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= 038175
(155 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 = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 68/138 (49%), Gaps = 23/138 (16%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG---------------SDGKSNNATIF 66
K+ D TG + GYGFV + D N+ +A+ +NG S +A ++
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIRDANLY 94
Query: 67 VGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQG 120
V L +S K++ +LFS +G I++ +I V +G GF++F R +AE A++ L G
Sbjct: 95 VSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Query: 121 TAI--GKQTVRLSWGHNP 136
+ + + + +NP
Sbjct: 155 QKPLGAAEPITVKFANNP 172
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 10/92 (10%)
Query: 57 DGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKD 110
D K+N + V L N++ + + LF G+I S K+ K G GFV +++ D
Sbjct: 2 DSKTN---LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPND 58
Query: 111 AEVALQKLQGTAIGKQTVRLSWGHNPGNKQWR 142
A+ A+ L G + +T+++S+ P + R
Sbjct: 59 ADKAINTLNGLKLQTKTIKVSYAR-PSSASIR 89
Score = 29.6 bits (65), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+++ +D TG ++G GF+RF E A+ +NG
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
>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 = 63.5 bits (153), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 47/149 (31%), Positives = 68/149 (45%), Gaps = 27/149 (18%)
Query: 7 SDITNSILQETFSRA------KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMN------ 54
D+T ++L E FS A +V D T + GY +V F + RA+ MN
Sbjct: 25 PDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG 84
Query: 55 -----------GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKG 99
S KS IF+ LD ++ +K L + FS FG ILS K+ KG
Sbjct: 85 KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG 144
Query: 100 CGFVQFANRKDAEVALQKLQGTAIGKQTV 128
GFV F ++ AE A++K+ G + + V
Sbjct: 145 YGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 6/88 (6%)
Query: 53 MNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI------PVGKGCGFVQFA 106
MN S A+++VG L +V++ L E FS G ILS+++ G +V F
Sbjct: 6 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 65
Query: 107 NRKDAEVALQKLQGTAIGKQTVRLSWGH 134
DAE AL + I + VR+ W
Sbjct: 66 QPADAERALDTMNFDVIKGKPVRIMWSQ 93
>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 = 63.2 bits (152), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 47/149 (31%), Positives = 68/149 (45%), Gaps = 27/149 (18%)
Query: 7 SDITNSILQETFSRA------KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMN------ 54
D+T ++L E FS A +V D T + GY +V F + RA+ MN
Sbjct: 20 PDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG 79
Query: 55 -----------GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKG 99
S KS IF+ LD ++ +K L + FS FG ILS K+ KG
Sbjct: 80 KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG 139
Query: 100 CGFVQFANRKDAEVALQKLQGTAIGKQTV 128
GFV F ++ AE A++K+ G + + V
Sbjct: 140 YGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 6/88 (6%)
Query: 53 MNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI------PVGKGCGFVQFA 106
MN S A+++VG L +V++ L E FS G ILS+++ G +V F
Sbjct: 1 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
Query: 107 NRKDAEVALQKLQGTAIGKQTVRLSWGH 134
DAE AL + I + VR+ W
Sbjct: 61 QPADAERALDTMNFDVIKGKPVRIMWSQ 88
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 60/120 (50%), Gaps = 21/120 (17%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG---------------SDGKSNNATIF 66
K+ D TG + GYGFV + D + +A+ +NG S +A ++
Sbjct: 33 KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLY 92
Query: 67 VGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQG 120
V L ++ K+L +LFS +G I++ +I V +G GF++F R +AE A++ L G
Sbjct: 93 VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 118
+ V L N++ ++ R LF GEI S K+ K G GFV + + KDAE A+ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 119 QGTAIGKQTVRLSWGHNPGNKQWR 142
G + +T+++S+ P + R
Sbjct: 65 NGLRLQTKTIKVSYAR-PSSASIR 87
Score = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 9 ITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+T L++ FS+ +++ +D TG ++G GF+RF E A+ +NG
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 42/154 (27%), Positives = 70/154 (45%), Gaps = 30/154 (19%)
Query: 9 ITNSILQETF------SRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNN 62
IT IL++ F + K+ ID N + Y FV + ++ + A+ +NG ++N
Sbjct: 12 ITEDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQTLNGKQIENNI 70
Query: 63 ATI-----------------FVGALDSNVSDKDLRELFSHFGEILS------VKIPVGKG 99
I FVG L+ NV D+ LR F F LS ++ +G
Sbjct: 71 VKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 130
Query: 100 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWG 133
GFV F ++ DA+ A+ +QG + + +R++W
Sbjct: 131 YGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKL 118
++VG LD +++ L++ F G I ++KI + K FV++ DA +ALQ L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 119 QGTAIGKQTVRLSWG 133
G I V+++W
Sbjct: 62 NGKQIENNIVKINWA 76
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 56.2 bits (134), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 43/72 (59%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 121
N T++ G + S ++D+ +R+ FS FG+I+ +++ KG FV+F+ + A A+ + GT
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 122 AIGKQTVRLSWG 133
I V+ WG
Sbjct: 85 TIEGHVVKCYWG 96
Score = 34.3 bits (77), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 3 YCQ--VSDITNSILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGS 56
YC S +T+ ++++TFS ++ KGY FVRF + A++ +NG+
Sbjct: 29 YCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 21/121 (17%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKS---------------NNATI 65
AK+ D GH+ GYGFV + + RA+ +NG +S +A +
Sbjct: 32 AKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 66 FVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQ 119
++ L ++ KD+ ++FS FG I++ ++ V +G F++F R +AE A+
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Query: 120 G 120
G
Sbjct: 152 G 152
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDA 111
G++N + V L N++ +LR LFS GE+ S K+ K G GFV + KDA
Sbjct: 1 GRTN---LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 57
Query: 112 EVALQKLQGTAIGKQTVRLSWGH 134
E A+ L G + +T+++S+
Sbjct: 58 ERAINTLNGLRLQSKTIKVSYAR 80
Score = 34.3 bits (77), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 9 ITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG--SDGKS 60
+T +++ FSR ++V +D TG ++G F+RF +E A+ NG G S
Sbjct: 100 MTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
Query: 61 NNATIFVGA 69
T+ A
Sbjct: 160 EPITVXFAA 168
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 21/121 (17%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKS---------------NNATI 65
AK+ D GH+ GYGFV + + RA+ +NG +S +A +
Sbjct: 32 AKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 66 FVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKLQ 119
++ L ++ KD+ ++FS FG I++ ++ V +G F++F R +AE A+
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Query: 120 G 120
G
Sbjct: 152 G 152
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDA 111
G++N + V L N++ +LR LFS GE+ S K+ K G GFV + KDA
Sbjct: 1 GRTN---LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 57
Query: 112 EVALQKLQGTAIGKQTVRLSWGH 134
E A+ L G + +T+++S+
Sbjct: 58 ERAINTLNGLRLQSKTIKVSYAR 80
Score = 33.5 bits (75), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 9 ITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG--SDGKS 60
+T +++ FSR ++V +D TG ++G F+RF +E A+ NG G S
Sbjct: 100 MTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
Query: 61 NNATIFVGA 69
T+ A
Sbjct: 160 EPITVKFAA 168
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 54 NGSDGKSNN-ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAE 112
+GS G+ T++VG L +++ DLR F FGEI ++ + + C F+QFA R+ AE
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAE 62
Query: 113 VALQK 117
VA +K
Sbjct: 63 VAAEK 67
>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 = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEV 113
SN+ +FVG L ++ +D++ F+ FG I ++ KG GFV F N+ DAE
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 114 ALQKLQGTAIGKQTVRLSW 132
A+Q++ G +G + +R +W
Sbjct: 73 AIQQMGGQWLGGRQIRTNW 91
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 8 DITNSILQETF------SRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+IT ++ F S A+V D TG +KGYGFV F ++ + A+ +M G
Sbjct: 26 EITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 79
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 9/77 (11%)
Query: 51 IEMNGSDGKSNNAT----IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-----KGCG 101
I+M +D + NNA +F+G + ++ D+R +FS FG+I +I G +GC
Sbjct: 80 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 139
Query: 102 FVQFANRKDAEVALQKL 118
FV F R A+ A++ +
Sbjct: 140 FVTFTTRAMAQTAIKAM 156
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 111
S+ +FVG + S+KDLRELF +G + + + P KGC FV F RK A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 44/79 (55%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 114
G + +FVG L ++++++D + LF +GE V I +G GF++ +R AE+A
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIA 74
Query: 115 LQKLQGTAIGKQTVRLSWG 133
+L GT + + +R+ +
Sbjct: 75 KAELDGTILKSRPLRIRFA 93
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 53/125 (42%), Gaps = 14/125 (11%)
