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= psy6353
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 143 bits (361), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 70/87 (80%), Positives = 75/87 (86%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T QSLGYGFVNY P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 99
Query: 92 MSQQELESLFSPYGRIITSRILCDNLA 118
M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVT 126
Score = 33.1 bits (74), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q+E SLF G I + +++ D + ++ Y
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGY 46
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA 71
T S G GF+ + + +AE+AI LNG + T I V +A
Sbjct: 126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 141 bits (356), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 71/96 (73%), Positives = 77/96 (80%), Gaps = 2/96 (2%)
Query: 22 DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
D E C + T QSLGYGFVNY P DA+KAINTLNGL+LQ KTIKVSYARPSS SI+
Sbjct: 30 DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIR 89
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD 125
Score = 32.0 bits (71), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q E +SLF G I + +++ D + ++ Y
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGY 48
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
+T S G GF+ + + +AE+AI LNG +
Sbjct: 127 ATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 127 bits (320), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 59/82 (71%), Positives = 71/82 (86%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMS 93
SLGYGFVNY +DAE+AINTLNGLRLQ+KTIKVSYARPSSE IK ANLY+SGLP+ M+
Sbjct: 42 HSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMT 101
Query: 94 QQELESLFSPYGRIITSRILCD 115
Q+++E +FS +GRII SR+L D
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVD 123
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 27/37 (72%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
NL V+ LP++M+Q EL SLFS G + +++++ D +A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVA 40
Score = 25.8 bits (55), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG 58
+T S G F+ + + +AE+AI + NG
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>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 = 127 bits (320), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 59/82 (71%), Positives = 71/82 (86%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMS 93
SLGYGFVNY +DAE+AINTLNGLRLQ+KTIKVSYARPSSE IK ANLY+SGLP+ M+
Sbjct: 42 HSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMT 101
Query: 94 QQELESLFSPYGRIITSRILCD 115
Q+++E +FS +GRII SR+L D
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVD 123
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 27/37 (72%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
NL V+ LP++M+Q EL SLFS G + +++++ D +A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVA 40
Score = 25.8 bits (55), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG 58
+T S G F+ + + +AE+AI + NG
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>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 = 89.0 bits (219), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 40/87 (45%), Positives = 58/87 (66%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T S GY FV++ D+++AI LNG+ ++NK +KVSYARP ESIK NLYV+ LP+
Sbjct: 52 TGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 111
Query: 92 MSQQELESLFSPYGRIITSRILCDNLA 118
++ +L+++F YG I+ IL D L
Sbjct: 112 ITDDQLDTIFGKYGSIVQKNILRDKLT 138
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ + +EL +LF G I T RI D
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRD 49
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGL 59
T + G FV Y++ E+A++AI+ LN +
Sbjct: 138 TGRPRGVAFVRYNKREEAQEAISALNNV 165
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 40/86 (46%), Positives = 58/86 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T S GY FV++ D+++AI LNG+ ++NK +KVSYARP ESIK NLYV+ LP+
Sbjct: 41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 100
Query: 92 MSQQELESLFSPYGRIITSRILCDNL 117
++ +L+++F YG I+ IL D L
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDKL 126
Score = 32.3 bits (72), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ M+ +EL +LF G I T RI+ D
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD 38
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGL 59
T + G FV Y++ E+A++AI+ LN +
Sbjct: 127 TGRPRGVAFVRYNKREEAQEAISALNNV 154
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 84.0 bits (206), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 42/60 (70%), Positives = 46/60 (76%), Gaps = 2/60 (3%)
Query: 22 DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
D E C + T QSLGYGFVNY P DA+KAINTLNGL+LQ KTIKVSYARPSS SI+
Sbjct: 30 DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIR 89
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
NL V+ LP++M+Q E +SLF G I + +++ D +
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKIT 42
>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 = 72.0 bits (175), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 34/42 (80%), Positives = 37/42 (88%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
