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= 037126
(192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 69/150 (46%), Gaps = 36/150 (24%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K++ D T ++ GYGFV + D N+ +A+ +NG+ ++ + + A P AS
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSAS------- 87
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP- 119
+A ++V L +S K++ + FS +G I++ +I
Sbjct: 88 -----------------------IRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILL 124
Query: 120 -----VGKGCGFVQFANRKDAEVALQKLQG 144
V +G GF++F R +AE A++ L G
Sbjct: 125 DQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 33.1 bits (74), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ + + F G+I S K+ K G GFV +++ DA+ A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 143 QGTAIGKQTVRLS 155
G + +T+++S
Sbjct: 67 NGLKLQTKTIKVS 79
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 79 GSDGESNN-ATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEV 137
GS GE T++VG L +++ DLR F FGEI ++ + + C F+QFA R+ AEV
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEV 63
Query: 138 ALQK 141
A +K
Sbjct: 64 AAEK 67
>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 = 57.0 bits (136), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 68/150 (45%), Gaps = 36/150 (24%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K++ D T ++ GYGFV + D + +A+ +NG+ ++ + + A P AS
Sbjct: 33 KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS------- 85
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
+A ++V L ++ K+L + FS +G I++ +I V
Sbjct: 86 -----------------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 121 ------GKGCGFVQFANRKDAEVALQKLQG 144
+G GF++F R +AE A++ L G
Sbjct: 123 DQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ ++ R F GEI S K+ K G GFV + + KDAE A+ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDAT 180
G + +T+++S P + R ++ + L + T
Sbjct: 65 NGLRLQTKTIKVSYAR-PSSASIRDANLYVSGLPKTMT 101
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 50/88 (56%), Gaps = 7/88 (7%)
Query: 72 SNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCG 125
S+G+ Q D SN+ +FVG L +++ +D++ F+ FG I ++ KG G
Sbjct: 2 SSGSSGQKKD-TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 126 FVQFANRKDAEVALQKLQGTAIGKQTVR 153
FV F N+ DAE A+Q++ G +G + +R
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIR 88
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
+V+ D T ++KGYGFV F ++ + A+ +M G + R + + AT K
Sbjct: 46 RVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 145
N T++ G + S ++D+ +R+ FS FG+I+ +++ KG FV+F+ + A A+ + GT
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 146 AIGKQTVRLSSG 157
I V+ G
Sbjct: 85 TIEGHVVKCYWG 96
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 12 KGYGFVRFGDENERSRAMIEMNGV 35
KGY FVRF + A++ +NG
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGT 84
>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 = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 43/156 (27%), Positives = 65/156 (41%), Gaps = 32/156 (20%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
+V D T R+ GY +V F + RA+ MN +P+ I + Q+
Sbjct: 41 RVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI---------MWSQRDP 91
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
S +S IF+ LD + +K L + FS FG ILS K+
Sbjct: 92 SLR-------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 132
Query: 121 ----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 152
KG GFV F ++ AE A++K+ G + + V
Sbjct: 133 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 140
A+++VG L DV++ L E FS G ILS+++ G +V F DAE AL
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 141 KLQGTAIGKQTVRL 154
+ I + VR+
Sbjct: 71 TMNFDVIKGKPVRI 84
>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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 43/156 (27%), Positives = 65/156 (41%), Gaps = 32/156 (20%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
+V D T R+ GY +V F + RA+ MN +P+ I + Q+
Sbjct: 46 RVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI---------MWSQRDP 96
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
S +S IF+ LD + +K L + FS FG ILS K+
Sbjct: 97 SLR-------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137
Query: 121 ----GKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 152
KG GFV F ++ AE A++K+ G + + V
Sbjct: 138 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCGFVQFANRKDAEVALQ 140
A+++VG L DV++ L E FS G ILS+++ G +V F DAE AL
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 141 KLQGTAIGKQTVRL 154
+ I + VR+
Sbjct: 76 TMNFDVIKGKPVRI 89
>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 = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 54/105 (51%), Gaps = 9/105 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 144
IF+ LD + +K L + FS FG ILS K+ KG GFV F ++ AE A++K+ G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 145 TAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYVNNRNFFP 189
+ + V + G K+ + L A A++ T V +NF P
Sbjct: 68 MLLNDRKVFV--GRFKSRKEREAE---LGARAKEFTNVYIKNFGP 107
Score = 33.5 bits (75), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSI 44
KV+ D N +KGYGFV F + RA+ +MNG+ + R + +
Sbjct: 36 KVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/150 (23%), Positives = 64/150 (42%), Gaps = 36/150 (24%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K+I D + GYGFV + + RA+ +NG+ S+ + + A P S
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP----------S 82
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
S+ + +A +++ L ++ KD+ + FS FG I++ ++ V
Sbjct: 83 SEVI--------------------KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 121 ------GKGCGFVQFANRKDAEVALQKLQG 144
+G F++F R +AE A+ G
Sbjct: 123 DQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 7/108 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ +LR FS GE+ S K+ K G GFV + KDAE A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYVNNRNFFPK 190
G + +T+++S P ++ + ++ + L + T + + F +
Sbjct: 65 NGLRLQSKTIKVSYAR-PSSEVIKDANLYISGLPRTMTQKDVEDMFSR 111
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYC--SSRPMSIDVA 47
+V++D T ++G F+RF +E A+ NG SS P+++ A
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/150 (23%), Positives = 64/150 (42%), Gaps = 36/150 (24%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K+I D + GYGFV + + RA+ +NG+ S+ + + A P S
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP----------S 82
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
S+ + +A +++ L ++ KD+ + FS FG I++ ++ V
Sbjct: 83 SEVI--------------------KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 121 ------GKGCGFVQFANRKDAEVALQKLQG 144
+G F++F R +AE A+ G
Sbjct: 123 DQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 7/108 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ +LR FS GE+ S K+ K G GFV + KDAE A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYVNNRNFFPK 190
G + +T+++S P ++ + ++ + L + T + + F +
Sbjct: 65 NGLRLQSKTIKVSYAR-PSSEVIKDANLYISGLPRTMTQKDVEDMFSR 111
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYC--SSRPMSIDVA 47
+V++D T ++G F+RF +E A+ NG SS P+++ A
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 42/161 (26%), Positives = 73/161 (45%), Gaps = 35/161 (21%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K++ID N ++ Y FV + ++ + A+ +NG + + I+ A +Q Q S
Sbjct: 31 KIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA-------FQSQQS 82
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILS----- 115
S SD N +FVG L+ +V D+ LR F F LS
Sbjct: 83 S------------------SDDTFN---LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 116 -VKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLS 155
++ +G GFV F ++ DA+ A+ +QG + + +R++
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKL 142
++VG LD +++ L++ F G I ++KI + K FV++ DA +ALQ L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 143 QGTAIGKQTVRLS 155
G I V+++