Query: 7 SDITNSILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNN---- 62
+DIT + F R + +G+GF+R A E++G+ KS
Sbjct: 32 TDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR 91
Query: 63 -----ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV-----GKGCGFVQFANRKDAE 112
A + V L VS++ L + FS FG + + V G GFV+FA + A
Sbjct: 92 FATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPAR 151
Query: 113 VALQK 117
AL++
Sbjct: 152 KALER 156
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 9/77 (11%)
Query: 51 IEMNGSDGKSNNAT----IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-----KGCG 101
I+M +D + NNA +F+G + ++ D+R +FS FG+I +I G +GC
Sbjct: 92 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 151
Query: 102 FVQFANRKDAEVALQKL 118
FV F R A+ A++ +
Sbjct: 152 FVTFTTRAMAQTAIKAM 168
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 111
+FVG + S+KDLRELF +G + + + P KGC FV F RK A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 72
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 56 SDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDA 111
++ KS + V + D DLR++F FG+IL V+I KG GFV F N DA
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82
Query: 112 EVALQKLQGTAI 123
+ A +KL GT +
Sbjct: 83 DRAREKLHGTVV 94
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 6/79 (7%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEV 113
SN+ +FVG L ++ +D++ F+ FG+I ++ KG GFV F N+ DAE
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 114 ALQKLQGTAIGKQTVRLSW 132
A+ + G +G + +R +W
Sbjct: 73 AIVHMGGQWLGGRQIRTNW 91
Score = 33.5 bits (75), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 8 DITNSILQETF------SRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+IT ++ F S A+V D TG +KGYGFV F ++ + A++ M G
Sbjct: 26 EITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 79
>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 = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILS------VKIPVGKGCGFVQFANRKDAEVALQKL 118
+FVG L+ NV D+ LR F F LS ++ +G GFV F ++ DA+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 119 QGTAIGKQTVRLSWG 133
QG + + +R++W
Sbjct: 64 QGQDLNGRPLRINWA 78
Score = 33.5 bits (75), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
V D TG ++GYGFV F +++ AM M G D
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVA 114
KS IF+ LD ++ +K L + FS FG ILS K+ KG GFV F ++ AE A
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 67
Query: 115 LQKLQGTAIGKQTV 128
++K+ G + + V
Sbjct: 68 IEKMNGMLLNDRKV 81
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 9 ITNSILQETFS------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNN 62
I N L +TFS KV D N +KGYGFV F + RA+ +MNG N+
Sbjct: 23 IDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGM--LLND 78
Query: 63 ATIFVGALDS 72
+FVG S
Sbjct: 79 RKVFVGRFKS 88
>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 = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDA 111
G++N + V L N++ +LR LFS GE+ S K+ K G GFV + KDA
Sbjct: 3 GRTN---LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 59
Query: 112 EVALQKLQGTAIGKQTVRLSWGH 134
E A+ L G + +T+++S+
Sbjct: 60 ERAINTLNGLRLQSKTIKVSYAR 82
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
AK+ D GH+ GYGFV + + RA+ +NG
Sbjct: 34 AKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 76 DKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQGTAI 123
D DLR++F FG+IL V+I KG GFV F N DA+ A +KL GT +
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV 80
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 118
+ V L N + +LR LFS GE+ S K+ K G GFV + KDAE A+ L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 119 QGTAIGKQTVRLSWGH 134
G + +T+++S+
Sbjct: 82 NGLRLQSKTIKVSYAR 97
Score = 30.4 bits (67), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
AK+ D GH+ GYGFV + + RA+ +NG
Sbjct: 49 AKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 120
IF+ LD ++ +K L + FS FG ILS K+ KG GFV F ++ AE A++K+ G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 121 TAIGKQTV 128
+ + V
Sbjct: 68 MLLNDRKV 75
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 9 ITNSILQETFS------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNN 62
I N L +TFS KV D N +KGYGFV F + RA+ +MNG N+
Sbjct: 17 IDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGM--LLND 72
Query: 63 ATIFVGALDS 72
+FVG S
Sbjct: 73 RKVFVGRFKS 82
>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 = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 8/91 (8%)
Query: 61 NNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK----GCGF--VQFANRKDAEVA 114
+ T++VG L +++ + ELFS G+I + + + K CGF V++ +R DAE A
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 115 LQKLQGTAIGKQTVRLSW--GHNPGNKQWRG 143
++ + GT + + +R W G G + RG
Sbjct: 98 MRYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVAL 115
+A ++V L +S K++ +LFS +G I++ +I V +G GF++F R +AE A+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 116 QKLQGTAI--GKQTVRLSWGHNP 136
+ L G + + + + +NP
Sbjct: 61 KGLNGQKPLGAAEPITVKFANNP 83
Score = 30.0 bits (66), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+++ +D TG ++G GF+RF E A+ +NG
Sbjct: 31 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 65
>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 = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 51 IEMNGSDGKSNNAT----IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-----KGCG 101
I+ +D + NNA +F+G + ++ D+R FS FG+I +I G +GC
Sbjct: 80 IQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCA 139
Query: 102 FVQFANRKDAEVALQ 116
FV F R A+ A++
Sbjct: 140 FVTFTTRAXAQTAIK 154
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 111
S+ FVG + S+KDLRELF +G + + + P KGC FV F RK A
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 112 EVALQKLQGTAIGKQTVRLSWGHNP 136
A L + L H+P
Sbjct: 61 LEAQNALHNXKV------LPGXHHP 79
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAE 112
++ +AT++VG LD VS+ L ELF G +++ +P + G GFV+F + +DA+
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 113 VALQKLQGTAIGKQTVRL 130
A++ + + + +R+
Sbjct: 72 YAIKIMDMIKLYGKPIRV 89
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 11/67 (16%)
Query: 9 ITNSILQETFSRAKVTI------DSNTGHTKGYGFVRFGDENERSRA-----MIEMNGSD 57
++ +L E F +A + D TG +GYGFV F E + A MI++ G
Sbjct: 27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86
Query: 58 GKSNNAT 64
+ N A+
Sbjct: 87 IRVNKAS 93
>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 = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI--------PVGKGCGFVQFANRKDA 111
S+ +FVG + S+KDLRELF +G + + + P KGC FV F RK A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>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 = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 5/76 (6%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK---GCGF--VQFANRKDAEVALQ 116
+ T++VG L +++ + ELFS G+I + + + K CGF V++ +R DAE A++
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 117 KLQGTAIGKQTVRLSW 132
+ GT + + +R W
Sbjct: 78 YINGTRLDDRIIRTDW 93
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 56/129 (43%), Gaps = 17/129 (13%)
Query: 25 IDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNNA-----TIFVG 68
+D G T+ +G+V F + +A+ I++ GK + T+
Sbjct: 40 VDVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAK 99
Query: 69 ALDSNVSDKDLRELFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQT 127
L V+ +L+E+F EI L K KG +++F DAE ++ QGT I ++
Sbjct: 100 NLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRS 159
Query: 128 VRLSWGHNP 136
+ L + P
Sbjct: 160 ISLYYTGEP 168
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 57 DGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 116
+G+ +N +FV +V + +L E+F FG + VKI G FV+F + A A++
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIE 83
Query: 117 KLQGTAIGKQTVRLSWGHNPGNKQWR 142
++ 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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKI---PVG--KGCGFVQFANRKDAEVALQKLQ 119
+FVG L+ S+ D+R LF FG I I P G KGC FV++++ +A+ A+ L
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 120 GT 121
G+
Sbjct: 78 GS 79
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 10/89 (11%)
Query: 55 GSDGKSNNAT----IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQ 104
GS G S AT ++VG L V DK L F FG+I ++IP+ +G FV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 105 FANRKDAEVALQKLQGTAIGKQTVRLSWG 133
F +DA A+ + + + +T+R++
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 54 NGSDGKSNNATIFVGALDSNVSDK-DLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAE 112
N +D KS N+ +F+G L++ + K D+ +FS +G + V KG FVQ++N + A
Sbjct: 19 NKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS--VHKGYAFVQYSNERHAR 76
Query: 113 VALQKLQGTAIGKQTVRLSWGHNP 136
A+ G + QT+ ++ P
Sbjct: 77 AAVLGENGRVLAGQTLDINMAGEP 100
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV-------GKGCGFVQFANRKDAEVALQK 117
+ +G L NV+ + E+FS +G+I + +PV KG +V+F N +AE AL+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 118 LQGTAIGKQTV 128
+ G I Q +
Sbjct: 67 MDGGQIDGQEI 77
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 32 TKGYGFVRFGDENERSRAMIEMNGS--DGKSNNATIFVGA 69
+KGY +V F + +E +A+ M+G DG+ AT +
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAP 85
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDAEVALQKLQG 120