SLGYGFVNY +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 58 GHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 28/40 (70%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
+G NL V+ LP++ +Q EL SLFS G + +++++ D +A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVA 57
>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 = 72.0 bits (175), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 34/42 (80%), Positives = 37/42 (88%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
SLGYGFVNY +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 43 GHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 27/37 (72%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
NL V+ LP++M+Q EL SLFS G + +++++ D +A
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVA 42
>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 = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 32/100 (32%), Positives = 61/100 (61%), Gaps = 7/100 (7%)
Query: 25 ICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGAN 82
+C +I T +SLGY +VN+ +P DAE+A++T+N ++ K +++ +++ PS N
Sbjct: 42 VCRDMI-TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
+++ L K + + L FS +G I++ +++CD ENG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 136
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
C + S GYGFV++ E AE+AI +NG+ L ++ + V
Sbjct: 128 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
PS+ S A+LYV L +++ L FSP G I++ R+ C ++ T
Sbjct: 3 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-CRDMIT 48
>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 = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 32/100 (32%), Positives = 61/100 (61%), Gaps = 7/100 (7%)
Query: 25 ICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGAN 82
+C +I T +SLGY +VN+ +P DAE+A++T+N ++ K +++ +++ PS N
Sbjct: 47 VCRDMI-TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
+++ L K + + L FS +G I++ +++CD ENG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 141
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
C + S GYGFV++ E AE+AI +NG+ L ++ + V
Sbjct: 133 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Score = 30.4 bits (67), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
PS+ S A+LYV L +++ L FSP G I++ R+ C ++ T
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-CRDMIT 53
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 62.4 bits (150), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/35 (82%), Positives = 31/35 (88%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD 36
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
+T S G GF+ + + +AE+AI LNG +
Sbjct: 38 ATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 67
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 24/50 (48%), Positives = 34/50 (68%)
Query: 68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
+SYARP ESIK NLYV+ LP+ ++ +L+++F YG I+ IL D L
Sbjct: 1 MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL 50
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGL 59
T + G FV Y++ E+A++AI+ LN +
Sbjct: 51 TGRPRGVAFVRYNKREEAQEAISALNNV 78
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/48 (52%), Positives = 34/48 (70%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
T S GY FV++ D+++AI LNG+ ++NK +KVSYARP ESIK
Sbjct: 41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIK 88
Score = 32.3 bits (72), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ M+ +EL +LF G I T RI+ D
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD 38
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 51/95 (53%), Gaps = 2/95 (2%)
Query: 23 AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGA- 81
A I + + +++ Y FV YH+ DA A+ TLNG +++N +K+++A S +S
Sbjct: 28 ANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDT 87
Query: 82 -NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL+V L ++ + L + F + ++ ++ D
Sbjct: 88 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 30/46 (65%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
++ + T S GYGFV++ +DA+ A++++ G L + +++++A
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
NLY+S LP M +QELE++ P+G++I++RIL D+ T G ++ + E+
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+T QS G+ F+++HR EDA +AI ++G + + V +A+PS+ S
Sbjct: 52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 50/100 (50%), Gaps = 6/100 (6%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQE 96
G+GF+ AE A L+ + L+ K ++V +A A+L V LP+++S +
Sbjct: 59 GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA------CHSASLTVRNLPQYVSNEL 112
Query: 97 LESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR 136
LE FS +G++ + ++ D+ +GK G+ R+
Sbjct: 113 LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARK 152
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 69 SYARPSSESI-KGANLYVSGLPKHMSQQELESLFSPYGR 106
++ +P ++ + + L+V LP ++++E+ LF YG+
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGK 48
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 15/97 (15%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
T + G+ FV Y PE A+ A+ +N + L + IKV RPS +E +
Sbjct: 66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 123