Sbjct: 62 NGKQIENNIVKIN 74
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
V+ D T ++GYGFV F +++ AM M G + RP+ I+ A
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 72 SNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCG 125
S+G+ Q D SN+ +FVG L +++ +D++ F+ FG+I ++ KG G
Sbjct: 2 SSGSSGQKKD-TSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 126 FVQFANRKDAEVALQKLQGTAIGKQTVR 153
FV F N+ DAE A+ + G +G + +R
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIR 88
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
+V+ D T ++KGYGFV F ++ + A++ M G + R + + AT K
Sbjct: 46 RVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 138
G + +FVG L +D++++D + F +GE V I +G GF++ +R AE+A
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIA 74
Query: 139 LQKLQGTAIGKQTVRL 154
+L GT + + +R+
Sbjct: 75 KAELDGTILKSRPLRI 90
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 52/138 (37%), Gaps = 41/138 (29%)
Query: 9 DRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQALVLAG 68
+R +G+GF+R A E++G SRP+ I AT
Sbjct: 55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-------------------- 94
Query: 69 GPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV-----GKG 123
+ A + V L VS++ L + FS FG + + V G
Sbjct: 95 ----------------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 138
Query: 124 CGFVQFANRKDAEVALQK 141
GFV+FA + A AL++
Sbjct: 139 KGFVEFAAKPPARKALER 156
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 144
IF+ LD + +K L + FS FG ILS K+ KG GFV F ++ AE A++K+ G
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 145 TAIGKQTV 152
+ + V
Sbjct: 74 MLLNDRKV 81
Score = 33.5 bits (75), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSI 44
KV+ D N +KGYGFV F + RA+ +MNG+ + R + +
Sbjct: 42 KVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 11/103 (10%)
Query: 50 KKASGYQQQCSSQALVLAGGPASNGTRVQGSDGESNNAT----IFVGALDSDVSDKDLRE 105
+KA+ Q VL G + +++ +D E NNA +F+G + ++ D+R
Sbjct: 57 RKAALEAQNALHNMKVLPG--MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 114
Query: 106 PFSHFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 143
FS FG+I +I G +GC FV F R A+ A++ +
Sbjct: 115 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 135
S+ +FVG + S+KDLRE F +G + + + P KGC FV F RK A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 136 EVALQKLQGTAIGKQTVRLSSGHNP 160
A L + L H+P
Sbjct: 61 LEAQNALHNMKV------LPGMHHP 79
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 11/103 (10%)
Query: 50 KKASGYQQQCSSQALVLAGGPASNGTRVQGSDGESNNAT----IFVGALDSDVSDKDLRE 105
+KA+ Q VL G + +++ +D E NNA +F+G + ++ D+R
Sbjct: 69 RKAALEAQNALHNMKVLPG--MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 126
Query: 106 PFSHFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 143
FS FG+I +I G +GC FV F R A+ A++ +
Sbjct: 127 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 40/96 (41%), Gaps = 14/96 (14%)
Query: 73 NGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI--------PVGKGC 124
NGT + + +FVG + S+KDLRE F +G + + + P KGC
Sbjct: 2 NGTLDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC 61
Query: 125 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSSGHNP 160
FV F RK A A L + L H+P
Sbjct: 62 CFVTFYTRKAALEAQNALHNMKV------LPGMHHP 91
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 2/53 (3%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNG-VYCSSRPMSIDVATPKKA 52
KV++D T +KGYGFV+F DE E+ RA+ E G V S+P+ + VA PK +
Sbjct: 41 KVVLD-QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKAS 92
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 79 GSDGESN-NATIFVGALDSDVSDKDLRE------PFSHFGEILSVKIPVGKGCGFVQFAN 131
GS G S ++FVG L DV D L E P G+++ + V KG GFV+F +
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 132 RKDAEVALQKLQG-TAIGKQTVRLS 155
+ + AL + QG +G + VRLS
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRLS 85
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 80 SDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDA 135
++ +S + V + D DLR+ F FG+IL V+I KG GFV F N DA
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82
Query: 136 EVALQKLQGTAIGKQTVRLSS 156
+ A +KL GT + + + +++
Sbjct: 83 DRAREKLHGTVVEGRKIEVNN 103
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
V I N +KG+GFV F + + RA +++G R + ++ AT +
Sbjct: 59 VEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 100 DKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAI 147
D DLR+ F FG+IL V+I KG GFV F N DA+ A +KL GT +
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV 80
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 11 TKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
+KG+GFV F + + RA +++G R + ++ AT +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 93
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 80 SDGESNNAT----IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG-----KGCGFVQFA 130
+D E NNA +F+G + ++ D+R FS FG+I +I G +GC FV F
Sbjct: 85 ADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFT 144
Query: 131 NRKDAEVALQ 140
R A+ A++
Sbjct: 145 TRAXAQTAIK 154
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 90 FVGALDSDVSDKDLREPFSHFGEILSVKI--------PVGKGCGFVQFANRKDAEVALQK 141
FVG + S+KDLRE F +G + + + P KGC FV F RK A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 142 LQGTAIGKQTVRLSSGHNP 160
L + L H+P
Sbjct: 67 LHNXKV------LPGXHHP 79
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 10/86 (11%)
Query: 79 GSDGESNNAT----IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQ 128
GS G S AT ++VG L +V DK L F FG+I ++IP+ +G FV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 129 FANRKDAEVALQKLQGTAIGKQTVRL 154
F +DA A+ + + + +T+R+
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRV 86
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 27/51 (52%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
++ +D T++ +G+ FV F + + A+ MN R + +++A P +
Sbjct: 43 QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 93
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 65/151 (43%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 38 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSRE--- 86
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
SQ P ++ T IFVG + D + LR+ F +G+I ++I
Sbjct: 87 DSQR------PGAHLT----------VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 130
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 131 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 161
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 64/151 (42%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 45 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSRED-- 94
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
+ P ++ T IFVG + D + LR+ F +G+I ++I
Sbjct: 95 -------SQRPGAHLT----------VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 138 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 65/151 (43%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 43 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSRE--- 91
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
SQ P ++ T IFVG + D + LR+ F +G+I ++I
Sbjct: 92 DSQR------PGAHLT----------VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 135
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 136 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 166
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/151 (25%), Positives = 61/151 (40%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 46 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSREDSQ 97
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
A + IFVG + D + LR+ F +G+I ++I
Sbjct: 98 RPGAHLTV-------------------KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 138
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 139 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 169
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 64/151 (42%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 44 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSRED-- 93