++V LD + D+ LR+ FS FG I S K+ + KG GFV F++ ++A A+ ++ G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 121 TAIGKQTVRLSWGHNPGNKQ 140
+ + + ++ +Q
Sbjct: 78 RIVATKPLYVALAQRKEERQ 97
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
T + AKV ++ G +KG+GFV F E ++A+ EMNG
Sbjct: 41 TITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEMNG 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDA 111
G + ++VG L V DK L F FG+I ++IP+ +G FV+F +DA
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 112 EVALQKLQGTAIGKQTVRLSWG 133
A+ + + + +T+R++
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 8/59 (13%)
Query: 7 SDITNSILQETFSRA-------KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDG 58
D+ + +L E F + KV +D TG +KGYGFV+F DE E+ RA+ E G+ G
Sbjct: 19 PDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTECQGAVG 76
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 55 GSDGKSNNA-TIFVGALDSNVSDKDLRELFSHF------GEILSVKIPVGKGCGFVQFAN 107
GS G S ++FVG L +V D L E F G+++ + V KG GFV+F +
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 108 RKDAEVALQKLQGTA-IGKQTVRLS 131
+ + AL + QG +G + VRLS
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRLS 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 47/83 (56%), Gaps = 6/83 (7%)
Query: 54 NGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFAN 107
N G + ++VG+L N+++ LR +F FG I S+++ + KG GF+ F++
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 108 RKDAEVALQKLQGTAIGKQTVRL 130
+ A+ AL++L G + + +++
Sbjct: 78 SECAKKALEQLNGFELAGRPMKV 100
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 6/54 (11%)
Query: 8 DITNSILQ---ETFSRA---KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+IT +L+ E F R ++ +DS TG +KGYGF+ F D +A+ ++NG
Sbjct: 37 NITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90
>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 = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 61/138 (44%), Gaps = 25/138 (18%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG--------------SDGKS-NNATIF 66
++ D TG++ GY FV F E + RA+ +NG G+S + ++
Sbjct: 45 RIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLY 104
Query: 67 VGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKLQG 120
V L ++D L +F +G I+ I K G FV++ R++A+ A+ L
Sbjct: 105 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 164
Query: 121 TAI--GKQ--TVRLSWGH 134
G Q +VRL+ H
Sbjct: 165 VIPEGGSQPLSVRLAEEH 182
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 119
+ + +FVG L +++++++R+LF +G+ V I KG GF++ R AE+A +L
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 120 GTAIGKQTVRLSWG 133
+ + +R+ +
Sbjct: 80 NMPLRGKQLRVRFA 93
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQ 119
+ + +FVG L +++++++R+LF +G+ V I KG GF++ R AE+A +L
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 120 GTAIGKQTVRLSWG 133
+ + +R+ +
Sbjct: 73 NMPLRGKQLRVRFA 86
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 19/92 (20%)
Query: 59 KSNNATIFVGALDSNVSDKDL---------RELFSHFGEILSVKIPVGKGCGFVQFANRK 109
+ N T++VG +D ++ K L R +FS G+I ++ K CGFV+F +
Sbjct: 133 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQA 192
Query: 110 DAEVALQKLQGTAIGKQTVRLSWGHNPGNKQW 141
+AE A + A+ QT+ L P +K+W
Sbjct: 193 NAEFAKE-----AMSNQTLLL-----PSDKEW 214
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIP-------VGKGCGFVQFANRKDA 111
K + I V + + +++RELFS FGE+ +V++P +G GFV F ++DA
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 112 EVALQKL 118
+ A L
Sbjct: 72 KKAFNAL 78
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 14/87 (16%)
Query: 56 SDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIP-----VGKGCGFVQFANRKD 110
+GK T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 111 AEVALQ--------KLQ-GTAIGKQTV 128
+ ++ KL+ G AI KQ +
Sbjct: 63 VQKIVESQINFHGKKLKLGPAIRKQNL 89
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 19/92 (20%)
Query: 59 KSNNATIFVGALDSNVSDKDL---------RELFSHFGEILSVKIPVGKGCGFVQFANRK 109
+ N T++VG +D ++ K L R +FS G+I ++ K CGFV+F +
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQA 190
Query: 110 DAEVALQKLQGTAIGKQTVRLSWGHNPGNKQW 141
+AE A + A+ QT+ L P +K+W
Sbjct: 191 NAEFAKE-----AMSNQTLLL-----PSDKEW 212
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 31/118 (26%), Positives = 53/118 (44%), Gaps = 21/118 (17%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG--------------SDGKS-NNATIF 66
++ D TG++ GY FV F E + RA+ +NG G+S + ++
Sbjct: 34 RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLY 93
Query: 67 VGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQKL 118
V L ++D L +F +G I+ I K G FV++ R++A+ A+ L
Sbjct: 94 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
>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 = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 14/85 (16%)
Query: 56 SDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIP-----VGKGCGFVQFANRKD 110
+GK T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 111 AEVALQ--------KLQ-GTAIGKQ 126
+ ++ KL+ G AI KQ
Sbjct: 63 VQKIVESQINFHGKKLKLGPAIRKQ 87
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFG---EILSVKIPVG--KGCGFVQFANRKDAEVALQKLQ 119
+FVG L+ S++D+ LF FG E ++ P G KGC FV+F++ +A+ A+ L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 120 GT 121
G+
Sbjct: 78 GS 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 51/124 (41%), Gaps = 6/124 (4%)
Query: 16 ETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALDSNVS 75
E S I SN + Y V + + + + ++VG L V
Sbjct: 17 ENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVD 76
Query: 76 DKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQKLQGTAIGKQTVR 129
DK L F FG+I ++IP+ +G FV+F +DA A+ + + + +T+R
Sbjct: 77 DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136
Query: 130 LSWG 133
++
Sbjct: 137 VNLA 140
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 13/92 (14%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDA 111
G S ++ ++VG+L N+++ LR +F FG+I ++ + KG GF+ F++ + A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 112 EVALQKLQG-------TAIGKQTVRLSWGHNP 136
AL++L G +G T RL G P
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDGGSGP 92
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
DS+TG +KGYGF+ F D RA+ ++NG
Sbjct: 40 DSDTGRSKGYGFITFSDSECARRALEQLNG 69
>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 = 1e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 63 ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GC-GFVQFANRKDAEVALQ 116
A +F+ L D+DL ++F FG ++S K+ + K C GFV + N A+ A+Q
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 117 KLQGTAIGKQTVRL 130
+ G IG + +++
Sbjct: 86 SMNGFQIGMKRLKV 99
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
AKV ID T +K +GFV + + A+ MNG
Sbjct: 55 AKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 123
T ++G + ++ DL LF +FG IL K KGC F+++ + A V + L
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPF 88
Query: 124 GKQTVRLSWG 133
+ +R WG
Sbjct: 89 QGRNLRTGWG 98
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKI---PVG--KGCGFVQFANRKDAEVALQKL 118
+FVG L +D+D+R++F FG I + P G KGC FV+F +A+ A+ L
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 36/142 (25%), Positives = 66/142 (46%), Gaps = 18/142 (12%)
Query: 14 LQETFSRAKV-TIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMN---GSDG 58
+ E F++ + +D TG + +G+V F + +A+ I++ G D
Sbjct: 34 ISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDS 93
Query: 59 KSNNA--TIFVGALDSNVSDKDLRELFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVAL 115
K A T+ L N+++ +L+E+F EI L + KG +++F + DAE L
Sbjct: 94 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 153
Query: 116 QKLQGTAIGKQTVRLSWGHNPG 137
++ QG I ++V L + G
Sbjct: 154 EEKQGAEIDGRSVSLYYTGEKG 175
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI------PVGKGCGFVQFANRKDAEV 113
S+ +FVG L + +++ L ++FS +G+I V + +G GFV F N DA+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 114 ALQKLQGTAIGKQTVRL 130
A+ + G ++ + +R+
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
Score = 30.0 bits (66), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 8 DITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
D L++ FS+ V D T ++G+GFV F + ++ AM+ MNG
Sbjct: 23 DTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG 76
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 117
++VG L V DK L F FG+I ++IP+ +G FV+F +DA A+
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 118 LQGTAIGKQTVRLSWG 133
+ + + +T+R++
Sbjct: 64 MNESELFGRTIRVNLA 79
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 117
++VG L V DK L F FG+I ++IP+ +G FV+F +DA A+
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 118 LQGTAIGKQTVRLSWG 133
+ + + +T+R++
Sbjct: 69 MNESELFGRTIRVNLA 84
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 14/83 (16%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIP-----VGKGCGFVQFANRKDAE 112
GK T+FVG +D + + ++R F+ +G + VKI V KG GFV F N D +
Sbjct: 6 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 65
Query: 113 VALQ--------KLQ-GTAIGKQ 126
++ KL+ G AI KQ
Sbjct: 66 KIVESQINFHGKKLKLGPAIRKQ 88
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 10/92 (10%)
Query: 57 DGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKD 110
D K+N + V L N++ + + LF G+I S K+ K G GFV +++ D
Sbjct: 2 DSKTN---LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPND 58
Query: 111 AEVALQKLQGTAIGKQTVRLSWGHNPGNKQWR 142
