADAEKTFEEKQGTEIDGRSISLYYTGEPKG 170
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 17/69 (24%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
K V+ + + ++ ++ F FG I+E+++ + KG+ F++F ++++A AI
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAI 78
Query: 189 IEMNGRMIQ 197
+ +NG I+
Sbjct: 79 VSVNGTTIE 87
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 224 QPARKN-KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS 282
Q + KN ++ + S + + + F+ FG I + +K F+ F + A HA+
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV 79
Query: 283 TMNGHVFKSKPLKVTLSGTKPGVS 306
++NG + +K P ++
Sbjct: 80 SVNGTTIEGHVVKCYWGKESPDMT 103
Score = 28.1 bits (61), Expect = 7.1, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
++ + + +Q + F FG + ++RV K G++ + F+T A A V +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-----GYSFVRFSTHESAAHAIVSVN 82
Query: 97 GHLIGSKPVIITFVELKPGQRSKP 120
G I V + + P S P
Sbjct: 83 GTTIEGHVVKCYWGKESPDMTSGP 106
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ KNL + E+ELK F + +E+++V ++GKSKG +I+F S AEK + E
Sbjct: 19 LLAKNLSFNITEDELKEVF---EDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 193 GRMIQHNSTFVSL 205
G I S VSL
Sbjct: 75 GAEIDGRS--VSL 85
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V+NL+ V + + F +FGTL+ V +++ S G A + F A+A KA + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 97 GHLIGSKPVIITFV 110
G + +P+ I V
Sbjct: 91 GVPLDGRPMNIQLV 104
Score = 35.0 bits (79), Expect = 0.053, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTM 284
K+ V+NL +++++ +ELFA FGT+ +++ D+ + F A A+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 285 NGHVFKSKPLKVTL 298
NG +P+ + L
Sbjct: 90 NGVPLDGRPMNIQL 103
Score = 31.6 bits (70), Expect = 0.62, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 192 NG 193
NG
Sbjct: 90 NG 91
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 126 KQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAA 184
K + K+F+ + +DE++LK F +FG I E+ +++D G KG F+ + ++A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 185 EKA 187
KA
Sbjct: 69 LKA 71
Score = 31.2 bits (69), Expect = 0.76, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG 267
K+F+ +P N++ + + LF FG I +++ D+ G
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTG 52
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 124 EEKQYKKD-KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYK 182
+EK KK ++V NL EE++ F K G+I ++ + D+ + GF F++++S
Sbjct: 11 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRA 70
Query: 183 AAEKAIIEMNG 193
AE A+ +NG
Sbjct: 71 DAENAMRYING 81
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
K+F+ NL E+E++S F ++G ++E I+++ +GF+ AAE AI
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDAI 59
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVF 289
K+F+ NLP E LF ++G + ++ K+ GF+ A A+ + H +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNL--HHY 65
Query: 290 KSKPLKVTLSGTKPGVSITNPTKAPKKPA 318
K + + + +K N +KA P+
Sbjct: 66 KLHGVNINVEASK------NKSKASSGPS 88
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIV-RDENGKSKGFGFIQFFSYKAAEKAI 188
VF++NL +EE L +FG++ V++V + SKG F QF + +AA+K +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKA 91
+ NL + +AL ++FG L+ VRV + + E S+G A F T A+K
Sbjct: 20 IRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
KV+V NL ++ EL+ F +G + V + R+ GF F++F + A A+ E+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVREL 130
Query: 192 NGRMIQHNSTFVSLA 206
+GR + V L+
Sbjct: 131 DGRTLCGCRVRVELS 145
>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 = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 44/183 (24%), Positives = 80/183 (43%), Gaps = 36/183 (19%)
Query: 37 LHVNNLEPS-VDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL P V Q+L F +G ++ V++ NK + A++ +A+ A +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHL 92
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKD------------------------ 131
NGH + KP+ IT + + Q + G E++ KD
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPRE-GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 132 -KVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGFIQFFSYKAAEKAII 189
+ + N+ +V EE+LK F G +++ K + K + IQ S + A +A+I
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALI 207
Query: 190 EMN 192
+++
Sbjct: 208 DLH 210
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 223 LQPARKNKIFVANL-PSNINNSEFEELFARFGTITSSS-LVSDKHIGFIEFIMPKHATHA 280