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
+ P ++ T IFVG + D + LR+ F +G+I ++I
Sbjct: 94 -------SQRPGAHLT----------VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 136
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 137 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 167
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 64/151 (42%), Gaps = 36/151 (23%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D NT R++G+GFV + E AM ++RP +D V PK+A +
Sbjct: 45 VMRDPNTKRSRGFGFVTYATVEEVDAAM--------NARPHKVDGRVVEPKRAVSRED-- 94
Query: 60 SSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP 119
+ P ++ T IFVG + D + LR+ F +G+I ++I
Sbjct: 95 -------SQRPGAHLT----------VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Query: 120 VGKGCG------FVQFANRKDAE-VALQKLQ 143
+G G FV F + + + +QK
Sbjct: 138 TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 8/82 (9%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVAL 139
+AT++VG LD VS+ L E F G +++ +P + G GFV+F + +DA+ A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 140 QKLQGTAIGKQTVRL--SSGHN 159
+ + + + +R+ +S HN
Sbjct: 75 KIMDMIKLYGKPIRVNKASAHN 96
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
D T + +GYGFV F E + A+ M+ + +P+ ++ KAS + + S
Sbjct: 50 DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN-----KASAHNKNLS 100
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
++++DS T R+KGYGF+ F D +A+ ++NG + RPM + T +
Sbjct: 57 QLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDA 135
G + ++VG+L ++++ LR F FG I S+++ + KG GF+ F++ + A
Sbjct: 22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 136 EVALQKLQGTAIGKQTVRLSSGH 158
+ AL++L G + + +++ GH
Sbjct: 82 KKALEQLNGFELAGRPMKV--GH 102
>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 = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 135
S+ +FVG + S+KDLRE F +G + + + P KGC FV F RK A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 136 EVALQKLQGTAIGKQTVRLSSGHNP 160
A L + L H+P
Sbjct: 61 LEAQNALHNMKV------LPGMHHP 79
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDA 135
G + ++VG L +V DK L F FG+I ++IP+ +G FV+F +DA
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 136 EVALQKLQGTAIGKQTVRLS 155
A+ + + + +T+R++
Sbjct: 61 AAAIDNMNESELFGRTIRVN 80
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
++ DS+T R+KGYGF+ F D RA+ ++NG + RPM + T + G
Sbjct: 37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGG 89
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 13/92 (14%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDA 135
G S ++ ++VG+L ++++ LR F FG+I ++ + KG GF+ F++ + A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 136 EVALQKLQG-------TAIGKQTVRLSSGHNP 160
AL++L G +G T RL G P
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDGGSGP 92
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 81 DGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 140
+GE +N +FV DV + +L E F FG + VKI G FV+F + A A++
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIE 83
Query: 141 KLQGTAIGKQTVRLSSGHNPGNKQWR 166
++ G + Q + + P K++R
Sbjct: 84 EVHGKSFANQPLEVVYSKLPA-KRYR 108
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 143
+FVG L+ S+ D+R F FG I I G KGC FV++++ +A+ A+ L
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 144 GT 145
G+
Sbjct: 78 GS 79
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCGFVQFANRKDAEV 137
S+ +FVG L D +++ L + FS +G+I V + +G GFV F N DA+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 138 ALQKLQGTAIGKQTVRL 154
A+ + G ++ + +R+
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
V+ D T R++G+GFV F + ++ AM+ MNG R + +D A
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILS------VKIPVGKGCGFVQFANRKDAEVALQKL 142
+FVG L+ +V D+ LR F F LS ++ +G GFV F ++ DA+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 143 QGTAIGKQTVRLS 155
QG + + +R++
Sbjct: 64 QGQDLNGRPLRIN 76
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
V+ D T ++GYGFV F +++ AM M G + RP+ I+ A
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 10/87 (11%)
Query: 74 GTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI------PVGKGCGFV 127
G +++G +G +F+ L + +D DL F FG ++S K+ + K GFV
Sbjct: 32 GKQIEGPEG----CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFV 87
Query: 128 QFANRKDAEVALQKLQGTAIGKQTVRL 154
F N A+VA++ + G +G + +++
Sbjct: 88 SFDNPDSAQVAIKAMNGFQVGTKRLKV 114
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDV 46
KV ID T +K +GFV F + + A+ MNG ++ + + +
Sbjct: 71 KVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVAL 139
+A ++V L +S K++ + FS +G I++ +I V +G GF++F R +AE A+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 140 QKLQG 144
+ L G
Sbjct: 61 KGLNG 65
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNG--VYCSSRPMSIDVA 47
++++D T ++G GF+RF E A+ +NG ++ P+++ A
Sbjct: 32 RILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFA 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
++VG L +V DK L F FG+I ++IP+ +G FV+F +DA A+
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 142 LQGTAIGKQTVRLS 155
+ + + +T+R++
Sbjct: 125 MNESELFGRTIRVN 138
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ +LR FS GE+ S K+ K G GFV + KDAE A+ L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 143 QGTAIGKQTVRLS 155
G + +T+++S
Sbjct: 67 NGLRLQSKTIKVS 79
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATP 49
K+I D + GYGFV + + RA+ +NG+ S+ + + A P
Sbjct: 35 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 83
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
++VG L +V DK L F FG+I ++IP+ +G FV+F +DA A+
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 142 LQGTAIGKQTVRLS 155
+ + + +T+R++
Sbjct: 69 MNESELFGRTIRVN 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
++VG L +V DK L F FG+I ++IP+ +G FV+F +DA A+
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 142 LQGTAIGKQTVRLS 155
+ + + +T+R++
Sbjct: 64 MNESELFGRTIRVN 77
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 10/87 (11%)
Query: 74 GTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGC------GFV 127
G++ +G +G A +F+ L + D+DL + F FG ++S K+ + K GFV
Sbjct: 17 GSQKEGPEG----ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 72
Query: 128 QFANRKDAEVALQKLQGTAIGKQTVRL 154
+ N A+ A+Q + G IG + +++
Sbjct: 73 SYDNPVSAQAAIQSMNGFQIGMKRLKV 99
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKAS 53
KV ID T+ +K +GFV + + A+ MNG + + + + K S
Sbjct: 56 KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 108
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 76 RVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDA 135
R G + + +FVG L D++++++R+ F +G+ V I KG GF++ R A
Sbjct: 12 RKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLA 71
Query: 136 EVALQKLQGTAI-GKQ 150
E+A +L + GKQ
Sbjct: 72 EIAKVELDNMPLRGKQ 87
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 19/89 (21%)
Query: 86 NATIFVGALDSDVSDKDL---------REPFSHFGEILSVKIPVGKGCGFVQFANRKDAE 136
N T++VG +D ++ K L R FS G+I ++ K CGFV+F + +AE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 137 VALQKLQGTAIGKQTVRLSSGHNPGNKQW 165
A + A+ QT+ L P +K+W
Sbjct: 196 FAKE-----AMSNQTLLL-----PSDKEW 214
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 19/89 (21%)
Query: 86 NATIFVGALDSDVSDKDL---------REPFSHFGEILSVKIPVGKGCGFVQFANRKDAE 136
N T++VG +D ++ K L R FS G+I ++ K CGFV+F + +AE
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 137 VALQKLQGTAIGKQTVRLSSGHNPGNKQW 165
A + A+ QT+ L P +K+W
Sbjct: 194 FAKE-----AMSNQTLLL-----PSDKEW 212
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 144
++V LD + D+ LR+ FS FG I S K+ + KG GFV F++ ++A A+ ++ G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 145 TAIGKQTVRLSSGHNPGNKQ 164
+ + + ++ +Q
Sbjct: 78 RIVATKPLYVALAQRKEERQ 97
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 10 RTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
R+KG+GFV F E ++A+ EMNG +++P+ + +A K+