A+ A+ L G + +T+++S+ P + R
Sbjct: 59 ADKAINTLNGLKLQTKTIKVSYAR-PSSASIR 89
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
K+ D TG + GYGFV + D N+ +A+ +NG
Sbjct: 34 CKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV-------GKGCGFVQFANRKD 110
G S ++ IF+G LD + +K L + FS FG IL + KG F+ FA+
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 111 AEVALQKLQGTAIGKQTVRLSW 132
++ A++ + G + + + +S+
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSY 82
Score = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 8 DITNSILQETFS-------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+I +L +TFS K+ D +TG++KGY F+ F + A+ MNG
Sbjct: 16 EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNG 70
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 8/66 (12%)
Query: 54 NGSDGKSNNATI--FVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQF 105
+GS G ++ I F+G + N+ +KDL+ LF FG+I + + + KGC F+ +
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 106 ANRKDA 111
R+ A
Sbjct: 63 CERESA 68
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 55/123 (44%), Gaps = 25/123 (20%)
Query: 8 DITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFG-----DENERSRAMIEMNGS 56
D T L+E F + K+ D TG ++G+GF+ F DE +++ +++
Sbjct: 14 DTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVI 73
Query: 57 DGK--------SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGF 102
D K IFVG + +V K+ E FS +G I+ ++ + K G GF
Sbjct: 74 DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133
Query: 103 VQF 105
V +
Sbjct: 134 VTY 136
Score = 29.3 bits (64), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 61 NNATIFVGALDSNVSDKDLRELFSHFGEILSVKI---PV---GKGCGFVQF 105
+ +F+G L+ + ++ +LRE F +G + +KI P +G GF+ F
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRK 109
G +G A + V LD VSD D++ELF+ FG + + + G V F R
Sbjct: 81 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 140
Query: 110 DAEVALQKLQGTAI 123
DA A+++ +G +
Sbjct: 141 DALKAMKQYKGVPL 154
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRK 109
G +G A + V LD VSD D++ELF+ FG + + + G V F R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 87
Query: 110 DAEVALQKLQGTAI 123
DA A+++ +G +
Sbjct: 88 DALKAMKQYKGVPL 101
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRK 109
G +G A + V LD VSD D++ELF+ FG + + + G V F R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 87
Query: 110 DAEVALQKLQGTAI 123
DA A+++ +G +
Sbjct: 88 DALKAMKQYKGVPL 101
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 61 NNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVA 114
+NATI V L + + DL+ELF FG I + + KG F+ F R+DA A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 115 LQKLQGTAIGKQTVRLSWGHNPGN 138
+ + G + + W N
Sbjct: 74 IAGVSGFGYDHLILNVEWAKPSTN 97
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 8 DITNSILQETF------SRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
D + LQE F SR + D TG +KG+ F+ F + +RA+ ++G
Sbjct: 26 DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
N + V L +++DLRE+FS +G I V I +G FV F N DA+ A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 116 QKLQGTAIGKQTVRLS 131
++ G + + +R+S
Sbjct: 75 ERANGMELDGRRIRVS 90
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 118
I+VG L + + + ++ELFS FG++ +VK+ KG GFV+ +E A+ KL
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 119 QGTAIGKQTVRLSWGHNP 136
T +T+R++ NP
Sbjct: 63 DNTDFMGRTIRVTEA-NP 79
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-KGCGFVQFANRKDAE 112
G S ++ +FVG ++++ +LRE FS +G+++ V IP + FV FA+ + A+
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
N + V L +++DLRE+FS +G I V I +G FV F N DA+ A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 116 QKLQGTAIGKQTVRLSW 132
++ G + + +R+ +
Sbjct: 75 ERANGMELDGRRIRVDF 91
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
N + V L +++DLRE+FS +G I V I +G FV F N DA+ A
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 116 QKLQGTAIGKQTVRLSW 132
++ G + + +R+ +
Sbjct: 106 ERANGMELDGRRIRVDF 122
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 61 NNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQG 120
+N +FV +V + +L E+F FG + VKI G FV+F + A A++++ G
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEVHG 60
Query: 121 TAIGKQTVRLSWG 133
+ Q + + +
Sbjct: 61 KSFANQPLEVVYS 73
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 52 EMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI------PVGKGCGFVQF 105
++ G +G +F+ L +D DL F FG ++S K+ + K GFV F
Sbjct: 34 QIEGPEG----CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 89
Query: 106 ANRKDAEVALQKLQGTAIGKQTVRL 130
N A+VA++ + G +G + +++
Sbjct: 90 DNPDSAQVAIKAMNGFQVGTKRLKV 114
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 8 DITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+ T++ L TF AKV ID T +K +GFV F + + A+ MNG
Sbjct: 51 EFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 50 MIEMNGSDGKSNNATIFVGALD-SNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANR 108
M EM+ KS +F+G L NVS +DL +FS +G I+ + I GF+QF N
Sbjct: 1 MTEMHNIPPKSR---LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNP 55
Query: 109 KDAEVALQ-KLQGTAIGKQTVRLSWGHNPGNKQWRGDH 145
+ A++ + Q GK+ + N + GDH
Sbjct: 56 QSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDH 93
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV ++ + +++E F +GEI ++ + + + GF V++ K A A + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 119 QGTAIGKQTVRLSWGHNPGNKQ 140
G I QT+++ W G K+
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPKR 110
>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 = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV ++ + +++E F +GEI ++ + + + GF V++ K A A + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 119 QGTAIGKQTVRLSWGHNPGNKQ 140
G I QT+++ W G K+
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKR 156
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
N + V L +++DLRE+FS +G I V I +G FV F N DA+ A
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 116 QKLQGTAIGKQTVRLSW 132
++ G + + +R+ +
Sbjct: 72 ERANGMELDGRRIRVDF 88
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 117
++ V L S LR +F +G + V IP +G FV+F +++DAE A+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 118 LQGTAIGKQTVRLS---WGHNP 136
+ G + + +R+ +G P
Sbjct: 132 MDGAVLDGRELRVQMARYGRPP 153
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNGS 56
D T ++G+ FVRF D+ + AM M+G+
Sbjct: 105 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGA 135
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 118
+FVG L ++ + F+ FG I ++ KG GFV F N+ DAE A+Q++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 119 QGTAIGKQTVRLSW 132
G +G + +R +W
Sbjct: 69 GGQWLGGRQIRTNW 82
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 19 SRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
S A+V D TG +KGYGFV F ++ + A+ +M G
Sbjct: 34 SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 117
++ V L S LR +F +G + V IP +G FV+F +++DAE A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 118 LQGTAIGKQTVRLS---WGHNP 136
+ G + + +R+ +G P
Sbjct: 109 MDGAVLDGRELRVQMARYGRPP 130
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGS--DGK 59
+ D T ++G+ FVRF D+ + AM M+G+ DG+
Sbjct: 79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 117
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 60 SNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKG---CGFVQFANRKDAEVALQ 116
+N+ I+VG L ++ KD+ ++F +G I + + +G FV+F + +DAE A+
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 79
Query: 117 KLQGTAIGKQTVRLSW 132
G +R+ +
Sbjct: 80 GRDGYDYDGYRLRVEF 95
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 8 DITNSILQETFS---RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNAT 64
D T L+E+F RA++ D TG +KG+GFV F E + A M + N T
Sbjct: 26 DTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT 85
Query: 65 I 65
+
Sbjct: 86 L 86
Score = 33.5 bits (75), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 64 TIFVGALDSNVSDKDLRELF--SHFGEILSVK-IPVGKGCGFVQFANRKDAEVALQKLQG 120
T+FV L + +++ L+E F S I++ + KG GFV F + +DA+ A + ++
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 121 TAIGKQTVRLSWGH 134
I V L W
Sbjct: 77 GEIDGNKVTLDWAK 90
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 86 NGQDLMGQPISVDW 99
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 55 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 89
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 54 NGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEV 113
+GS G + +FV L + V+++ L + FS FG++ VK K F+ F R A
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVK 60
Query: 114 ALQKLQGTAIGKQTVRLSWGHNPGNKQ 140
A++++ G + + + + + P K+
Sbjct: 61 AMEEMNGKDLEGENIEIVFAKPPDQKR 87
Score = 31.2 bits (69), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 9 ITNSILQETFSR-AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATI 65
+T IL++ FS+ K+ K Y F+ F + + +AM EMNG D + N I
Sbjct: 23 VTEEILEKAFSQFGKL---ERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEI 77
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 54 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 88
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKD 110
GS G S IFV L + + K L++ F+ G +L I + KGCG V+F + +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60
Query: 111 AEVALQKLQGTAIGKQTVRLSWGHN 135
AE A + + G + + + + N