Query: 80 GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N +YV+ + + +S +++S+F +G+I ++ + D
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T + GYGF+ Y + + ++ A++++N L + ++V A
Sbjct: 162 TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 49/97 (50%), Gaps = 15/97 (15%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
T + G+ FV Y PE A+ A+ +N + L + IKV RPS +E +
Sbjct: 51 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 108
Query: 80 GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N +YV+ + + +S +++S+F +G+I + + D
Sbjct: 109 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARD 145
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T + GYGF+ Y + + ++ A++++N L + ++V A
Sbjct: 147 TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T ++VH SD E+ + + G FV E AE AIN + RL+ + + V
Sbjct: 35 TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 91
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+P+ A L V+ LP ++QQ+ E L P+G +
Sbjct: 92 QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 122
Score = 33.5 bits (75), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 13 YEKVHLGFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+E++ F E C + S T QS GYGF Y + + A +A + L G L +T+ V +
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQSL--------------GYGFVNYHRPEDAEK 51
L ++ +++ GF+D + +S S G+ + Y E AE+
Sbjct: 182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE 241
Query: 52 AINTLNGLRLQNKTIKVSYARP 73
A +GL L ++VS+ P
Sbjct: 242 AQQQADGLSLGGSHLRVSFCAP 263
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T ++VH SD E+ + + G FV E AE AIN + RL+ + + V
Sbjct: 33 TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 89
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+P+ A L V+ LP ++QQ+ E L P+G +
Sbjct: 90 QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 120
Score = 33.5 bits (75), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 13 YEKVHLGFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+E++ F E C + S T QS GYGF Y + + A +A + L G L +T+ V +
Sbjct: 110 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 169
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQSL--------------GYGFVNYHRPEDAEK 51
L ++ +++ GF+D + +S S G+ + Y E AE+
Sbjct: 180 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE 239
Query: 52 AINTLNGLRLQNKTIKVSYARP 73
A +GL L ++VS+ P
Sbjct: 240 AQQQADGLSLGGSHLRVSFCAP 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T ++VH SD E+ + + G FV E AE AIN + RL+ + + V
Sbjct: 35 TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 91
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+P+ A L V+ LP ++QQ+ E L P+G +
Sbjct: 92 QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 122
Score = 33.5 bits (75), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 13 YEKVHLGFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+E++ F E C + S T QS GYGF Y + + A +A + L G L +T+ V +
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQSL--------------GYGFVNYHRPEDAEK 51
L ++ +++ GF+D + +S S G+ + Y E AE+
Sbjct: 182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE 241
Query: 52 AINTLNGLRLQNKTIKVSYARP 73
A +GL L ++VS+ P
Sbjct: 242 AQQQADGLSLGGSHLRVSFCAP 263
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 23 AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSES 77
+E+ + T++S G+ F+ + P DA+ A +NG L K IKV A +PS +S
Sbjct: 35 SEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 15/97 (15%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
T + G+ FV Y PE A+ A+ N + L + IKV RPS +E +
Sbjct: 50 TXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 107
Query: 80 GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N +YV+ + + +S +++S+F +G+I + + D
Sbjct: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARD 144
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 24/41 (58%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T + GYGF+ Y + + ++ A+++ N L + ++V A
Sbjct: 146 TTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 2 VYQTLLNKLFTYEKVHLGF------SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINT 55
V+ L+ T E + F SDA + V ++T +S GYGFV++ DAE AI
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 56 LNGLRLQNKTIKVSYAR---PSSESIKGANLYVSG 87
+ G L + I+ ++A P+ +S +N SG
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSG 111
Score = 32.7 bits (73), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
+++V L ++ +++++ F+P+GRI +R++ D +AT K Y
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKD-MATGKSKGY 59
>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 = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
SDA + V ++T +S GYGFV++ DAE AI + G L + I+ ++A
Sbjct: 34 SDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%)
Query: 68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ A E +GANL++ LP+ Q+L +F P+G ++++++ D
Sbjct: 13 IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
+GFV+Y P A+ AI ++NG ++ K +KV R ++S G
Sbjct: 69 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 25/40 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T QS GYGFV + A++AI LNG + NK +KV+ A
Sbjct: 80 TRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119
Score = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ +P + + +L LF YG I + +I+CD