Sbjct: 53 RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKE 94
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L + + +LR FS GE+ S K+ K G GFV + KDAE A+ L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 143 QGTAIGKQTVRLS 155
G + +T+++S
Sbjct: 82 NGLRLQSKTIKVS 94
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATP 49
K+I D + GYGFV + + RA+ +NG+ S+ + + A P
Sbjct: 50 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 98
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 143
+ + +FVG L D++++++R+ F +G+ V I KG GF++ R AE+A +L
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 144 GTAI-GKQ 150
+ GKQ
Sbjct: 73 NMPLRGKQ 80
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 66/162 (40%), Gaps = 25/162 (15%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQAL 64
DS T + KG+ FV + A+ +MN V R +I V P Q A
Sbjct: 63 DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR--NIKVGRPSNIGQAQPIIDQLA- 119
Query: 65 VLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI---PVG 121
+ + N I+V ++ D+SD D++ F FG+I S + P
Sbjct: 120 ---------------EEARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTT 163
Query: 122 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSSGHNP 160
KG GF+++ + ++ A+ + +G Q +R+ P
Sbjct: 164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 51/100 (51%), Gaps = 6/100 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
++VG++ ++ + +R+ F+ FG I S+ + KG FV++ + A++AL+++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYV 182
+G + +++ N G Q D + A A + YV
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 130
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 66/162 (40%), Gaps = 25/162 (15%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQAL 64
DS T + KG+ FV + A+ +MN V R +I V P Q A
Sbjct: 48 DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR--NIKVGRPSNIGQAQPIIDQLA- 104
Query: 65 VLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI---PVG 121
+ + N I+V ++ D+SD D++ F FG+I S + P
Sbjct: 105 ---------------EEARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTT 148
Query: 122 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSSGHNP 160
KG GF+++ + ++ A+ + +G Q +R+ P
Sbjct: 149 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 190
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 51/100 (51%), Gaps = 6/100 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
++VG++ ++ + +R+ F+ FG I S+ + KG FV++ + A++AL+++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYV 182
+G + +++ N G Q D + A A + YV
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 115
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 48/90 (53%), Gaps = 8/90 (8%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK----GCGF--VQFANRKDAEVAL 139
+ T++VG L +++ + E FS G+I + + + K CGF V++ +R DAE A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 140 QKLQGTAIGKQTVR--LSSGHNPGNKQWRG 167
+ + GT + + +R +G G + RG
Sbjct: 99 RYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQK 141
+ +G L +V+ + E FS +G+I + +PV KG +V+F N +AE AL+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 142 LQGTAIGKQTV 152
+ G I Q +
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 9/92 (9%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKD 134
GS G S IFV L D + K L++ F+ G +L I + KGCG V+F + +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60
Query: 135 AEVALQ-----KLQGTAIGKQTVRLSSGHNPG 161
AE A + KL G I + R +SG + G
Sbjct: 61 AERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
I ++KG G V+F RA MNG+ S R IDV + ASG
Sbjct: 40 IKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGR--EIDVRIDRNASG 88
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV-------GKGCGFVQFANRKD 134
G S ++ IF+G LD ++ +K L + FS FG IL + KG F+ FA+
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 135 AEVALQKLQGTAIGKQTVRLS 155
++ A++ + G + + + +S
Sbjct: 61 SDAAIEAMNGQYLCNRPITVS 81
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
K++ D +T +KGY F+ F + A+ MNG Y +RP+++ A K + G
Sbjct: 37 KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG-----KGCGFVQFANRKDAEVALQKLQ 143
+FVG L +D+D+R+ F FG I + G KGC FV+F +A+ A+ L
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 16/92 (17%)
Query: 81 DGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP-----VGKGCGFVQFANRKDA 135
+G+ T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 136 EVALQ--------KLQ-GTAIGKQTVRLSSGH 158
+ ++ KL+ G AI KQ LS+ H
Sbjct: 64 QKIVESQINFHGKKLKLGPAIRKQN--LSTYH 93
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 89 IFVGALDSDVSDKD---LREPFSHFGEILSVKIPVG--KGCGFVQFANRKDAEVALQKLQ 143
+FVG L+ S++D L +PF E ++ P G KGC FV+F++ +A+ A+ L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 144 GT 145
G+
Sbjct: 78 GS 79
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 5/73 (6%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK---GCGF--VQFANRKDAEVALQ 140
+ T++VG L +++ + E FS G+I + + + K CGF V++ +R DAE A++
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 141 KLQGTAIGKQTVR 153
+ GT + + +R
Sbjct: 78 YINGTRLDDRIIR 90
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 80 SDGESNNATIFVGALDSDVSDK-DLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 138
+D +S N+ +F+G L++ + K D+ FS +G + V KG FVQ++N + A A
Sbjct: 21 NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS--VHKGYAFVQYSNERHARAA 78
Query: 139 LQKLQGTAIGKQTVRLSSGHNP 160
+ G + QT+ ++ P
Sbjct: 79 VLGENGRVLAGQTLDINMAGEP 100
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 77 VQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFA 130
+ S E + FVG L D S KDL++ F+ FGE++ I +G GF+ F
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 131 NRKDAEVAL----QKLQGTAI 147
+ E L +L G I
Sbjct: 62 DAASVEKVLDQKEHRLDGRVI 82
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG-KGCGFVQFANRKDAE 136
G S ++ +FVG D+++ +LRE FS +G+++ V IP + FV FA+ + A+
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 81 DGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP-----VGKGCGFVQFANRKDA 135
+G+ T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 136 E 136
+
Sbjct: 64 Q 64
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 11/75 (14%)
Query: 79 GSDGE----SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP-------VGKGCGFV 127
GS G+ + I V + + +++RE FS FGE+ +V++P +G GFV
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 128 QFANRKDAEVALQKL 142
F ++DA+ A L
Sbjct: 64 DFITKQDAKKAFNAL 78
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIP-----VGKGCGFVQFANRKDAE 136
T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 65
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 83 ESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKL 142
E +N +FV DV + +L E F FG + VKI G FV+F + A A++++
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEV 58
Query: 143 QGTAIGKQTVRL 154
G + Q + +
Sbjct: 59 HGKSFANQPLEV 70
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 139
N + V L +++DLRE FS +G I V I +G FV F N DA+ A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 140 QKLQGTAIGKQTVRLS 155
++ G + + +R+S
Sbjct: 75 ERANGMELDGRRIRVS 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 31/53 (58%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKAS 53
K++ D T ++ GYGFV + D N+ +A+ +NG+ ++ + + A P AS
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSAS 87
Score = 33.9 bits (76), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 142
+ V L +++ + + F G+I S K+ K G GFV +++ DA+ A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 143 QGTAIGKQTVRLS 155
G + +T+++S
Sbjct: 67 NGLKLQTKTIKVS 79
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 58/148 (39%), Gaps = 36/148 (24%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
+++ D T + GY FV F E + RA+ +NG+ ++ + + A P
Sbjct: 34 RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP----------- 82
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
GG + T ++V L ++D L F +G I+ I