L A + + V+NL P + LF +G + L + K ++ A A
Sbjct: 29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLA 88
Query: 281 VSTMNGHVFKSKPLKVTLS 299
+S +NGH KP+++TLS
Sbjct: 89 MSHLNGHKLHGKPIRITLS 107
>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 = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V+NL+ V + + F +FGTL+ V +++ S G A + F A+A KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 97 GHLIGSKPVIITFV 110
G + +P I V
Sbjct: 92 GVPLDGRPXNIQLV 105
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTM 284
K+ V+NL +++++ +ELFA FGT+ +++ D+ + F A A
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 285 NGHVFKSKPLKVTL 298
NG +P + L
Sbjct: 91 NGVPLDGRPXNIQL 104
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 192 NG 193
NG
Sbjct: 91 NG 92
>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 = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 192 NGR 194
NG+
Sbjct: 70 NGQ 72
Score = 29.6 bits (65), Expect = 2.6, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 285 NGHVFKSKPLKV 296
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 192 NGR 194
NG+
Sbjct: 70 NGQ 72
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 285 NGHVFKSKPLKV 296
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 192 NGR 194
NG+
Sbjct: 72 NGQ 74
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 285 NGHVFKSKPLKV 296
NG +P+ V
Sbjct: 72 NGQDLMGQPISV 83
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 82/190 (43%), Gaps = 36/190 (18%)
Query: 37 LHVNNLEPS-VDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL P V Q+L F +G ++ V++ NK + A++ +A+ A +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHL 61
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKD------------------------ 131
NGH + KP+ IT + + Q + G E++ KD
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPRE-GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 132 -KVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGFIQFFSYKAAEKAII 189
+ + N+ +V EE+LK F G +++ K + K + IQ S + A +A+I
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALI 176
Query: 190 EMNGRMIQHN 199
+++ + N
Sbjct: 177 DLHNHDLGEN 186
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 231 IFVANL-PSNINNSEFEELFARFGTITSSS-LVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
+ V+NL P + LF +G + L + K ++ A A+S +NGH
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 289 FKSKPLKVTLS 299
KP+++TLS
Sbjct: 66 LHGKPIRITLS 76
>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 = 36.6 bits (83), Expect = 0.021, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 192 NGR 194
NG+
Sbjct: 70 NGQ 72
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 285 NGHVFKSKPLKV 296
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 192 NGR 194
NG+
Sbjct: 86 NGQ 88
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 285 NGHVFKSKPLKV 296
NG +P+ V
Sbjct: 86 NGQDLMGQPISV 97
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V+NL+ V + + F +FGTL+ V +++ S G A + F A+A KA +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 97 GHLIGSKPVIITFV 110
G + +P+ I V
Sbjct: 98 GVPLDGRPMDIQLV 111
Score = 35.0 bits (79), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTM 284
K+ V+NL +++++ +ELFA FGT+ +++ D+ + F A A+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 285 NGHVFKSKPLKVTL 298
G +P+ + L
Sbjct: 97 KGVPLDGRPMDIQL 110
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 192 NG 193
G
Sbjct: 97 KG 98
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V+NL+ V + + F +FGTL+ V +++ S G A + F A+A KA +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 97 GHLIGSKPVIITFV 110
G + +P+ I V
Sbjct: 98 GVPLDGRPMDIQLV 111
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTM 284
K+ V+NL +++++ +ELFA FGT+ +++ D+ + F A A+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 285 NGHVFKSKPLKVTL 298
G +P+ + L
Sbjct: 97 KGVPLDGRPMDIQL 110
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 192 NG 193
G
Sbjct: 97 KG 98
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKA 187
++V L +T+ E +L++HF +FG I + +V+ + FIQF + +AAE A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ-----CAFIQFATRQAAEVA 64
>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 = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L++ NL + + + + F K+G +R +RV E+RG A +V+ +AK A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 97 GHLIGSKPVIITF 109
G + ++ +++ +
Sbjct: 79 GFNVCNRYLVVLY 91
