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= psy1757
(348 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 115 bits (288), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 75 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 134
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 135 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 180
>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 = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 67 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 126
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 127 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172
>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 = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 73 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 132
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 133 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 178
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 115 bits (287), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 115 bits (287), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 90/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP T +SRGF FVTY T + VD +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEITEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 72 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 131
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + D+++ + G +V++
Sbjct: 132 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 177
>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 = 111 bits (278), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 56/161 (34%), Positives = 96/161 (59%), Gaps = 2/161 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+F+GGL+ +T E + +YF +YG V + I DP TG+SRGF F+++ +VD+++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDK 136
H + K IDPKR R K KIFVGG+ ++ ++ ++FSQ+G+I + Q DK
Sbjct: 65 -QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 137 SKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVK 177
+GF F+++D + D+V +N +++++KR +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE 164
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 50/75 (66%), Gaps = 1/75 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
CK+F+GGL + TE ++R+YF +YG++T+ + D + +GF F+SF+ + D+V+K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 161 NPKQVICGKEVDVKR 175
+ ++ GK +D KR
Sbjct: 64 T-QHILDGKVIDPKR 77
>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 = 77.8 bits (190), Expect = 9e-15, Method: Composition-based stats.
Identities = 33/73 (45%), Positives = 51/73 (69%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
+F+GGL +T +K++ DYFS++GEV ++K DP TG+SRGF FV + ++VD ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 DHYIGNKKIDPKR 91
+H + K IDPKR
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+F+GGL+ + T++D++DYFS++G + + D +GF F+ F + D+V+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 163 KQVICGKEVDVKR 175
+ + GK +D KR
Sbjct: 62 EHKLNGKVIDPKR 74
>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 = 75.5 bits (184), Expect = 4e-14, Method: Composition-based stats.
Identities = 34/83 (40%), Positives = 52/83 (62%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
A D K FVGGL +T +K++ DYF+++GEV +IK DP TG+SRGF F+ +
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
+V+ +L +H + + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K FVGGL+ + +++D++DYF+++G + + D + +GF FI F D ++VL
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 162 PKQVICGKEVDVKR 175
+ + G+ +D K+
Sbjct: 73 KEHRLDGRVIDPKK 86
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 75.1 bits (183), Expect = 5e-14, Method: Composition-based stats.
Identities = 33/73 (45%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVT+ Q VD +LA
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPK 90
H + +K IDPK
Sbjct: 62 SRHELDSKTIDPK 74
Score = 58.5 bits (140), Expect = 6e-09, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
CK+F+GGL+ + T++ +R+YF Q+G + E D +GF F++F DQ D+VL
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVK 174
+ + K +D K
Sbjct: 61 QSRHELDSKTIDPK 74
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 73.9 bits (180), Expect = 1e-13, Method: Composition-based stats.
Identities = 35/82 (42%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVT+ Q VD +LA
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 78 GDHYIGNKKIDPK-RVTKRVNP 98
H + +K IDPK +R P
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQP 108
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
CK+F+GGL+ + T++ +R+YF Q+G + E D +GF F++F DQ D+VL
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
Query: 161 NPKQVICGKEVDVK 174
+ + K +D K
Sbjct: 86 QSRHELDSKTIDPK 99
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 71.6 bits (174), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 49/79 (62%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
RKLF+GGL T E+ + +Y+ Q+G++ + DP + +SRGF FVT+++ VD +A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 77 AGDHYIGNKKIDPKRVTKR 95
A H I + ++PKR R
Sbjct: 88 ARPHSIDGRVVEPKRAVAR 106
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 43/81 (53%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K+F+GGL+ E TE+ +R+Y+ Q+G +T+ D + +GF F++F D +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 162 PKQVICGKEVDVKRVKFNPET 182
I G+ V+ KR E+
Sbjct: 89 RPHSIDGRVVEPKRAVAREES 109
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 68.9 bits (167), Expect = 4e-12, Method: Composition-based stats.