Sbjct: 83 -------GGESIKDT------------NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 123
Query: 121 GK------GCGFVQFANRKDAEVALQKL 142
K G FV++ R++A+ A+ L
Sbjct: 124 DKLTGRPRGVAFVRYNKREEAQEAISAL 151
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 65/168 (38%), Gaps = 40/168 (23%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
++ D T + GY FV F E + RA+ +NG+ ++ + + A P
Sbjct: 45 RIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARP----------- 93
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
GG + T ++V L ++D L F +G I+ I
Sbjct: 94 -------GGESIKDT------------NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 134
Query: 121 GK------GCGFVQFANRKDAEVALQKLQGTAI--GKQ--TVRLSSGH 158
K G FV++ R++A+ A+ L G Q +VRL+ H
Sbjct: 135 DKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAEEH 182
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
I+VG L + + ++E FS FG++ +VK+ KG GFV+ +E A+ KL
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 143 QGTAIGKQTVRLSSGHNP 160
T +T+R++ NP
Sbjct: 63 DNTDFMGRTIRVTEA-NP 79
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKA 52
K+I D T + KG+GFV +E+ S A+ +++ R + + A PKK+
Sbjct: 32 KLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKS 82
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQGTAI 147
++VG L + +L FS++G + +V I G FV+F + +DAE A++ L G I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 148 GKQTVR--LSSG 157
VR LS+G
Sbjct: 63 CGSRVRVELSTG 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 85 NNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVA 138
+NATI V L D + DL+E F FG I + + KG F+ F R+DA A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 139 LQKLQG 144
+ + G
Sbjct: 74 IAGVSG 79
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV----GKGCGFVQFANRKDAEV 137
G S ++ IFV L D + K L++ F+ G +L I + KGCG V+F + + AE
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 138 ALQKLQGTAIGKQTV 152
A + + G + + +
Sbjct: 61 ACRMMNGMKLSGREI 75
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
I ++KG G V+F RA MNG+ S R IDV + ASG
Sbjct: 37 IKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGR--EIDVRIDRNASG 85
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 46/102 (45%), Gaps = 7/102 (6%)
Query: 60 SSQALVLAGGPASNGTRVQGSDGESN-NATIFVGALDSDVSDKDLREPFSHFGEILSVKI 118
S A + G G+R G+ + N + V L +++DLRE FS +G I V I
Sbjct: 19 SHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78
Query: 119 PV------GKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 154
+G FV F N DA+ A ++ G + + +R+
Sbjct: 79 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 26/50 (52%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
++ D + R++G+ FV F + ++ A NG+ R + +D + K+
Sbjct: 78 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
++FVG + + +++ L++ FS G ++S ++ KG GF ++ +++ A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 142 LQGTAIGKQTVRLSSGHNPGNKQ 164
L G + +R+ + + NK+
Sbjct: 70 LNGREFSGRALRVDNAASEKNKE 92
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
+++ D T + KGYGF + D+ AM +NG S R + +D A +K
Sbjct: 39 RLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK 89
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRK 133
G +G A + V LD VSD D++E F+ FG + + + G V F R
Sbjct: 81 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 140
Query: 134 DAEVALQKLQGTAI 147
DA A+++ +G +
Sbjct: 141 DALKAMKQYKGVPL 154
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 89 IFVGALDSDVSDKDL-REPFSHFGEILSVKIPVGKG-------CGFVQFANRKDAEVALQ 140
I + L +++ D++L RE F FG I + IP G+ C F F N+ AE ALQ
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 139
N + V L +++DLRE FS +G I V I +G FV F N DA+ A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 140 QKLQGTAIGKQTVRL 154
++ G + + +R+
Sbjct: 75 ERANGMELDGRRIRV 89
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 26/50 (52%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
++ D + R++G+ FV F + ++ A NG+ R + +D + K+
Sbjct: 47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 96
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKG---CGFVQFANRKDAEVALQ 140
+N+ I+VG L D+ KD+ + F +G I + + +G FV+F + +DAE A+
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 79
Query: 141 KLQGTAIGKQTVRLS 155
G +R+
Sbjct: 80 GRDGYDYDGYRLRVE 94
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
IFVG L D ++ +RE F FGE+ S+++P+ +G F+ F + + ++K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 141
IFVG L D ++ +RE F FGE+ S+++P+ +G F+ F + + ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 64/162 (39%), Gaps = 25/162 (15%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQAL 64
DS T + KG+ FV + A+ + N V R +I V P Q A
Sbjct: 47 DSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGR--NIKVGRPSNIGQAQPIIDQLA- 103
Query: 65 VLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKI---PVG 121
+ + N I+V ++ D+SD D++ F FG+I S + P
Sbjct: 104 ---------------EEARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTT 147
Query: 122 ---KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSSGHNP 160
KG GF+++ + ++ A+ +G Q +R+ P
Sbjct: 148 GKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTP 189
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 49/100 (49%), Gaps = 6/100 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
++VG++ ++ + +R+ F+ FG I S+ KG FV++ + A++AL++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 143 QGTAIGKQTVRLSSGHNPGNKQWRGDHINLIALAQDATYV 182
+G + +++ N G Q D + A A + YV
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 114
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRK 133
G +G A + V LD VSD D++E F+ FG + + + G V F R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 87
Query: 134 DAEVALQKLQGTAI 147
DA A+++ +G +
Sbjct: 88 DALKAMKQYKGVPL 101
>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 = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL--- 139
+F+G L D + KDL++ FS FGE++ + + +G GFV F + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 140 -QKLQGTAI 147
KL G I
Sbjct: 62 EHKLNGKVI 70
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 139
N + V L +++DLRE FS +G I V I +G FV F N DA+ A
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 140 QKLQGTAIGKQTVRL 154
++ G + + +R+
Sbjct: 72 ERANGMELDGRRIRV 86
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 26/50 (52%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
++ D + R++G+ FV F + ++ A NG+ R + +D + K+
Sbjct: 44 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 93
>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 = 0.008, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRK 133
G +G A + V LD VSD D++E F+ FG + + + G V F R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 87
Query: 134 DAEVALQKLQGTAI 147
DA A+++ +G +
Sbjct: 88 DALKAMKQYKGVPL 101
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 54/135 (40%), Gaps = 38/135 (28%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K++ D T R++G+GF+ F +P S+D +
Sbjct: 34 KIMKDPATGRSRGFGFLSF-------------------EKPSSVD-----------EVVK 63
Query: 61 SQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV 120
+Q ++ G + R D + IFVG + DV K+ E FS +G I+ ++ +
Sbjct: 64 TQHIL--DGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121
Query: 121 GK------GCGFVQF 129
K G GFV +
Sbjct: 122 DKDTGQSRGFGFVTY 136
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 85 NNATIFVGALDSDVSDKDLREPFSHFGEILSVKI---PV---GKGCGFVQF 129
+ +F+G L+ D ++ +LRE F +G + +KI P +G GF+ F
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV ++ + + +++E F +GEI ++ + + + GF V++ K A A + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 143 QGTAIGKQTVRL 154
G I QT+++
Sbjct: 89 NGAEIMGQTIQV 100
>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 = 0.012, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV ++ + + +++E F +GEI ++ + + + GF V++ K A A + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 143 QGTAIGKQTVRL 154
G I QT+++
Sbjct: 135 NGAEIMGQTIQV 146