Sbjct: 61 AERACRMMNGMKLSGREIDVRIDRN 85
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 41 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 75
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 53 MNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFA 106
+N S + + FVG L + S KDL++ F+ FGE++ I +G GF+ F
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 107 NRKDAEVALQKLQ 119
+ E L + +
Sbjct: 62 DAASVEKVLDQKE 74
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 8 DITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGD 42
D + L++ F++ + D NTG ++G+GF+ F D
Sbjct: 22 DTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 55 GSDGKSNNA-TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEV 113
GS G S N IFVG + + + ++LR LF G + ++ V K FV DA+
Sbjct: 1 GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKA 58
Query: 114 ALQKLQGTAI 123
A+ +L G +
Sbjct: 59 AIAQLNGKEV 68
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 39 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 39 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV-GKGCGFVQFANRKDAEVALQKLQGTAI 123
++VG L + +L FS++G + +V I G FV+F + +DAE A++ L G I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 124 GKQTVRL 130
VR+
Sbjct: 63 CGSRVRV 69
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 58 GKSNNAT-IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 116
GK+N T ++VG L N S L F FG I ++ G ++Q+ + A+ A
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71
Query: 117 KLQGTAIGKQTVRL 130
K++G +G RL
Sbjct: 72 KMRGFPLGGPDRRL 85
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGF------VQFANRKDAEVALQKL 118
+FV + +++D+ + F+ +GEI ++ + + + G+ V++ K+A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 QGTAIGKQTVRLSW 132
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 23 VTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ +D TG+ KGY V + E AM +NG D
Sbjct: 39 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 117
++FVG + +++ L+++FS G ++S ++ KG GF ++ +++ A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 118 LQGTAIGKQTVRLSWGHNPGNKQ 140
L G + +R+ + NK+
Sbjct: 70 LNGREFSGRALRVDNAASEKNKE 92
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 8 DITNSILQETFSRA------KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSD 57
+ T L++ FS ++ D TG KGYGF + D+ AM +NG +
Sbjct: 19 EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74
>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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 45/88 (51%), Gaps = 6/88 (6%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKL 118
++VG++ + + +R+ F+ FG I S+ + KG FV++ + A++AL+++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 119 QGTAIGKQTVRLSWGHNPGNKQWRGDHI 146
+G + +++ N G Q D +
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQL 118
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 51/97 (52%), Gaps = 7/97 (7%)
Query: 46 RSRAMIEMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI---PVG---KG 99
+++ +I+ + ++ N I+V ++ ++SD D++ +F FG+I S + P KG
Sbjct: 110 QAQPIIDQLAEEARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168
Query: 100 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGHNP 136
GF+++ + ++ A+ + +G Q +R+ P
Sbjct: 169 YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMN 54
A + D TG KGYGF+ + A+ MN
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 52/112 (46%), Gaps = 15/112 (13%)
Query: 41 GDENERSRAMIEMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIP----- 95
G +R RA+ M ++VG++ + + +R+ F+ FG I S+ +
Sbjct: 1 GAMAQRQRALAIM---------CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 51
Query: 96 -VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGHNPGNKQWRGDHI 146
KG FV++ + A++AL+++ +G + +++ N G Q D +
Sbjct: 52 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 103
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 32/143 (22%), Positives = 59/143 (41%), Gaps = 32/143 (22%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG--------SDGKSNNA-------------- 63
DS T KG+ FV + A+ +MN G+ +N
Sbjct: 48 DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 107
Query: 64 ----TIFVGALDSNVSDKDLRELFSHFGEILSVKI---PVG---KGCGFVQFANRKDAEV 113
I+V ++ ++SD D++ +F FG+I S + P KG GF+++ + ++
Sbjct: 108 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQD 167
Query: 114 ALQKLQGTAIGKQTVRLSWGHNP 136
A+ + +G Q +R+ P
Sbjct: 168 AVSSMNLFDLGGQYLRVGKAVTP 190
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVALQKLQGTA 122
T+ L N+++ +L+E+F EI L + KG +++F + DAE L++ QG
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 123 IGKQTVRLSWGHNPG 137
I ++V L + G
Sbjct: 78 IDGRSVSLYYTGEKG 92
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 10/90 (11%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 118
+ V + + V + LR+LF +G I SVKI +G GFV+F + A+ A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 119 QGTAIGKQTVRLSW---GHN-PGNKQWRGD 144
G I + ++++ GH PG GD
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGAVGD 134
Score = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 14 LQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
L++ F R K+ D T ++GYGFV+F + +A+ +NG
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 32 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 91
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 152 VDKIVIQK 159
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQK 117
T+ V L S LR +F +G + V IP +G FV+F +R+DA+ A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 118 LQGTAIGKQTVRL 130
+ G + + +R+
Sbjct: 75 MDGAELDGRELRV 87
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 39 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 159 VDKIVIQK 166
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 37 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 96
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 97 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 156
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 157 VDKIVIQK 164
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 117
IFVG L + ++ +RE F FGE+ S+++P+ +G F+ F + + ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDA 111
G S ++ +++ L +D+DL +L +G+I+S K + KG GFV F + A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 112 EVALQKLQGTAIGKQTVRLS 131
+ A+ L+ + + Q + S
Sbjct: 61 QKAVTALKASGVQAQMAKQS 80
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGS 56
K +D T KGYGFV F + +A+ + S
Sbjct: 36 KAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS 70
>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 = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG------KGCGFVQFANRKDAEVALQK 117
IFVG L + ++ +RE F FGE+ S+++P+ +G F+ F + + ++K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 38 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 97
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 98 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 157
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 158 VDKIVIQK 165
>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 = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 39 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 159 VDKIVIQK 166
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAM-----------IEMNGSDGKSNN--- 62
T + V D NT ++G+GFV + E AM +E + + ++
Sbjct: 40 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 99
Query: 63 ------ATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCG------FVQFANRKD 110
IFVG + + + LR+ F +G+I ++I +G G FV F +
Sbjct: 100 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 159
Query: 111 AE-VALQK 117
+ + +QK
Sbjct: 160 VDKIVIQK 167
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 63
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 64 LRSMQGFPFYDKPMRIQYA 82
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 65
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 66 LRSMQGFPFYDKPMRIQYA 84
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 64
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 65 LRSMQGFPFYDKPMRIQYA 83
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 63 LRSMQGFPFYDKPMRIQYA 81
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 11/85 (12%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK---------GCGFVQFANR 108
G S ++ +F+ L+ + +++ L+ +FS G I S I K G GFV++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 109 KDAEVALQKLQGTAIG--KQTVRLS 131
+ A+ AL++LQG + K VR+S
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRIS 85
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQKL 118
IFVG L + +D LR+ F FG+I + +G GFV A+R AE A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 119 QGTAIGKQT-VRLSW-GHNPGNKQ 140
G++ V L++ G P + Q
Sbjct: 80 NPIIDGRKANVNLAYLGAKPRSLQ 103
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG-SDGKSNNATI-FVGA 69
A V D TG ++GYGFV D RA + N DG+ N + ++GA
Sbjct: 47 AVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGA 97
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV-----GKGCGFVQFANRKDAEVALQKL 118
T++VG L +V++ + +LFS G S K+ C FV+F +DA AL +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYC-FVEFYEHRDAAAALAAM 75
Query: 119 QGTAIGKQTVRLSWGHNPGNKQ 140
G I + V+++W P +++
Sbjct: 76 NGRKILGKEVKVNWATTPSSQK 97
>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 = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 70 LDSNVSDKDLRELFSHFGEILSVKIPVGKG-------CGFVQFANRKDAEVALQ 116