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T +S G+ FV +H DAE A++ ++G L + ++V AR
Sbjct: 85 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T +S G+ FV +H DAE A++ ++G L + ++V AR
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 6/100 (6%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQE 96
G+GF+ AE A L+G L+++ +++ +A GA L V L +S +
Sbjct: 59 GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA------THGAALTVKNLSPVVSNEL 112
Query: 97 LESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR 136
LE FS +G + + ++ D+ GK + + R+
Sbjct: 113 LEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARK 152
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 3/90 (3%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS--YARPSSES 77
F+ ++ V + + +G+V++ ED EKA+ L GL++ IK+ + S +
Sbjct: 32 FAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGKDSKKE 90
Query: 78 IKGANLYVSGLPKHMSQQELESLFSPYGRI 107
L LP ++Q EL+ +F I
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEI 120
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 4 QTLLNKLFTY----EKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGL 59
+TLL K Y +++ F DA + +S G ++ + DAEK G
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGT 153
Query: 60 RLQNKTIKVSY-ARPSSESIK 79
+ ++I + Y P E ++
Sbjct: 154 EIDGRSISLYYTGEPKGEGLE 174
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 9/84 (10%)
Query: 2 VYQTLLNKLFTYEKVHLGF------SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINT 55
V+ L+ T E + F SDA + V ++T +S GYGFV+++ DAE AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARV-VKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 56 LNGLRLQNKTIKVSYA--RPSSES 77
+ G L + I+ ++A +P + S
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPS 100
Score = 32.3 bits (72), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
+++V L ++ ++++S F+P+G+I +R++ D +AT K Y
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKD-MATGKSKGY 59
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
T +S G+GFV + +DA+ A+ +NG + + I+V A SS++ G
Sbjct: 50 TQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSG 98
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V GL ++Q LE +FS YG+I ++ D
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD 47
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 30/46 (65%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
++ + T S GYGFV++ +DA+ A++++ G L + +++++A
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 31/51 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
T Q GYGFV + EDA+ AI ++ ++L K I+V+ A ++++ G +
Sbjct: 53 TGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPS 103
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 25/40 (62%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
E +G NL++ LP+ + +L S F P+G +I++++ D
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFID 75
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T+ S +GFV++ P+ A+ AI +NG ++ K +KV +
Sbjct: 78 TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S GYGF+ + E A+KA+ LNG L + +KV +
Sbjct: 64 TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
LYV L ++++ L +F P+GRI + +++ D+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS 62
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T S GY F+N+ + ++ AI +NG L N+ I VSYA
Sbjct: 44 TGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 83
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
C + S GYGFV++ E AE+AI +NG+ L ++ + V + E
Sbjct: 41 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 91
Score = 34.7 bits (78), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
A PS N+++ L K + + L FS +G I++ +++CD ENG
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 49
>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 = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 36 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 94
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 132
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 43 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 101
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 139
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 41 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 99
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 100 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 137
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 43 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 101
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 139
>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 = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
C + S GYGFV++ E AE+AI +NG+ L ++ + V + E
Sbjct: 35 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 85
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
N+++ L K + + L FS +G I++ +++CD ENG
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 43
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+ +S G G V + PE AE+A +NG++L + I V R +S
Sbjct: 42 MENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS 87
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 42 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 100
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 101 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 138