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L++ NL + + + + F K+G +R +RV E+RG A +V+ +AK A ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 97 GHLIGSKPVIITF 109
G + ++ +++ +
Sbjct: 69 GFNVSNRYLVVLY 81
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 36.2 bits (82), Expect = 0.024, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 226 ARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATH 279
A + V LP ++ + E LF G I + ++ D G F++F +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 280 AVSTMNGHVFKSKPLKVTLSGTKPG 304
A+ +NG ++K LKV+ + +PG
Sbjct: 61 AIKVLNGITVRNKRLKVSYA--RPG 83
Score = 32.0 bits (71), Expect = 0.51, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEM 95
L VN L + ++ L F+ G + R+ R+ K S G+A + F + ++++A +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGHLIGSKPVIITFVELKPGQRS 118
NG + +K + +++ +PG S
Sbjct: 66 NGITVRNKRLKVSYA--RPGGES 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 8/71 (11%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKA---- 187
VF +L T E +L+ F K+G I +V IV D+ + S+GF F+ F + A++A
Sbjct: 51 VFGLSLYTT--ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 188 -IIEMNGRMIQ 197
+E++GR I+
Sbjct: 109 NGMELDGRRIR 119
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 55 FKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITF 109
F K+G + DV + ++ SRGFA + F +AK+A+ NG + + + + F
Sbjct: 67 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS--KGFGFIQFF 179
G K+ K+ V+N+ ++ E++ F FG + V++ + G +GFGF+ F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 180 SYKAAEKAI 188
+ + A+KA
Sbjct: 67 TKQDAKKAF 75
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLV-------SDKHIGFIEFIMPKHATHAV 281
+KI V N+P N E ELF+ FG + + L + + GF++FI + A A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 282 STM 284
+ +
Sbjct: 76 NAL 78
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 44 PSVDNQALINE-FKKFGTLRDVRVARNKNDES--RGFAIIVFNTPAEAKKA--RVEMNGH 98
P NQ I E F FG L+ VR+ + RGF + F T +AKKA + + H
Sbjct: 24 PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH 83
Query: 99 LIGSKPVI 106
L G + V+
Sbjct: 84 LYGRRLVL 91
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 6/77 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYK---AAEKAI 188
+FV ++ E E+E++ F +G I + + D G SKG+ +++ ++K AA++A+
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 189 --IEMNGRMIQHNSTFV 203
E+ G+ IQ + FV
Sbjct: 135 NGAEIMGQTIQVDWCFV 151
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV ++ E +E F +G I + L D+ GF +E+ K A A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 285 NGHVFKSKPLKVTLS 299
NG + ++V
Sbjct: 135 NGAEIMGQTIQVDWC 149
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 36.2 bits (82), Expect = 0.030, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 6/60 (10%)
Query: 144 EEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAI-----IEMNGRMIQ 197
E +L+ F K+G I +V IV D+ + S+GF F+ F + A++A +E++GR I+
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Score = 34.7 bits (78), Expect = 0.075, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 55 FKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITF 109
F K+G + DV + ++ SRGFA + F +AK+A+ NG + + + + F
Sbjct: 33 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 88
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
KV+V NL ++ EL+ F +G + V + R+ GF F++F + A A+ ++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRDL 130
Query: 192 NGRMIQHNSTFVSLA 206
+GR + V L+
Sbjct: 131 DGRTLCGCRVRVELS 145
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 6/60 (10%)
Query: 144 EEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAI-----IEMNGRMIQ 197
E +L+ F K+G I +V IV D+ + S+GF F+ F + A++A +E++GR I+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 55 FKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEMNG 97
F K+G + DV + ++ SRGFA + F +AK+A+ NG
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTM 284
K+ V+NL +++++ +ELFA FGT+ +++ D+ + F A A+
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 149
Query: 285 NGHVFKSKPLKVTL 298
G +P+ + L
Sbjct: 150 KGVPLDGRPMDIQL 163
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L V+NL+ V + + F +FGTL+ V +++ S G A + F A+A KA +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 97 GHLIGSKPVIITFV 110
G + +P+ I V
Sbjct: 151 GVPLDGRPMDIQLV 164
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 149
Query: 192 NG 193
G
Sbjct: 150 KG 151