LD N+ LRE F FG I + IP G+ C F F N+ AE ALQ
Sbjct: 223 LDENL----LRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQG 120
+ ++VG L +N + +L F ++G + SV + G FV+F + +DA A+++L G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
Query: 121 TAIGKQTVRL 130
+ VR+
Sbjct: 133 RTLCGCRVRV 142
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ +QG + +R+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 10 TNSILQETFS------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGK 59
T L+E FS +V D TGH+KG+GFVRF + + + M + + DG+
Sbjct: 28 TEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGR 83
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 61 NNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFAN 107
+ + V L +++DL+E FS FGE+L V++ KG GFV+F
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDA 111
+FVG + + ++DL+ LF FG I + + + KGC F+ + R A
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 58 GKSNNATIFVGALD-SNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 116
G + +F+G L NVS +DL +FS +G I+ + I GF+QF N + A++
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 75
Query: 117 -KLQGTAIGKQTV 128
+ Q GK+ +
Sbjct: 76 XESQEMNFGKKLI 88
>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 = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 50/97 (51%), Gaps = 7/97 (7%)
Query: 46 RSRAMIEMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKI---PVG---KG 99
+++ +I+ + ++ N I+V ++ ++SD D++ +F FG+I S + P KG
Sbjct: 94 QAQPIIDQLAEEARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKG 152
Query: 100 CGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGHNP 136
GF+++ + ++ A+ +G Q +R+ P
Sbjct: 153 YGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTP 189
Score = 33.9 bits (76), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 6/88 (6%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVK------IPVGKGCGFVQFANRKDAEVALQKL 118
++VG++ + + +R+ F+ FG I S+ KG FV++ + A++AL++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 119 QGTAIGKQTVRLSWGHNPGNKQWRGDHI 146
+G + +++ N G Q D +
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQL 102
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 79 LRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAIGKQTVRL 130
LR FS FG I+ + + + C FV + + A+ A+ +L GT + ++V+L
Sbjct: 30 LRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV--ESVQL 79
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/101 (22%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 41 GDENERSRAMIEMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHF----GEILSVKIPV 96
G E R + + + N +++ L V+++DL LF+ F G + ++
Sbjct: 4 GSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT 63
Query: 97 G--KGCGFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGHN 135
G +G F+ F N++ A AL + G + + + + +G N
Sbjct: 64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 54 NGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEI---LSVKIPVGK---GCGFVQFAN 107
GS S+ +F+G L + + LRE F FGE+ L ++ P+ K G GFV F +
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Query: 108 RKDAEVAL 115
+ + L
Sbjct: 77 QAGVDKVL 84
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 58 GKSNNATIFVGALD-SNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ 116
G + +F+G L NVS +DL +FS +G I+ + I GF+QF N + A++
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 75
Query: 117 -KLQGTAIGKQTV 128
+ Q GK+ +
Sbjct: 76 CESQEMNFGKKLI 88
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 63 ATIFVGALD-SNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQ-KLQG 120
+ +F+G L NVS +DL +FS +G I+ + I GF+QF N + A++ + Q
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIECESQE 60
Query: 121 TAIGKQTV 128
GK+ +
Sbjct: 61 MNFGKKLI 68
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 65 IFVGALDSNVSDKDLRELFSHFG---EILSVKIPVGK--GCGFVQFANRKDAEVALQKLQ 119
+F+G L+ ++K L+ +F G E+L +K K G F+ F N DA+ A + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 120 GTAIGKQTVRLSWGHNP 136
G ++ + +++ P
Sbjct: 70 GKSLHGKAIKVEQAKKP 86
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 58 GKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV----GKGCGFVQFANRKDAEV 113
G S ++ IFV L + + K L++ F+ G +L I + KGCG V+F + + AE
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 114 ALQKLQGTAIGKQTVRLSWGHN 135
A + + G + + + + N
Sbjct: 61 ACRMMNGMKLSGREIDVRIDRN 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-KGCGFVQFANRKDAEVALQKLQG 120
+ ++VG L +N + +L F ++G + SV + G FV+F + +DA A++ L G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDG 132
Query: 121 TAIGKQTVRL 130
+ VR+
Sbjct: 133 RTLCGCRVRV 142
>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 = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKI---PV---GKGCGFVQFANRKDAEVAL--- 115
+F+G L + + KDL++ FS FGE++ + P+ +G GFV F + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 116 -QKLQGTAI 123
KL G I
Sbjct: 62 EHKLNGKVI 70
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 8 DITNSILQETFSR------AKVTIDSNTGHTKGYGFVRFGDENERSRAM 50
D T L++ FS+ + +D TG ++G+GFV F + + M
Sbjct: 10 DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 79 LRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 123
LR FS FG I+ + + + C FV + + A+ A+ +L GT +
Sbjct: 54 LRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 98
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-KGCGFVQFANRKDAE 112
+FVG +++ ++L++ F +GE++ V IP + FV FA+ K A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62
>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 = 34.3 bits (77), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFG---EILSVKIPVGKGCGFVQFANRKDAEVA 114
N TI++ ++ + ++L+ LFS FG +I+++K +G FV F + A
Sbjct: 6 NHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNA 65
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L++LQG + +R+ +
Sbjct: 66 LRQLQGFPFYGKPMRIQYA 84
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 114
GS G S +++G L V+ DLR+LF L+ ++ + G FV + ++ A A
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRA 60
Query: 115 LQKLQG 120
++ L G
Sbjct: 61 IETLSG 66
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.5 bits (75), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKLQ 119
+ V LD VSD D++ELF+ FG + + + G V F + DA A+++
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 120 GTAI 123
G +
Sbjct: 91 GVPL 94
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 65
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ QG + R+ +
Sbjct: 66 LRSXQGFPFYDKPXRIQYA 84
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 67
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ QG + R+ +
Sbjct: 68 LRSXQGFPFYDKPXRIQYA 86
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 62 NATIFVGALDSNVSDKDLRE----LFSHFGEILSVKIPVG---KGCGFVQFANRKDAEVA 114
N TI++ L+ + +L++ +FS FG+IL + + +G FV F A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 68
Query: 115 LQKLQGTAIGKQTVRLSWG 133
L+ QG + R+ +
Sbjct: 69 LRSXQGFPFYDKPXRIQYA 87
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.1 bits (74), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 10/84 (11%)
Query: 54 NGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFAN 107
N S + + T+F L + + +DL + FS G++ V+I KG +V+F
Sbjct: 17 NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
Query: 108 RKDAEVAL----QKLQGTAIGKQT 127
+ +A+ Q+L G I Q
Sbjct: 77 IQSVPLAIGLTGQRLLGVPIIVQA 100
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 32.7 bits (73), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFAN 107
+FVG LD + + + LR FS +GE++ I K G GFV+F +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 25.8 bits (55), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 26 DSNTGHTKGYGFVRFGDEN 44
D T ++G+GFV+F D N
Sbjct: 51 DKTTNQSRGFGFVKFKDPN 69
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.7 bits (73), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGE------ILSVKIPVGKGCGFVQFANRKDAE 112
+ +A + V L +++ + EL FG + S + KG GF ++ + A
Sbjct: 92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151
Query: 113 VALQKLQGTAIGKQTVRLSW 132
A L G +G +T+ + W
Sbjct: 152 RAKSDLLGKPLGPRTLYVHW 171
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 6 VSDITNSILQETFS----------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
V+++ S+ Q+ F R + TG +KGYGF + ++ +RA ++ G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
>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 = 32.3 bits (72), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 117
+++G++ + +++ + +L S+ G ++++K+ KG F++F + + + A++
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 118 LQGTAIGKQTVRLSWGHN 135
L G +G + ++ + N
Sbjct: 65 LNGYQLGSRFLKCGYSSN 82
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
K+ D TG +KGY F+ F D + A+ +NG
Sbjct: 34 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 67
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 32.3 bits (72), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGE------ILSVKIPVGKGCGFVQFANRKDAE 112
+ +A + V L +++ + EL FG + S + KG GF ++ + A
Sbjct: 90 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 149
Query: 113 VALQKLQGTAIGKQTVRLSW 132
A L G +G +T+ + W
Sbjct: 150 RAKSDLLGKPLGPRTLYVHW 169
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 6 VSDITNSILQETFS----------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