Identities = 36/78 (46%), Positives = 45/78 (57%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
KLFVGGL +T ++ + YFSQYGEV I D T QSRGF FV + V +LA+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
H + + IDPK T R
Sbjct: 78 RPHTLDGRNIDPKPCTPR 95
Score = 58.2 bits (139), Expect = 6e-09, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 41/73 (56%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K+FVGGL T++ +R YFSQYG + + DK+ N +GF F+ F D N VL +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 162 PKQVICGKEVDVK 174
+ G+ +D K
Sbjct: 78 RPHTLDGRNIDPK 90
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 70/143 (48%), Gaps = 2/143 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V L +N + E+ FS GEVES + D G S G+ FV Y T K + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79 DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDK 136
+ + +K I +K +++ GL +T++DV D FS++G I + D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVADQVL 159
+ + +G FI FD ++ A++ +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAI 147
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
L++ GL R +K++ D FS++G + + + D TG SRG AF+ + + ++ + +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>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 = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 70/143 (48%), Gaps = 2/143 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V L +N + E+ FS GEVES + D G S G+ FV Y T K + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79 DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDK 136
+ + +K I +K +++ GL +T++DV D FS++G I + D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVADQVL 159
+ + +G FI FD ++ A++ +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAI 147
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
L++ GL R +K++ D FS++G + + + D TG SRG AF+ + + ++ + +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/161 (29%), Positives = 78/161 (48%), Gaps = 21/161 (13%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG--QSRGFAFVTYTTQKAV 71
+D K+FVG + R EK++ + F QYG V I++ D QS+G FVT+ T+KA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72 DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEITEQDVRD 119
+ +L H I K D ++ V R K+F+G ++ + TE D+R
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
FS +G I E + + +G F++F + +A +K
Sbjct: 115 MFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
++RKLF+G + + E +I FS +G++E I P G SRG AFVT+TT+
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 152
Query: 75 LAA 77
+ A
Sbjct: 153 IKA 155
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/160 (30%), Positives = 77/160 (48%), Gaps = 21/160 (13%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG--QSRGFAFVTYTTQKAVD 72
D K+FVG + R EK++ + F QYG V I++ D QS+G FVT+ T+KA
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 73 D---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEITEQDVRDY 120
+ +L H I K D ++ V R K+F+G ++ + TE D+R
Sbjct: 74 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRVM 127
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
FS +G I E + + +G F++F + +A +K
Sbjct: 128 FSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
>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 = 64.7 bits (156), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 49/165 (29%), Positives = 77/165 (46%), Gaps = 21/165 (12%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG--QSRGFAFVTYTTQKAV 71
+D K FVG + R EK++ + F QYG V I++ D QS+G FVT+ T+KA
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72 DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEITEQDVRD 119
+ +L H I K D ++ V R K+F+G ++ + TE D+R
Sbjct: 61 LEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDR------KLFIGXISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQ 164
FS +G I E + + +G F++F + A +K Q
Sbjct: 115 XFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQ 158
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 44/148 (29%), Positives = 69/148 (46%), Gaps = 10/148 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT----TQKAVDDL 74
L V L +N ++E F GE+ES + D TGQS G+ FV Y +KA++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 75 --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQ 132
L I P + R ++V GL +T++++ FSQYG I +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 133 PFDKSKNMKKGFCFISFDDQNVADQVLK 160
D+ + +G FI FD + A++ +K
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
>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 = 62.0 bits (149), Expect = 5e-10, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
+K+FVGGL +T E++I +YF +GEVESI + D T + RGF F+T+ ++ V ++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 77 AGDHYIGNKKIDPK 90
H +G K + K
Sbjct: 62 KKYHNVGLSKCEIK 75
Score = 59.3 bits (142), Expect = 3e-09, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 38/59 (64%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
KIFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 46/76 (60%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
KIFVGG+ E ++R+YF ++G +TE +D K +GF FI+F+D+ DQ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 PKQVICGKEVDVKRVK 177