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 79 GSDGESNNATI--FVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFA 130
GS G ++ I F+G + ++ +KDL+ F FG+I + + + KGC F+ +
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 131 NRKDA 135
R+ A
Sbjct: 64 ERESA 68
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 142
+FVG L +++ + F+ FG I ++ KG GFV F N+ DAE A+Q++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 143 QGTAIGKQTVR 153
G +G + +R
Sbjct: 69 GGQWLGGRQIR 79
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
+V+ D T ++KGYGFV F ++ + A+ +M G + R + + AT K
Sbjct: 37 RVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 97 DVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 154
D++ LR FS FG I+ + + + C FV + + A+ A+ +L GT + ++V+L
Sbjct: 24 DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV--ESVQL 79
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 80 SDGESNNATIFVGALDSDVSDKDLREPFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVA 138
S E + T+ L V+ +L+E F EI L K KG +++F DAE
Sbjct: 87 SKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKT 146
Query: 139 LQKLQGTAIGKQTVRLSSGHNP 160
++ QGT I +++ L P
Sbjct: 147 FEEKQGTEIDGRSISLYYTGEP 168
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 78 QGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEI---LSVKIPVGK---GCGFVQFAN 131
+GS S+ +F+G L + + LRE F FGE+ L ++ P+ K G GFV F +
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Query: 132 RKDAEVAL 139
+ + L
Sbjct: 77 QAGVDKVL 84
>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 = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 143 QGTAIGKQTVRL 154
G + Q + +
Sbjct: 86 NGQDLMGQPISV 97
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 57 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>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 = 0.019, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 143 QGTAIGKQTVRL 154
G + Q + +
Sbjct: 85 NGQDLMGQPISV 96
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 56 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 97
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 103 LREPFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 154
LR F +G + V IP +G FV+F +++DAE A+ + G + + +R+
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
D T ++G+ FVRF D+ + AM M+G R + + +A
Sbjct: 105 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 97 DVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 147
D++ LR FS FG I+ + + + C FV + + A+ A+ +L GT +
Sbjct: 48 DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 98
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 138
GS G + +FV L + V+++ L + FS FG++ VK K F+ F R A A
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKA 61
Query: 139 LQKLQGTAIGKQTVRLSSGHNPGNKQ 164
++++ G + + + + P K+
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKR 87
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 10 RTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQALVLAGG 69
+ K Y F+ F + + +AM EMNG + I A P +++ QA A G
Sbjct: 43 KLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQA---ASG 99
Query: 70 PAS 72
P+S
Sbjct: 100 PSS 102
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 11/85 (12%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK---------GCGFVQFANR 132
G S ++ +F+ L+ +++ L+ FS G I S I K G GFV++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 133 KDAEVALQKLQGTAI--GKQTVRLS 155
+ A+ AL++LQG + K VR+S
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRIS 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 143 QGTAIGKQTV 152
G + Q +
Sbjct: 70 NGQDLMGQPI 79
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + KG V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 143 QGTAIGKQTV 152
G + Q +
Sbjct: 70 NGQDLMGQPI 79
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 143 QGTAIGKQTV 152
G + Q +
Sbjct: 70 NGQDLMGQPI 79
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 41 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 142
+FV + + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 143 QGTAIGKQTV 152
G + Q +
Sbjct: 72 NGQDLMGQPI 81
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
+D T KGY V + E AM +NG +P+S+D
Sbjct: 43 LDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 10/90 (11%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 142
+ V + + V + LR+ F +G I SVKI +G GFV+F + A+ A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 143 QGTAIGKQTVRL---SSGHN-PGNKQWRGD 168
G I + +++ +SGH PG GD
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGAVGD 134
Score = 33.9 bits (76), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQ 57
K++ D T +++GYGFV+F + +A+ +NG ++ + + +A ASG+Q+
Sbjct: 73 KIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA----ASGHQR 125
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 35.0 bits (79), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 32/70 (45%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 147
T ++G + ++ DL F +FG IL K KGC F+++ + A V + L
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPF 88
Query: 148 GKQTVRLSSG 157
+ +R G
Sbjct: 89 QGRNLRTGWG 98
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 34.7 bits (78), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 89 IFVGALDSDVSDKDLREPFSHFG---EILSVKIPVGK--GCGFVQFANRKDAEVALQKLQ 143
+F+G L+ + ++K L+ F G E+L +K K G F+ F N DA+ A + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 144 GTAIGKQTVRLSSGHNP 160
G ++ + +++ P
Sbjct: 70 GKSLHGKAIKVEQAKKP 86
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
++I T +++G+ F+ F + + A +MNG + + ++ A
Sbjct: 38 LLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 34.7 bits (78), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 79 GSDGESNNA-TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEV 137
GS G S N IFVG + + + ++LR F G + ++ V K FV DA+
Sbjct: 1 GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKA 58
Query: 138 ALQKLQGTAI 147
A+ +L G +
Sbjct: 59 AIAQLNGKEV 68
>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 = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQ 140
++ V L S LR F +G + V IP +G FV+F +++DAE A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 141 KLQGTAIGKQTVRL 154
+ G + + +R+
Sbjct: 108 AMDGAVLDGRELRV 121
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
D T ++G+ FVRF D+ + AM M+G R + + +A
Sbjct: 82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 34.7 bits (78), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 82 GESNNAT-IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 140
G++N T ++VG L + S L F FG I ++ G ++Q+ + A+ A
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71
Query: 141 KLQGTAIGKQTVRL 154
K++G +G RL
Sbjct: 72 KMRGFPLGGPDRRL 85
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 34.7 bits (78), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQG 144
+ ++VG L ++ + +L F ++G + SV + G FV+F + +DA A+++L G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
Query: 145 TAIGKQTVR--LSSGH 158
+ VR LS+G
Sbjct: 133 RTLCGCRVRVELSNGE 148
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQ 140
IFVG L +D LR+ F FG+I + +G GFV A+R AE A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 11/54 (20%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGV-----------YCSSRPMSI 44
VI D T +++GYGFV D RA + N + Y ++P S+
Sbjct: 49 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSL 102
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 141
T+ V L S LR F +G + V IP +G FV+F +R+DA+ A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 142 LQGTAIGKQTVRL 154
+ G + + +R+
Sbjct: 75 MDGAELDGRELRV 87
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 5 DSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVA 47
+ +T +G+ FVRF D + A M+G R + + VA
Sbjct: 48 EPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 85 NNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFAN 131
+ + V L +++DL+E FS FGE+L V++ KG GFV+F