V+++ S+ Q+ F R + TG +KGYGF + ++ +RA ++ G
Sbjct: 98 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 157
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.3 bits (72), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGE------ILSVKIPVGKGCGFVQFANRKDAE 112
+ +A + V L +++ + EL FG + S + KG GF ++ + A
Sbjct: 92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151
Query: 113 VALQKLQGTAIGKQTVRLSW 132
A L G +G +T+ + W
Sbjct: 152 RAKSDLLGKPLGPRTLYVHW 171
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 6 VSDITNSILQETFS----------RAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
V+++ S+ Q+ F R + TG +KGYGF + ++ +RA ++ G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
>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 = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 117
+++G++ + +++ + +L S+ G ++++K+ KG F++F + + + A++
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 118 LQGTAIGKQTVRLSWGHN 135
L G +G + ++ + N
Sbjct: 66 LNGYQLGSRFLKCGYSSN 83
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
K+ D TG +KGY F+ F D + A+ +NG
Sbjct: 35 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 68
>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 = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-----GCGFVQFANRKDAEVALQKLQ 119
+ V LD VSD D++ELF+ FG + + + G V F + DA A ++
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 120 GTAI 123
G +
Sbjct: 92 GVPL 95
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 63 ATIFVGALDSNVSDKDLRELFSHFGE-ILSVKIP------VGKGCGFVQFANRKDAEVAL 115
A++++G L+ + + + F+ GE ++SVKI + G FV+FA+ AE L
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 116 QKLQGTAIGKQT 127
K+ G + T
Sbjct: 70 HKINGKPLPGAT 81
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKI-------PVGKGCGFVQFANRKDAEVALQ 116
T+FVG L++ V ++ L ELF G + V I P K GFV F + + A+
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP--KSFGFVCFKHPESVSYAIA 75
Query: 117 KLQGTAIGKQTVRLS 131
L G + + + +S
Sbjct: 76 LLNGIRLYGRPINVS 90
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQF-----ANRKDAEV 113
+FV L S++DL +LFS +G + + P+ KG FV F A + AEV
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 114 ALQKLQGTAI 123
Q QG +
Sbjct: 71 DGQVFQGRML 80
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 22 KVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
K+ D TG +KGY F+ F D + A+ +NG
Sbjct: 33 KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/78 (17%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVALQK 117
+++G++ + +++ + +L S+ G ++++K+ KG F++F + + + A++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 118 LQGTAIGKQTVRLSWGHN 135
L G +G + ++ + N
Sbjct: 64 LNGYQLGSRFLKCGYSSN 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 = 0.15, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEI---LSVKIPVGK---GCGFVQFANRKDAEVAL 115
+F+G L + + LRE F FGE+ L ++ P+ K G GFV F ++ + L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
IFVG + N + +LRE F FG + V + +G GF+ F + + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 31.6 bits (70), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 63 ATIFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAE 112
+T++V L ++++ DL +FS +G+++ V I KG F+ F ++ A+
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 31.2 bits (69), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRKDAEVAL 115
T+F+ L + ++ L E+ FG++ V++ + KGC F QF ++ A+ L
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
++ D TG++ GY FV F E + RA+ +NG
Sbjct: 33 CRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
>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 = 0.44, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 77 KDLRELFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 128
+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 = 30.4 bits (67), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 77 KDLRELFSHFGEILSVKIPVG------KGCG--FVQFANRKDAEVALQKLQGTAIGKQTV 128
+D+R+ S +G + S++IP GCG FV+F + D + A+Q L G + V
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
>pdb|2FWM|X Chain X, Crystal Structure Of E. Coli Enta, A 2,3-Dihydrodihydroxy
Benzoate Dehydrogenase
Length = 250
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 13/89 (14%)
Query: 21 AKVTIDSNTGHTKGYGFVRFGDENERSRAM-----IEMNGSDGKSNNATIFVGALDSN-- 73
A VT+ S+ HT G +G +++ +E+ GS + N + G+ D++
Sbjct: 127 AIVTVASDAAHTPRIGMSAYGASKAALKSLALSVGLELAGSGVRCN--VVSPGSTDTDMQ 184
Query: 74 ----VSDKDLRELFSHFGEILSVKIPVGK 98
VSD + FGE + IP+GK
Sbjct: 185 RTLWVSDDAEEQRIRGFGEQFKLGIPLGK 213
>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 = 30.0 bits (66), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 51 IEMNGSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKG-CGFVQFANRK 109
I + G G N+ + V+ + L LF +G++ VKI K VQ A+
Sbjct: 24 IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGN 83
Query: 110 DAEVALQKLQGTAIGKQTVRLSW 132
A++A+ L G + + +R++
Sbjct: 84 QAQLAMSHLNGHKLHGKPIRITL 106
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 30.0 bits (66), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 57 DGKSNNATIFVGALDSNVSDKDLRELFSHFGEI-LSVKIPVGKGCGFVQFANRKDAEVAL 115
+G A ++VG L + DL+ G + L + + F+ + + A+ A+
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 116 QKLQGTAIGKQTVRLSWGHNPGNK 139
LQG +G T+R++ +K
Sbjct: 74 SCLQGLRLGTDTLRVALARQQRDK 97
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIP-----VGKGCGFVQFANRKDAEVALQKL 118
T+ + L + +++ L+E+F +K+P KG F++FA+ +DA+ AL
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 119 QGTAIGKQTVRL 130
I + +RL
Sbjct: 74 NKREIEGRAIRL 85
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 10 TNSILQETFSRA---KVTIDSNTGHTKGYGFVRFGDENERSRAM 50
T LQE F +A KV + N G +KGY F+ F + A+
Sbjct: 28 TEETLQEVFEKATFIKVPQNQN-GKSKGYAFIEFASFEDAKEAL 70
>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 = 29.6 bits (65), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/116 (20%), Positives = 49/116 (42%), Gaps = 20/116 (17%)
Query: 33 KGYGFVRFGDENERSRAM----IEMNGSDGKSNNA----------TIFVGALDSNVSDKD 78
K + F+ F +E ++AM I G K +F+G L + ++D
Sbjct: 53 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQ 112
Query: 79 LRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 128
++EL + FG + + + + KG F ++ + + A+ L G +G + +
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 168
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
DS TG +KGY F + D N +A+ +NG
Sbjct: 131 DSATGLSKGYAFCEYVDINVTDQAIAGLNG 160
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 29.6 bits (65), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/116 (20%), Positives = 49/116 (42%), Gaps = 20/116 (17%)
Query: 33 KGYGFVRFGDENERSRAM----IEMNGSDGKSNNA----------TIFVGALDSNVSDKD 78
K + F+ F +E ++AM I G K +F+G L + ++D
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQ 110
Query: 79 LRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKLQGTAIGKQTV 128
++EL + FG + + + + KG F ++ + + A+ L G +G + +
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
DS TG +KGY F + D N +A+ +NG
Sbjct: 129 DSATGLSKGYAFCEYVDINVTDQAIAGLNG 158
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 9 ITNSILQETFSR-AKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
+T IL+++FS K+ K Y FV F D +AM EMNG
Sbjct: 27 VTEEILEKSFSEFGKL---ERVKKLKDYAFVHFEDRGAAVKAMDEMNG 71
Score = 29.3 bits (64), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 123
+FV L + V+++ L + FS FG++ VK K FV F +R A A+ ++ G I
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVK--KLKDYAFVHFEDRGAAVKAMDEMNGKEI 74
Query: 124 GKQTVRLSWGHNPGNKQ 140
+ + + P K+
Sbjct: 75 EGEEIEIVLAKPPDKKR 91
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 29.3 bits (64), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
DS TG +KGY F + D N +A+ +NG
Sbjct: 36 DSATGLSKGYAFCEYVDINVTDQAIAGLNG 65
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKL 118
+F+G L + ++D ++EL + FG + + + + KG F ++ + + A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 119 QGTAIGKQTV 128
G +G + +
Sbjct: 64 NGMQLGDKKL 73
>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 = 29.3 bits (64), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 117
T+FV ++ + ++ LR F +G I + + K G F+++ + +D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 118 LQGTAIGKQTV 128
G I + V
Sbjct: 164 ADGKKIDGRRV 174
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAEVALQK 117
T+FV ++ + ++ LR F +G I + + K G F+++ + +D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 118 LQGTAIGKQTV 128
G I + V
Sbjct: 164 ADGKKIDGRRV 174
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 DSNTGHTKGYGFVRFGDENERSRAMIEMNG 55
DS TG +KGY F + D N +A+ +NG
Sbjct: 149 DSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIP------VGKGCGFVQFANRKDAEVALQKL 118
+F+G L + ++D ++EL + FG + + + + KG F ++ + + A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 119 QGTAIGKQTV 128
G +G + +
Sbjct: 177 NGMQLGDKKL 186
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 63 ATIFVGALDSNVSDKDLRELFSHFG-----EILSVKIPVGKGCGFVQFANRKDAEVALQK 117
+T+FV LD V K L+E+FS G +IL K +G G V F +A A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 118 LQGTAI 123
G +
Sbjct: 76 FNGQLL 81
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 28/70 (40%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGTAI 123
I L + +++E FS FG + V +P G V+F +A A + L +
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF 71