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 26 CVFL--ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK-GAN 82
CV + +T +S G+GFV Y E+ + A+N ++ + ++ A +S + GA+
Sbjct: 44 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAH 102
Query: 83 L-----YVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L +V G+ + + L F YG+I I+ D
Sbjct: 103 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 140
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T + G+ FV + EDA AI+ +N L +TI+V+ A+P
Sbjct: 50 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP 91
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+ +S G G V + PE AE+A +NG++L + I V R +S
Sbjct: 39 MENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS 84
>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 = 0.007, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
S+G+GFV Y +PE A+KA+ L G + ++V + +++ G
Sbjct: 49 SMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASG 94
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 29 LISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
++ +S G+GFV + PE+A KA+ +NG + K + V+ A+ E G
Sbjct: 48 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSG 99
Score = 30.8 bits (68), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NLYV L + + L FSP+G I +++++ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME 50
>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 = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQ 94
+ G+ FV Y+ DAE A+ +NG RL ++ I+ + E + G + +
Sbjct: 80 ACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYR 139
Query: 95 QELESLFSPYGRI 107
Q+ ++ YG++
Sbjct: 140 QDYDAGRGGYGKL 152
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSG 87
T +S GYGF+ + E A +A+ LNG L + ++V + +E + G + SG
Sbjct: 43 TGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV---TERLDGGSGPSSG 95
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 12 TYEKVHLGFSDA----EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
T E+++ FS + +I + L + G+ FV Y+ DAE A+ +NG RL ++ I+
Sbjct: 31 TEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR 90
Query: 68 VSY 70
+
Sbjct: 91 TDW 93
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP-SSESI 78
F+ ++ V + T + +G+V++ ED EKA+ L GL++ IK+ + S+ +
Sbjct: 38 FAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKV 96
Query: 79 KGA-NLYVSGLPKHMSQQELESLF 101
+ A L L ++++ EL+ +F
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVF 120
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANL 83
+F T +S GY F+ + E + A+ LNG +L ++ +K Y+ S+ I G +L
Sbjct: 35 MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS--SNSDISGVSL 89
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T S G+GFV+++ EDA+ A + + + + +A+P
Sbjct: 50 TGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
Y FV++ EDA +A+ LNG L I+V+ A+P + G
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.5 bits (75), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
+GFV + PE AI LNG+RL + I VS
Sbjct: 59 FGFVCFKHPESVSYAIALLNGIRLYGRPINVS 90
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.1 bits (74), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L++ LP+ ++QE+ SLF YG+++ I+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII 41
>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 = 33.1 bits (74), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + G+ FV + EDA AI+ +N L +TI+V+ A+
Sbjct: 45 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.1 bits (74), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + G+ FV + EDA AI+ +N L +TI+V+ A+
Sbjct: 43 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 83
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.3 bits (72), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ LY+ GL + Q+L L PYG+I++++ + D
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD 40
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+T + GYGFV++ P A+KA+ L +Q + K S PSS
Sbjct: 42 TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS--GPSS 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.3 bits (72), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G+ FV + EDA AI+ +N L +TI+V+ A
Sbjct: 101 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 32.3 bits (72), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G+ FV + EDA AI+ +N L +TI+V+ A
Sbjct: 39 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
+F T +S GY F+ + E + A+ LNG +L ++ +K Y+ S+ I G +
Sbjct: 36 MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS--SNSDISGVS 89
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 25/42 (59%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
Y F+++ + A KA+ +NG L+ + I++ +A+P + K
Sbjct: 47 YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRK 88
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ +YVS LP ++ +L +FS YG+++ I+ D
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD 51
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
T G+ FV +H DA+ A ++G L + ++V AR + G +
Sbjct: 51 TKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+F T +S GY F+ + E + A+ LNG +L ++ +K Y+
Sbjct: 37 MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 81