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.9 bits (76), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 86 NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQG 144
+ ++VG L ++ + +L F ++G + SV + G FV+F + +DA A++ L G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDG 132
Query: 145 TAIGKQTVR--LSSGH 158
+ VR LS+G
Sbjct: 133 RTLCGCRVRVELSNGE 148
>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 = 0.068, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
K++ D T R+KGY F+ F D + A+ +NG SR + ++ SG
Sbjct: 34 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISG 87
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 141
+++G++ D +++ + + S+ G ++++K+ KG F++F + + + A++
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 142 LQGTAIGKQTVRLSSGHN 159
L G +G + ++ N
Sbjct: 65 LNGYQLGSRFLKCGYSSN 82
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.5 bits (75), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG-KGCGFVQFANRKDAE 136
+FVG D++ ++L++ F +GE++ V IP + FV FA+ K A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.5 bits (75), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
K++ D T R+KGY F+ F D + A+ +NG SR + ++ SG
Sbjct: 33 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISG 86
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 141
+++G++ D +++ + + S+ G ++++K+ KG F++F + + + A++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 142 LQGTAIGKQTVRLSSGHN 159
L G +G + ++ N
Sbjct: 64 LNGYQLGSRFLKCGYSSN 81
>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 = 0.096, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSR 40
K++ D T R+KGY F+ F D + A+ +NG SR
Sbjct: 35 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 74
Score = 29.6 bits (65), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 141
+++G++ D +++ + + S+ G ++++K+ KG F++F + + + A++
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 142 LQGTAIGKQTVRLSSGHN 159
L G +G + ++ N
Sbjct: 66 LNGYQLGSRFLKCGYSSN 83
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 82 GESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDA 135
G S ++ +++ L +D+DL + +G+I+S K + KG GFV F + A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 136 EVALQKLQGTAIGKQTVRLS 155
+ A+ L+ + + Q + S
Sbjct: 61 QKAVTALKASGVQAQMAKQS 80
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 23/72 (31%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCS 60
K I+D T++ KGYGFV F + +A+ + KASG Q Q +
Sbjct: 36 KAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL------------------KASGVQAQMA 77
Query: 61 SQALVLAGGPAS 72
Q+ GP+S
Sbjct: 78 KQS-----GPSS 84
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA 146
T+ L ++++ +L+E F EI L + KG +++F + DAE L++ QG
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 147 IGKQTVRL 154
I ++V L
Sbjct: 78 IDGRSVSL 85
>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 = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA 146
T+ L ++++ +L+E F EI L + KG +++F + DAE L++ QG
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 147 IGKQTVRL 154
I ++V L
Sbjct: 161 IDGRSVSL 168
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFAN 131
+FVG LD + + LR FS +GE++ I K G GFV+F +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 8/44 (18%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID 45
++ D T++++G+GFV+F D N G +SRP ++D
Sbjct: 48 IMKDKTTNQSRGFGFVKFKDPN--------CVGTVLASRPHTLD 83
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 141
T+FV ++ D ++ LR F +G I + + K G F+++ + +D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 142 LQGTAIGKQTV 152
G I + V
Sbjct: 164 ADGKKIDGRRV 174
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFGE-ILSVKIP------VGKGCGFVQFANRKDAEVAL 139
A++++G L+ + + + F+ GE ++SVKI + G FV+FA+ AE L
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 140 QKLQGTAIGKQT 151
K+ G + T
Sbjct: 70 HKINGKPLPGAT 81
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEI---LSVKIPVGK---GCGFVQFANRKDAEVAL 139
+F+G L + + LRE F FGE+ L ++ P+ K G GFV F ++ + L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 81 DGESNNATIFVGALDSDVSDKDLREPFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVAL 139
+G A ++VG L D DL+ G + L + + F+ + + A+ A+
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 140 QKLQGTAIGKQTVRLSSGHNPGNK 163
LQG +G T+R++ +K
Sbjct: 74 SCLQGLRLGTDTLRVALARQQRDK 97
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 88 TIFVGALDSDVSDKDLREPF--SHFGEILSVK-IPVGKGCGFVQFANRKDAEVALQKLQG 144
T+FV L D +++ L+E F S I++ + KG GFV F + +DA+ A + ++
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 145 TAIGKQTVRL 154
I V L
Sbjct: 77 GEIDGNKVTL 86
Score = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPK 50
+++ D T +KG+GFV F E + A M +++D A PK
Sbjct: 43 RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 84 SNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRKDAEV 137
+ T+F+ L D ++ L E FG++ V++ + KGC F QF ++ A+
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 138 AL 139
L
Sbjct: 73 CL 74
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFANRKDA 135
+FVG + + ++DL+ F FG I + + + KGC F+ + R A
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
+++ D +TD+ KG+ +V F DE + + + +G R + +D+A +K
Sbjct: 45 RLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIAEGRK 94
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSID--VATPKKASGYQQQC 59
V+ D + R++G+GFV F E AM ++RP SID V PK+A ++
Sbjct: 59 VMRDPASKRSRGFGFVTFSSMAEVDAAM--------AARPHSIDGRVVEPKRAVAREESG 110
Query: 60 S 60
S
Sbjct: 111 S 111
>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 = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 141
T+FV ++ D ++ LR F +G I + + K G F+++ + +D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 142 LQGTAIGKQTV 152
G I + V
Sbjct: 164 ADGKKIDGRRV 174
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 1 KVIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATP 49
+++ D T + GY FV F E + RA+ +NG+ ++ + + A P
Sbjct: 34 RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%)
Query: 79 GSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 138
GS G S +++G L V+ DLR+ F L+ ++ + G FV + ++ A A
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRA 60
Query: 139 LQKLQG 144
++ L G
Sbjct: 61 IETLSG 66
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKLQ 143
+ V LD VSD D++E F+ FG + + + G V F + DA A+++
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 144 GTAI 147
G +
Sbjct: 91 GVPL 94
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 10 RTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVAT 48
R+ G V F + + +AM + NGV RPM+I + T
Sbjct: 67 RSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 105
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 86 NATIFVGALDSDVSDKDLREP----FSHFG---EILSVKIPVGKGCGFVQFANRKDAEVA 138
N TI++ ++ + ++L+ FS FG +I+++K +G FV F + A
Sbjct: 6 NHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNA 65
Query: 139 LQKLQGTAIGKQTVRL 154
L++LQG + +R+
Sbjct: 66 LRQLQGFPFYGKPMRI 81
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 30.4 bits (67), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 101 KDLREPFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 152
+D+R+ S +G + S++IP GCG FV+F + D + A+Q L G + V
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 30.0 bits (66), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 101 KDLREPFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 152
+D+R+ S +G + S++IP GCG FV+F + D + A+Q L G + V
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.0 bits (66), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 80 SDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQFANRK 133
S E + T+F L + + +DL + FS G++ V+I KG +V+F +
Sbjct: 19 SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Query: 134 DAEVAL----QKLQGTAIGKQT 151
+A+ Q+L G I Q
Sbjct: 79 SVPLAIGLTGQRLLGVPIIVQA 100
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFGEILSVKIP------VGKGCGFVQFANRKDAE 136
+T++V L +++ DL FS +G+++ V I KG F+ F ++ A+