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFIQFFSYKAAEKAIIEM 191
++++ L +++L +G I+ K + D+ K KG+GF+ F S AA+KA+ +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 192 NGRMIQ 197
+Q
Sbjct: 68 KASGVQ 73
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 6/60 (10%)
Query: 144 EEELKSHFIKFGNIIEVKIVRDENGK-SKGFGFIQFFSYKAAEKAI-----IEMNGRMIQ 197
E +L+ F K+G I +V IV D+ + S+GF F+ F + A++A +E++GR I+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Score = 34.3 bits (77), Expect = 0.091, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 55 FKKFGTLRDVRVARNKNDE-SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITF 109
F K+G + DV + ++ SRGFA + F +AK+A+ NG + + + + F
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES-RGFAIIVFNTPAEAKKARVEM 95
L V+NL +L F+K+G + DV + R + ++ RGFA + F+ +A+ A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 96 NG 97
+G
Sbjct: 76 DG 77
Score = 34.7 bits (78), Expect = 0.074, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 135 VKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS-KGFGFIQFFSYKAAEKAIIEMNG 193
V NL + L+ F K+G + +V I R+ + K+ +GF F++F + A+ A M+G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
>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 = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E EE++ F ++G I + + D G KG+ +++ +YK A+ A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 192 NGR 194
NG+
Sbjct: 85 NGQ 87
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV + + + FA +G I + L D+ G+ +E+ K A A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 285 NGHVFKSKPLKVTLS 299
NG +P+ V
Sbjct: 85 NGQDLMGQPISVDWC 99
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/75 (16%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES-RGFAIIVFNTPAEAKKARVEM 95
L V + + + ++F ++G ++++ + ++ +G+ ++ + T EA+ A +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 96 NGHLIGSKPVIITFV 110
NG + +P+ + +
Sbjct: 85 NGQDLMGQPISVDWC 99
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.4 bits (80), Expect = 0.050, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L++ NL + + + + F K+G +R +RV E+RG A +V+ +AK A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNACDHLS 72
Query: 97 GHLIGSKPVIITF 109
G + ++ +++ +
Sbjct: 73 GFNVCNRYLVVLY 85
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.0 bits (79), Expect = 0.065, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 6/77 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYK---AAEKAI 188
+FV ++ E E+E++ F +G I + + D G SKG+ +++ ++K AA++A+
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 189 --IEMNGRMIQHNSTFV 203
E+ G+ IQ + FV
Sbjct: 89 NGAEIMGQTIQVDWCFV 105
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF------IEFIMPKHATHAVSTM 284
+FV ++ E +E F +G I + L D+ GF +E+ K A A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 285 NGHVFKSKPLKV 296
NG + ++V
Sbjct: 89 NGAEIMGQTIQV 100
>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 = 34.7 bits (78), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L + NL + + + + F K+G +R +RV E+RG A +V+ +AK A ++
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 97 GHLIGSKPVIITF 109
G + ++ +++ +
Sbjct: 79 GFNVCNRYLVVLY 91
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGH 287
K I NLP+ +E +E F+RFG++ L +EF+ P A A +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 288 VFKSKPL 294
F PL
Sbjct: 70 KFHHVPL 76
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
KV+V NL + EL+ F +G + V I R+ GF F++F + AE A+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 192 NGRMIQHNSTFVSLA 206
+G++I + V L+
Sbjct: 58 DGKVICGSRVRVELS 72
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS----KGFGFIQF---FSYKAA 184
KVFV L +DE+E+ + F +FG ++ V KS KG+ F+ F S +A
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 185 EKAIIEMNGRM 195
A +E +G++
Sbjct: 69 IDACLEEDGKL 79
>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 = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 144 EEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNG 193
EE++ G +I +K++ D + G+SKG+ FI+F +++ A+ +NG
Sbjct: 17 EEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 67
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 144 EEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNG 193
EE++ G +I +K++ D + G+SKG+ FI+F +++ A+ +NG
Sbjct: 16 EEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66
Score = 27.7 bits (60), Expect = 8.5, Method: Composition-based stats.