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE----SIKGANLYVSGLP 89
QS G FV ++ + A +A N L+ +++ +P+ +++ L++ +
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 104
Query: 90 KHMSQQELESLFSPYGRIITSRIL 113
K ++ ++ +FS +G+I RIL
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRIL 128
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
FV Y + E A++A+ LNG ++++ +KV+ AR
Sbjct: 53 FVTYEKMESADQAVAELNGTQVESVQLKVNIAR 85
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE----SIKGANLYVSGLP 89
QS G FV ++ + A +A N L+ +++ +P+ +++ L++ +
Sbjct: 57 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 116
Query: 90 KHMSQQELESLFSPYGRIITSRIL 113
K ++ ++ +FS +G+I RIL
Sbjct: 117 KKCTENDIRVMFSSFGQIEECRIL 140
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
L+V +P+ + +Q+L+ LF +GRI +L D L
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRL 52
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
FV Y + E A++A+ LNG ++++ +KV+ AR
Sbjct: 77 FVTYEKMESADQAVAELNGTQVESVQLKVNIAR 109
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V+ + +S G+ FV + +DA++A NG+ L + I+V ++
Sbjct: 48 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V+ + +S G+ FV + +DA++A NG+ L + I+V ++
Sbjct: 45 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V+ + +S G+ FV + +DA++A NG+ L + I+V ++
Sbjct: 79 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V Y + A +A++ LNG +L+N T+KV+Y
Sbjct: 59 VTYSSKDQARQALDKLNGFQLENFTLKVAY 88
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.8 bits (68), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
V+ + +S G+ FV + +DA++A NG+ L + I+VS
Sbjct: 48 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+S GY F+ + EDA++A+N+ N ++ + I++ P
Sbjct: 51 KSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP 90
>pdb|3DAF|A Chain A, The Crystal Structure Of [fe]-Hydrogenase Holoenzyme (Hmd)
From Methanocaldococcus Jannaschii Cocrystallized With
Cyanide
pdb|3DAG|A Chain A, The Crystal Structure Of [fe]-Hydrogenase Holoenzyme (Hmd)
From Methanocaldococcus Jannaschii
Length = 358
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFS---PYGRIITSRILCDNLATENGKYYSGLGGRE 132
E+++GA++ ++ LPK Q ++ F+ P G I+T C T+ K + L GRE
Sbjct: 137 EAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHA--CTIPTTKFAKIFKDL-GRE 193
Query: 133 RL 134
L
Sbjct: 194 DL 195
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 30.4 bits (67), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V+ T + GYGF Y E A A+ LNG + ++V A
Sbjct: 41 VYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA 85
>pdb|2B0J|A Chain A, The Crystal Structure Of The Apoenzyme Of The
Iron-Sulfur-Cluster-Free Hydrogenase (Hmd)
pdb|3F47|A Chain A, The Crystal Structure Of [fe]-Hydrogenase (Hmd) Holoenzyme
From Methanocaldococcus Jannaschii
Length = 358
Score = 30.4 bits (67), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFS---PYGRIITSRILCDNLATENGKYYSGLGGRE 132
E+++GA++ ++ LPK Q ++ F+ P G I+T C T+ K + L GRE
Sbjct: 137 EAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHA--CTIPTTKFAKIFKDL-GRE 193
Query: 133 RL 134
L
Sbjct: 194 DL 195
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
S GY +V + P++AEKA+ ++G ++ + I +
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT 80
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
F+ ++ V + T + +G+V++ ED EKA+ L GL++ IK+ +
Sbjct: 42 FAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 93
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 22 DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
D EI + + S G+GFV + DA++A L+G ++ + I+V+ A
Sbjct: 58 DVEI---IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 22 DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
D EI + + S G+GFV + DA++A L+G ++ + I+V+ A
Sbjct: 44 DVEI---IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
GY FV + E A AI ++NG ++ +K + + S + G +
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
S K +Y G+ ++ Q + FSP+G+I+ R+
Sbjct: 22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF 58
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSESIK 79
V L T S GYGFV + + ++A+ G + L +K +++S A P + +K
Sbjct: 42 VVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK 95
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + G V+Y P A+ A+ +G Q +KVS AR
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
>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 = 29.3 bits (64), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE----SIKGANLYVSGLP 89
QS G FV ++ + A +A N L+ ++ +P+ +++ L++ +
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXIS 104
Query: 90 KHMSQQELESLFSPYGRIITSRIL 113
K ++ ++ FS +G+I RIL
Sbjct: 105 KKCTENDIRVXFSSFGQIEECRIL 128
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 29.3 bits (64), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+ FV + P DAE A+ L+G + ++V
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 83 LYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
L++ LP K++S+++L +FSPYG I+ I
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 35
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN 121
L+V GL +Q+ L S FS YG ++ I+ D ++
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQS 57
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
Y FV+ + DA+ AI LNG ++ K I V