Query: 124 GKQTVRLSWG 133
+ L W
Sbjct: 72 HHVPLYLEWA 81
>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 = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 64 TIFVGALDSNVSDKDLRELFSHFGEILSVKIPV------GKGCGFVQFANRK--DAEVAL 115
+++VG +D + +DL FS G I + I KG +++FA R DA VA+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 116 QK 117
+
Sbjct: 98 DE 99
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDEN 44
+ +R + D +GH KGY ++ F + N
Sbjct: 62 SINRITILCDKFSGHPKGYAYIEFAERN 89
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 62 NATIFVGALDSNVSDK----DLRELFSHFGEIL---SVKIPVGKGCGFVQFANRKDAEVA 114
N TI++ L+ + + L +FS FG+IL ++K +G FV F A A
Sbjct: 6 NQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNA 65
Query: 115 LQKLQGTAIGKQTVRLSWGHN 135
L+ +QG + +++++ +
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKS 86
>pdb|1EPW|A Chain A, Crystal Structure Of Clostridium Neurotoxin Type B
pdb|1F31|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With A Trisaccharide
pdb|1I1E|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With Doxorubicin
pdb|1G9A|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 3)
pdb|1G9B|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 1)
pdb|1G9C|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 4)
pdb|1G9D|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 2)
pdb|1S0B|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 4.0
pdb|1S0C|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.0
pdb|1S0D|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.5
pdb|1S0E|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 6.0
pdb|1S0F|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 7.0
pdb|1S0G|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B Apo Form
pdb|2NP0|A Chain A, Crystal Structure Of The Botulinum Neurotoxin Type B
Complexed With Synaptotagamin-Ii Ectodomain
Length = 1290
Score = 28.5 bits (62), Expect = 1.6, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 61 NNATIFV-GALDSNVSDKDLRELFSHFGEIL 90
NNA I++ G L+SN KD+RE+ ++ GEI+
Sbjct: 1011 NNAKIYINGKLESNTDIKDIREVIAN-GEII 1040
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 114
G + + + V L + S +DL++ G++ + G G V+F ++D A
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYA 67
Query: 115 LQKLQGT 121
++KL T
Sbjct: 68 VRKLDNT 74
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 55 GSDGKSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVA 114
G + + + V L + S +DL++ G++ + G G V+F ++D A
Sbjct: 8 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYA 66
Query: 115 LQKLQGT 121
++KL T
Sbjct: 67 VRKLDNT 73
>pdb|1Z0H|A Chain A, N-Terminal Helix Reorients In Recombinant C-Fragment Of
Clostridium Botulinum Type B
pdb|1Z0H|B Chain B, N-Terminal Helix Reorients In Recombinant C-Fragment Of
Clostridium Botulinum Type B
Length = 438
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 61 NNATIFV-GALDSNVSDKDLRELFSHFGEIL 90
NNA I++ G L+SN KD+RE+ ++ GEI+
Sbjct: 159 NNAKIYINGKLESNTDIKDIREVIAN-GEII 188
>pdb|2NM1|A Chain A, Structure Of BontB IN COMPLEX WITH ITS PROTEIN RECEPTOR
Length = 436
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 61 NNATIFV-GALDSNVSDKDLRELFSHFGEIL 90
NNA I++ G L+SN KD+RE+ ++ GEI+
Sbjct: 155 NNAKIYINGKLESNTDIKDIREVIAN-GEII 184
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK------GCGFVQFANRKDAE 112
IFVG L N + +D++ F FG++ + K G GFV F + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE 55
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 101 GFVQFANRKDAEVALQKLQGTAIGKQTVRLSWGHNPGNKQWRG 143
FV F+NR+DA A++ L G + + ++ P +K G
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK-PVDKDSSG 95
>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 = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 25 IDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSN 61
+ + G KG +V + +E++ S+A+++M+G K N
Sbjct: 50 VTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN 86
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus
Complex With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus
Complex With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus
Complex With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 26.9 bits (58), Expect = 4.8, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 5 QVSDITNSILQETFSRAKVTIDSNTGHTKG 34
+++D TNSIL + FSR K + +G KG
Sbjct: 44 KITDYTNSILVKMFSRDKEDAELMSGVKKG 73
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 66 FVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANR 108
F G LD +DL LFS+ GEI + G G + F +
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEK 65
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 65 IFVGALDSNVSDKDLRELFSHFGEILSVKIPVGKGCGFVQFANRKDAEVALQKLQGT 121
+ V L + S +DL++ G++ + G G V+F ++D A++KL T
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDNT 73
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 26.6 bits (57), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGS 56
+ +R + D +GH KG+ ++ F D+ E R + ++ S
Sbjct: 31 SVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLALDES 69
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-------KGCGFVQF 105
KS T F+G L +V+++ ++E F I +V++P KG G+ +F
Sbjct: 16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 26.6 bits (57), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 17 TFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGS 56
+ +R + D +GH KG+ ++ F D+ E R + ++ S
Sbjct: 32 SVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLALDES 70
>pdb|3DI5|A Chain A, Crystal Structure Of A Dinb-Like Protein (Bce_4655) From
Bacillus Cereus Atcc 10987 At 2.01 A Resolution
Length = 168
Score = 26.6 bits (57), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 56 SDGKSNNATIFVGALDSNVSDKDLRELFSHFG 87
+DG T FV AL S +DKDL + FG
Sbjct: 82 ADGYRKVNTAFVEALQSEWTDKDLTTINDFFG 113
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 26.2 bits (56), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 62 NATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVGK-GCGFVQFANRKDAEVALQKLQG 120
N +F+ L ++ L LF+ F V++ G+ FV+F N A A LQG
Sbjct: 13 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQG 72
Query: 121 TAIGK-QTVRLSWG 133
I + +++S+
Sbjct: 73 FKITQNNAMKISFA 86
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 59 KSNNATIFVGALDSNVSDKDLRELFSHFGEILSVKIPVG-------KGCGFVQF 105
KS T F+G L +V+++ ++E F I +V++P KG G+ +F
Sbjct: 12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|3M8B|A Chain A, Crystal Structure Of Spin-Labeled Btub V10r1 In The Apo
State
pdb|3M8D|A Chain A, Crystal Structure Of Spin-Labeled Btub V10r1 With Bound
Calcium And Cyanocobalamin
Length = 594
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 155 STQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 207
Query: 72 SNVSD 76
N +D
Sbjct: 208 HNFTD 212
>pdb|3RGN|A Chain A, Crystal Structure Of Spin-Labeled Btub W371r1
Length = 594
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 155 STQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 207
Query: 72 SNVSD 76
N +D
Sbjct: 208 HNFTD 212
>pdb|1NQE|A Chain A, Outer Membrane Cobalamin Transporter (btub) From E. Coli
pdb|1NQG|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
With Bound Calcium
pdb|1NQH|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
With Bound Calcium And Cyanocobalamin (Vitamin B12)
Substrate
pdb|1UJW|A Chain A, Structure Of The Complex Between Btub And Colicin E3
Receptor Binding Domain
pdb|2GUF|A Chain A, In Meso Crystal Structure Of The Cobalamin Transporter,
Btub
pdb|2YSU|A Chain A, Structure Of The Complex Between Btub And Colicin E2
Receptor Binding Domain
Length = 594
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 155 STQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 207
Query: 72 SNVSD 76
N +D
Sbjct: 208 HNFTD 212
>pdb|2GSK|A Chain A, Structure Of The Btub:tonb Complex
Length = 590
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 151 STQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 203
Query: 72 SNVSD 76
N +D
Sbjct: 204 HNFTD 208
>pdb|1NQF|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
Methionine Substiution Construct For Se-Met Sad Phasing
Length = 594
Score = 25.8 bits (55), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 155 STQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 207
Query: 72 SNVSD 76
N +D
Sbjct: 208 HNFTD 212
>pdb|3RGM|A Chain A, Crystal Structure Of Spin-Labeled Btub T156r1
Length = 594
Score = 25.8 bits (55), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 12 SILQETFSRAKVTIDSNTGHTKGYGFVRFGDENERSRAMIEMNGSDGKSNNATIFVGALD 71
S Q+ + +VT+ + HT GY V +G N ++A + +G K+ GAL+
Sbjct: 155 SCQQQLGDKTRVTLLGDYAHTHGYDVVAYG--NTGTQAQTDNDGFLSKT-----LYGALE 207
Query: 72 SNVSD 76
N +D
Sbjct: 208 HNFTD 212
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,006,466
Number of Sequences: 62578
Number of extensions: 198878
Number of successful extensions: 823
Number of sequences better than 100.0: 210
Number of HSP's better than 100.0 without gapping: 147
Number of HSP's successfully gapped in prelim test: 63
Number of HSP's that attempted gapping in prelim test: 474
Number of HSP's gapped (non-prelim): 326
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
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: 47 (22.7 bits)