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKL 142
IFVG + + + +LRE F FG + V + +G GF+ F + + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 143 QGTAIGKQT 151
+GK+
Sbjct: 73 FHDIMGKKV 81
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 144
+FV L + V+++ L + FS FG++ VK K FV F +R A A+ ++ G
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAMDEMNG 71
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 10 RTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATP--KKASG 54
+ K Y FV F D +AM EMNG + I +A P KK SG
Sbjct: 47 KLKDYAFVHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRSG 93
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCG----FVQFANRKDAEVALQKLQ 143
T++VG L DV++ + + FS G S K+ FV+F +DA AL +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 144 GTAIGKQTVRLSSGHNPGNKQ 164
G I + V+++ P +++
Sbjct: 77 GRKILGKEVKVNWATTPSSQK 97
>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 = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 83 ESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVG------KGCGFVQFANRK--D 134
E + +++VG +D + +DL FS G I + I KG +++FA R D
Sbjct: 33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
Query: 135 AEVALQK 141
A VA+ +
Sbjct: 93 AAVAMDE 99
>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 = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKLQ 143
+ V LD VSD D++E F+ FG + + + G V F + DA A ++
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 144 GTAI 147
G +
Sbjct: 92 GVPL 95
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 4 IDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKK 51
IDS T + KG+ FV F +A E++G R + + +T KK
Sbjct: 42 IDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK 89
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 11/70 (15%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPV------GKGCGFVQF-----ANRKDAEV 137
+FV L S++DL + FS +G + + P+ KG FV F A + AEV
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 138 ALQKLQGTAI 147
Q QG +
Sbjct: 71 DGQVFQGRML 80
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVAT 48
++ DS T +KGY F + D N +A+ +NG+ + + + A+
Sbjct: 33 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 79
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 101 KDLREPFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 152
+D+R+ S +G + S++IP GCG FV+F + D + A Q L G + V
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 101 KDLREPFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 152
+D+R+ S +G + S++IP GCG FV+F + D + A Q L G + V
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 58/136 (42%), Gaps = 16/136 (11%)
Query: 12 KGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQALVL-AGGP 70
K V+ D N+ AM +NG +P+ I ++ + ++ Q L G
Sbjct: 41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNS 100
Query: 71 ASNGTRVQGSDGESN----NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGF 126
+ + GS N +AT+ + + VS++DL+ FS G ++ KG F
Sbjct: 101 PLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV-------KGFKF 153
Query: 127 VQFANRKDAEVALQKL 142
Q KD ++AL ++
Sbjct: 154 FQ----KDRKMALIQM 165
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 10 RTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATP--KKASG 54
+ + Y FV F + + AM +NG P+ + +A P K +SG
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 88 TIFVGALDSDVSDKDLREPFSHFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQKL 142
T+ + L +++ L+E F +K+P KG F++FA+ +DA+ AL
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 143 QGTAIGKQTVRL 154
I + +RL
Sbjct: 74 NKREIEGRAIRL 85
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 87 ATIFVGALDSDVSDKDLREPFSHFG-----EILSVKIPVGKGCGFVQFANRKDAEVALQK 141
+T+FV LD V K L+E FS G +IL K +G G V F +A A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 142 LQGTAI 147
G +
Sbjct: 76 FNGQLL 81
>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 = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 57/132 (43%), Gaps = 16/132 (12%)
Query: 16 FVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQALVL-AGGPASNG 74
V+ D N+ AM +NG +P+ I ++ + ++ Q L G +
Sbjct: 76 LVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHR 135
Query: 75 TRVQGSDGESN----NATIFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFA 130
+ GS N +AT+ + + VS++DL+ FS G ++ KG F Q
Sbjct: 136 FKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV-------KGFKFFQ-- 186
Query: 131 NRKDAEVALQKL 142
KD ++AL ++
Sbjct: 187 --KDRKMALIQM 196
>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 = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVAT 48
++ DS T +KGY F + D N +A+ +NG+ + + + A+
Sbjct: 128 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVAT 48
++ DS T +KGY F + D N +A+ +NG+ + + + A+
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>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 = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 2 VIIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVAT 48
++ DS T +KGY F + D N +A+ +NG+ + + + A+
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 26/156 (16%), Positives = 66/156 (42%), Gaps = 17/156 (10%)
Query: 3 IIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASGYQQQCSSQ 62
++ ++ K + F+ F +E ++AM +G+ + + I ++ YQ
Sbjct: 42 VLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI-----RRPHDYQPLPG-- 93
Query: 63 ALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSDKDLREPFSHFGEILSVKIP--- 119
++ P+ V + + +F+G L + ++D ++E + FG + + +
Sbjct: 94 ---MSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150
Query: 120 ---VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 152
+ KG F ++ + + A+ L G +G + +
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186
>pdb|4G59|A Chain A, Crystal Structure Of The Murine Cytomegalovirus Mhc-I
Homolog M152 With Ligand Rae-1 Gamma
pdb|4G59|B Chain B, Crystal Structure Of The Murine Cytomegalovirus Mhc-I
Homolog M152 With Ligand Rae-1 Gamma
Length = 205
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 25/59 (42%)
Query: 42 MSIDVATPKKASGYQQQCSSQALVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSD 100
++I TP Y+ +C +++ N T G GE+ NAT L V+D
Sbjct: 12 LTIKAPTPADPLWYEAKCLVDEILILHLSNINKTMTSGDPGETANATEVGECLTQPVND 70
>pdb|1Q2B|A Chain A, Cellobiohydrolase Cel7a With Disulphide Bridge Added
Across Exo-Loop By Mutations D241c And D249c
Length = 434
Score = 26.9 bits (58), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 39/99 (39%), Gaps = 17/99 (17%)
Query: 44 IDVATPKKASGYQQQCSSQA---LVLAGGPASNGTRVQGSDGESNNATIFVGALDSDVSD 100
+ A K +GY C SQ L G A V+G + SNNA +G S S+
Sbjct: 160 TNTAGAKYGTGY---CDSQCPRDLKFINGQA----NVEGWEPSSNNANTGIGGHGSCCSE 212
Query: 101 KDLREPFS-------HFGEILSVKIPVGKGCGFVQFANR 132
D+ E S H + +I G GCG NR
Sbjct: 213 MDIWEANSISEALTPHPCTTVGQEICEGCGCGGTYSCNR 251
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 89 IFVGALDSDVSDKDLREPFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 145
+ V L S +DL++ G++ + G G V+F ++D A++KL T
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDNT 74
>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 = 26.6 bits (57), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/52 (19%), Positives = 30/52 (57%)
Query: 3 IIDSNTDRTKGYGFVRFGDENERSRAMIEMNGVYCSSRPMSIDVATPKKASG 54
++ + + KG +V + +E++ S+A+++M+G+ + + ++ +SG
Sbjct: 49 LVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100
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
0.315 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,936,448
Number of Sequences: 62578
Number of extensions: 235782
Number of successful extensions: 778
Number of sequences better than 100.0: 180
Number of HSP's better than 100.0 without gapping: 132
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 456
Number of HSP's gapped (non-prelim): 310
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
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: 49 (23.5 bits)