Sbjct: 45 YAFVHMEKEADAKAAIAQLNGKEVKGKRINV 75
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
K ++L V GLP ++Q+L+ FS +G ++ ++ D
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD 50
>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 = 28.9 bits (63), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
S S++ L++SGLP +++ELE + +G + R++ + G Y
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAY 62
Score = 25.8 bits (55), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV--SYARPSS 75
G +V Y A +A+ ++G+ ++ IKV S + PSS
Sbjct: 59 GLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 81 ANLYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
+ L++ LP K++S+++L +FSPYG I+ I
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 83 LYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
L++ LP K++S+++L +FSPYG I+ I
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 83 LYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
L++ LP K++S+++L +FSPYG I+ I
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.9 bits (63), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNKTIKV--------SYARPSS 75
+V Y R EDA +AI +N + + +T+K SY+ PSS
Sbjct: 66 AYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSGPSS 110
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 23 AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
++C + Q G G V Y R ED E A+ L+ + ++ + SY R E G +
Sbjct: 40 GDVC---YADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPS 96
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYA 71
GY FV+Y A +AI TL+G + L K ++V Y+
Sbjct: 45 GYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS 80
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 29 LISTAQSLGYGFVNYHRPEDAEKAINTL 56
+ T G+GFV++ +DA+KA N L
Sbjct: 51 MTGTGAHRGFGFVDFITKQDAKKAFNAL 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
Y FV+ R EDA +AI L+ Q K + V
Sbjct: 46 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHV 76
>pdb|3AHR|A Chain A, Inactive Human Ero1
Length = 465
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 91 HMSQQELESLFSPYGRIITS 110
H+++QE+ SLF+ +GRI TS
Sbjct: 431 HLTRQEIVSLFNAFGRISTS 450
>pdb|3AHQ|A Chain A, Hyperactive Human Ero1
Length = 465
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 91 HMSQQELESLFSPYGRIITS 110
H+++QE+ SLF+ +GRI TS
Sbjct: 431 HLTRQEIVSLFNAFGRISTS 450
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 13/66 (19%)
Query: 16 VHLGFSDAEI-------------CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ 62
+ G SDA+I V + +SLG V++ R DA KA+ NG+ L
Sbjct: 36 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD 95
Query: 63 NKTIKV 68
+ + +
Sbjct: 96 GRPMNI 101
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSE 76
C + + Y FV ++ DA A+ +NG ++ K +KV++A PSS+
Sbjct: 45 CKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 96
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+T S GY F Y ++AI LNG++L +K + V A +++
Sbjct: 38 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 84
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/36 (25%), Positives = 22/36 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
L++ +P+++ +++L+ LF +G+I +L D
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF 50
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T S GY F Y ++AI LNG++L +K + V A
Sbjct: 131 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>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 = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T S GY F Y ++AI LNG++L +K + V A
Sbjct: 133 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
G FV + D +KA+ L G + N+ + Y P S
Sbjct: 59 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
G FV + D +KA+ L G + N+ + Y P S
Sbjct: 59 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
T S GY V Y + A A LNG + +TI+V +
Sbjct: 64 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+ FV + P DA A+ L+G L ++V
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRV 142
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+T S GY F Y ++AI LNG++L +K + V A
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>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 = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGR 106
+ L+V LP ++++E+ LF YG+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGK 41
>pdb|3UX1|A Chain A, Structural Characterization Of Adeno-Associated Virus
Serotype 9
Length = 518
Score = 27.3 bits (59), Expect = 2.8, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 55 TLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQ 95
T+NG +T+K S A PS+ +++G N Y+ G P + Q+
Sbjct: 232 TINGSGQNQQTLKFSVAGPSNMAVQGRN-YIPG-PSYRQQR 270
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+ FV + P DA A+ L+G L ++V
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142
>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 = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S++G L+V+G+ + +++++ F+ YG I
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEI 34
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 2 VYQTLLNKLFTYEKVHL---GFSDAEICVFLIS-TAQSLGYGFVNYHRPEDAEKAINTLN 57
++ +LNK + + V F + E C L S G FV Y +A+ AIN L+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 58 G 58
G
Sbjct: 78 G 78