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVSTM 284
+++ ++P + + +L + G + + ++ D G FIEF + + AV +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 285 NGHVFKSKPLKVTLSGTK--PGVSI 307
NG+ S+ LK S GVS+
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISGVSL 89
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 5/91 (5%)
Query: 108 TFVELKPGQRSKPVGPEEKQYKKDK----VFVKNLVETVDEEELKSHFIKFGNIIEVKIV 163
++VEL + G E+Q K K ++V NL EE++ F K G+I ++ +
Sbjct: 13 SYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72
Query: 164 RDENGKSK-GFGFIQFFSYKAAEKAIIEMNG 193
D+ K+ GF F++++S AE A+ +NG
Sbjct: 73 LDKMKKTACGFCFVEYYSRADAENAMRYING 103
>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 = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 144 EEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNG 193
EE++ G +I +K++ D + G+SKG+ FI+F +++ A+ +NG
Sbjct: 18 EEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 68
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 67
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 68 MQGFPFYDKPMRIQYAKTDSDI 89
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 65
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 66 RSMQGFPFYDKPMRIQYAK 84
>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 = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 66 MQGFPFYDKPMRIQYAKTDSDI 87
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 68
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 69 MQGFPFYDKPMRIQYAKTDSDI 90
Score = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 66
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 67 RSMQGFPFYDKPMRIQYAK 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 = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 71 MQGFPFYDKPMRIQYAKTDSDI 92
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 68
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
>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 = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 66
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 67 MQGFPFYDKPMRIQYAKTDSDI 88
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 64
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
>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 = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDI 93
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 69
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
>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 = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 71 MQGFPFYDKPMRIQYAKTDSDI 92
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 68
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 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 = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDI 93
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 69
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
>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 = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F+RFG I S + + F+ F AT+A+ +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 71 MQGFPFYDKPMRIQYAKTDSDI 92
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 68
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F++FG I S + + F+ F AT+A+ +
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 284 MNGHVFKSKPLKVTLSGT 301
M G F KP+++ + T
Sbjct: 71 MQGFPFYDKPMRIQYAKT 88
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDN----QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + ++L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 68
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDN----QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + ++L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 69
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F++FG I S + + F+ F AT+A+ +
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 284 MNGHVFKSKPLKVTLSGTKPGV 305
M G F KP+++ + T +
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDI 93
>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 = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQF 178
++V N+ EEL++HF G++ V I+ D+ +G KGF +I+F
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 55
>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 = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQF 178
++V N+ EEL++HF G++ V I+ D+ +G KGF +I+F
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 54
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.0 bits (71), Expect = 0.45, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 133 VFVKNLVETVDEEELKSHFIKFG-NIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIE 190
+++ +L +DE + F G ++ VKI+R+ G G+ F++F AEK + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 191 MNGR 194
+NG+
Sbjct: 72 INGK 75
>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 = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 71/154 (46%), Gaps = 22/154 (14%)
Query: 64 VRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
+R+ + + SR FA I + +A+ ++NG I ++ +K P
Sbjct: 148 IRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV-----------TKVSNP 196
Query: 124 EEKQYKKD-------KVFVKNL-VETVDEEELKSHFIKFGNIIEVKIV--RDENGKSKGF 173
EK + D ++ ++NL E +DE L+ F FG+I ++ I + E+ +
Sbjct: 197 LEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC 256
Query: 174 GFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F F + +AE+A ++ N ++ + VSLA+
Sbjct: 257 AFXVFENKDSAERA-LQXNRSLLGNREISVSLAD 289
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-IGFIEFIMPKHATHAVSTMNGHVF 289
+F+ NLP N LF +F LV ++H I F+EF + A + G F
Sbjct: 11 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQG--F 68
Query: 290 KSKP---LKVTLS 299
K P +K+T +
Sbjct: 69 KITPTHAMKITFA 81
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAE 185
KVFV E + EEL+ F ++G +++V I + + F F+ F K A+
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFADDKVAQ 62
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
P + N ++V ++ + F+ FG I S+ ++ F+ + + A AV+ +
Sbjct: 36 PRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 93
Query: 285 NGHVFKSKPLKVTLSGTKP 303
NG +S LKV ++ +P
Sbjct: 94 NGTQVESVQLKVNIARKQP 112
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAI--- 188
+FV L E++K +F +FG + + ++ D+ + +GFGF+ F S EK
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 189 -IEMNGRMIQ 197
E+N +M++
Sbjct: 62 FHEINNKMVE 71
>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 = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDN----QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + ++L F +FG + D+ V+R+ + RG A ++F + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 69
Query: 93 VEMNGHLIGSKPVIITFVE 111
M G KP+ I + +
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 231 IFVANLPSNINNSEFEE----LFARFGTITS---SSLVSDKHIGFIEFIMPKHATHAVST 283
I++ NL I E ++ +F++FG I S + + F+ F AT+A+ +
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 284 MNGHVFKSKPLKVTLSGT 301
M G F KP+++ + T
Sbjct: 72 MQGFPFYDKPMRIQYAKT 89
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
P + N ++V ++ + F+ FG I S+ ++ F+ + + A AV+ +
Sbjct: 12 PRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 69
Query: 285 NGHVFKSKPLKVTLSGTKP 303
NG +S LKV ++ +P
Sbjct: 70 NGTQVESVQLKVNIARKQP 88
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V N+ T +EL++ F ++G +IE IV+D + F+ + A +AI +
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGL 64
Query: 192 NGRMIQHNSTFVSLA 206
+ Q V L+
Sbjct: 65 DNTEFQGKRMHVQLS 79
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG--FAIIVFNTPAEAKKARVE 94
L V L P+ AL EF +FG++R + D +G FA I + + A+ A +
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTI-------DHVKGDSFAYIQYESLDAAQAACAK 72
Query: 95 MNGHLIG 101
M G +G
Sbjct: 73 MRGFPLG 79
>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 = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQF 178
K+FV L EE+++ +F FG + +++ D + K +GF FI F
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVAR-NKNDESRGFAIIVFNTPAEAKKARVEM 95
+ V L P + + F FG + + + NK ++ RGF I F KK +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 62
Query: 96 NGHLIG 101
H +G
Sbjct: 63 KYHNVG 68
>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 = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E +L+ F +G I + +V + +GK +G+ FI++ + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 192 NGRMIQHNSTFVSL 205
+G+ I V +
Sbjct: 165 DGKKIDGRRVLVDV 178
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E +L+ F +G I + +V + +GK +G+ FI++ + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 192 NGRMIQHNSTFVSL 205
+G+ I V +
Sbjct: 165 DGKKIDGRRVLVDV 178
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 142 VDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQ 197
V ++ L S F K G ++ ++ DE GK+KGF F++ S A+K I +G+ +
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 142 VDEEELKSHFIKFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQ 197
V ++ L S F K G ++ ++ DE GK+KGF F++ S A+K I +G+ +
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 39 VNNLEPSVDN---QALINEFKKF-GTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVE 94
+ N+ P V QAL+ G + D+ V + +D++ G A IVF T E+ +A VE
Sbjct: 34 ITNINPEVPKEKLQALLYALASSQGDILDIVV--DLSDDNSGKAYIVFAT-QESAQAFVE 90
Query: 95 -MNGHLIGSKPVIITFVELKPGQ 116
G+ P++ITF E Q
Sbjct: 91 AFQGYPFQGNPLVITFSETPQSQ 113
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 151 FIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTF 202
F KFG I +E+GK+KG+ F+++ S A A+ +G + TF
Sbjct: 28 FSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 31/66 (46%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVFK 290
+FV+ P +++++ E F FG + S + DK + I + A AV + + H
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLG 70
Query: 291 SKPLKV 296
L+V
Sbjct: 71 GHRLRV 76
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 151 FIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTF 202
F KFG I +E+GK+KG+ F+++ S A A+ +G + TF
Sbjct: 42 FSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.9 bits (63), Expect = 3.9, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLV----SDKHIGFIEFIMPKHATHAVSTMNG 286
++V NL ++ +LF++ G S ++ S+ F+EF + A A++ MNG
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 287 HVFKSKPLKVTLSGTKPGVSITNPT 311
K +KV + T P + P+
Sbjct: 78 RKILGKEVKVNWA-TTPSSQKSGPS 101
>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
Length = 507
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 223 LQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS 282
LQP R + + V P S+ +LF+ FG I S + D F+ P+ AV+
Sbjct: 435 LQPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVN 491
Query: 283 T 283
T
Sbjct: 492 T 492
>pdb|1WHV|A Chain A, Solution Structure Of The Rna Binding Domain From
Hypothetical Protein Bab23382
pdb|2ROK|A Chain A, Solution Structure Of The Cap-Binding Domain Of Parn
Complexed With The Cap Analog
Length = 100
Score = 28.5 bits (62), Expect = 5.0, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 223 LQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS 282
LQP R + + V P S+ +LF+ FG I S + D F+ P+ AV+
Sbjct: 11 LQPKRDHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVN 67
Query: 283 T 283
T
Sbjct: 68 T 68
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQF 178
+FV L EE+++ +F FG + +++ D + K +GF FI F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVAR-NKNDESRGFAIIVFNTPAEAKKARVEM 95
+ V L P + + F FG + + + NK ++ RGF I F KK +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60
Query: 96 NGHLIG 101
H +G
Sbjct: 61 KYHNVG 66
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 264 KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
+ F+ F + A A+ +NG V P++VTL+
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
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 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,990,396
Number of Sequences: 62578
Number of extensions: 339727
Number of successful extensions: 1584
Number of sequences better than 100.0: 201
Number of HSP's better than 100.0 without gapping: 122
Number of HSP's successfully gapped in prelim test: 79
Number of HSP's that attempted gapping in prelim test: 1044
Number of HSP's gapped (non-prelim): 439
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
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: 52 (24.6 bits)