>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 = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S++G L+V+G+ + +++++ F+ YG I
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEI 49
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
T S GY V Y + A A LNG + +TI+V +
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 19 GFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGL---RLQNKTIKVSYARP 73
GF D E V + T +S GYGFV AE+A N + R N + A+P
Sbjct: 40 GFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKP 99
Query: 74 SS 75
S
Sbjct: 100 RS 101
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N+YV L + ++++ LFS +G++ +++ D
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD 36
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G V++ P A+ AI+ +G IKVS+A
Sbjct: 53 TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S++G L+V+G+ + +++++ F+ YG I
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEI 34
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2HE7|A Chain A, Ferm Domain Of Epb41l3 (Dal-1)
Length = 283
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 4 QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL----NGL 59
+ L +K+ K H G + AE + + A+ L V+ H +D+E L +GL
Sbjct: 154 KELEDKVIELHKSHRGMTPAEAEMHFLENAKKLSMYGVDLHHAKDSEGVEIMLGVCASGL 213
Query: 60 RLQNKTIKVS-YARPSSESI--KGANLYVSGLPKHMSQQE 96
+ ++++ +A P I K N Y+ P Q E
Sbjct: 214 LIYRDRLRINRFAWPKVLKISYKRNNFYIKIRPGEFEQFE 253
>pdb|3GFO|A Chain A, Structure Of Cbio1 From Clostridium Perfringens: Part Of
The Abc Transporter Complex Cbionq
Length = 275
Score = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 14 EKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPED 48
E + + F D + +F S Q + +G VN PED
Sbjct: 84 ESIGIVFQDPDNQLFSASVYQDVSFGAVNMKLPED 118
>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 = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/50 (22%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 59 LRLQNKTIKVSYARPSSE-SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+R +++ P + S++G L+V+G+ + +++++ F+ YG I
Sbjct: 1 MREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEI 50
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 1 MVYQTLLNKLFTYEKVHLGFSD-AEICVFLIS----TAQSLGYGFVNYHRPEDAEKAINT 55
+++ T +++ T E +H F++ EI ++ T GY V Y ++A+ A+
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 56 LNGLRLQNKTIKVSY 70
LNG L + I V +
Sbjct: 85 LNGQDLMGQPISVDW 99
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE---SIKG 80
+ + T + G FV + A A+ T+ G +K ++++Y++ S+ IKG
Sbjct: 40 IVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKG 96
>pdb|3BIN|A Chain A, Structure Of The Dal-1 And Tslc1 (372-383) Complex
Length = 283
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 4 QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL----NGL 59
+ L +K+ K H G + AE + + A+ L V+ H +D+E L +GL
Sbjct: 154 KELEDKVIELHKSHRGMTPAEAEMHFLENAKKLSMYGVDLHHAKDSEGVEIMLGVCASGL 213
Query: 60 RLQNKTIKVS-YARPSSESI--KGANLYVSGLPKHMSQQE 96
+ ++++ +A P I K N Y+ P Q E
Sbjct: 214 LIYRDRLRINRFAWPKVLKISYKRNNFYIKIRPGEFEQFE 253
>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 = 26.6 bits (57), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S++G L+V+G+ + +++++ F+ YG I
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEI 34
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>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 = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S++G L+V+G+ + +++++ F+ YG I
Sbjct: 6 SVEGWILFVTGVHEEATEEDIHDKFAEYGEI 36
Score = 26.2 bits (56), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 52 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|3LGO|A Chain A, Structure Of Gse1p, Member Of The GseEGO COMPLEX
Length = 172
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQS---LGYGFVNYHRPEDAEKAINTLNGLRLQ 62
L N L Y+ + F + + +I TA + L Y N P+++ IN++N L++
Sbjct: 23 LENTLKPYDLHSVDFKTSSLQSSMIITATNGGILSYATSNNDVPKNSINEINSVNNLKMM 82
Query: 63 NKTIKVSYARPSSES 77
+ IK ++ +++
Sbjct: 83 SLLIKDKWSEDENDT 97
>pdb|4FTX|A Chain A, Crystal Structure Of Ego3 Homodimer
pdb|4FTX|B Chain B, Crystal Structure Of Ego3 Homodimer
Length = 170
Score = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQS---LGYGFVNYHRPEDAEKAINTLNGLRLQ 62
L N L Y+ + F + + +I TA + L Y N P+++ IN++N L++
Sbjct: 13 LENTLKPYDLHSVDFKTSSLQSSMIITATNGGILSYATSNNDVPKNSINEINSVNNLKMM 72
Query: 63 NKTIKVSYARPSSES 77
+ IK ++ +++
Sbjct: 73 SLLIKDKWSEDENDT 87
>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 = 25.8 bits (55), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
I ++YV + + Q+LE+ FS G I ILCD +
Sbjct: 34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINT 55
E+ + T S GYGFV+++ D +K + +
Sbjct: 39 EVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
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
0.318 0.136 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,919,466
Number of Sequences: 62578
Number of extensions: 144829
Number of successful extensions: 573
Number of sequences better than 100.0: 156
Number of HSP's better than 100.0 without gapping: 127
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 354
Number of HSP's gapped (non-prelim): 244
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)