I GK+V+VKR +
Sbjct: 72 HFHDIMGKKVEVKRAE 87
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K+FVGG+ N GE E+ +YF ++G V + + D + RGF F+T+ +++VD +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 78 GDHYIGNKKIDPKRVTKR 95
H I KK++ KR R
Sbjct: 72 HFHDIMGKKVEVKRAEPR 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 42/148 (28%), Positives = 69/148 (46%), Gaps = 10/148 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT----TQKAVDDL 74
L V L +N + E F G++ES + D TGQS G+ FV Y+ KA++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 75 --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQ 132
L I P + R ++V GL ++++++ FSQYG I +
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 133 PFDKSKNMKKGFCFISFDDQNVADQVLK 160
D++ + +G FI FD + A++ +K
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIK 150
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 59.3 bits (142), Expect = 3e-09, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 44/72 (61%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
+FVGGL +T E++I +YF +GEVESI + D T + RGF F+T+ ++ V ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 DHYIGNKKIDPK 90
H +G K + K
Sbjct: 62 YHNVGLSKCEIK 73
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
IFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 58.9 bits (141), Expect = 4e-09, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 6/73 (8%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK-- 160
IFVGGL+ T +DV+ YF Q+G + + FDK+ N +GF F++F+ +++ ++V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 161 ----NPKQVICGK 169
N K V C K
Sbjct: 62 FHEINNKMVECKK 74
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 43/73 (58%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
+FVGGL NT +++ YF Q+G+V+ + D T + RGF FVT+ ++ V+ +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 79 DHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 62 FHEINNKMVECKK 74
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+DE KLFVGGL +T E+ + FS+YG++ + + D T +SRGF FVT+ D
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 74 LLAAGDHYIGNKKIDPKRV 92
+ A + K +D +++
Sbjct: 70 AMMA----MNGKSVDGRQI 84
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 4/78 (5%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K+FVGGL+ + EQ + FS+YG I+E D+ +GF F++F +N+ D K+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF--ENIDDA--KD 69
Query: 162 PKQVICGKEVDVKRVKFN 179
+ GK VD ++++ +
Sbjct: 70 AMMAMNGKSVDGRQIRVD 87
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 45/166 (27%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT----TQKAVD-- 72
L+VG LH + E + + FS G + SI + D T +S G+A+V + ++A+D
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 73 --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEF 130
D++ I + DP V IF+ L I + + D FS +G+I
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 133
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVADQ-------VLKNPKQVICGK 169
+ D +N KG+ F+ F+ Q A++ +L N ++V G+
Sbjct: 134 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 5/91 (5%)
Query: 90 KRVTKRVNP-LKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
+ V R NP C + V GL+ TE+D+R+ FS+YG I + +D+ +GF F+
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 149 FDDQNVADQVLKNPKQVICGKEVDVKRVKFN 179
F +NV D K K+ G E+D +R++ +
Sbjct: 95 F--ENVDDA--KEAKERANGMELDGRRIRVD 121
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV + VDD A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 105
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 106 ERANG-MELDGRRI 118
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 45/166 (27%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT----TQKAVD-- 72
L+VG LH + E + + FS G + SI + D T +S G+A+V + ++A+D
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 73 --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEF 130
D++ I + DP V IF+ L I + + D FS +G+I
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 128
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVADQ-------VLKNPKQVICGK 169
+ D +N KG+ F+ F+ Q A++ +L N ++V G+
Sbjct: 129 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
>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 = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 67/146 (45%), Gaps = 13/146 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV Y +A L
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 78 GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEITEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++++ D++ F +
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFD 150
G I D + KG+ FI ++
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYE 175
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ Y ++ D +++
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 187 MNLFDLGGQYL---RVGKAVTP 205
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 99 LKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQV 158
+ +++VG + E+ E +R F+ +G I +D KGF F+ ++ A
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 159 LKNPKQVIC-GKEVDVKR 175
L+ V+ G+ + V R
Sbjct: 87 LEQMNSVMLGGRNIKVGR 104
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 67/146 (45%), Gaps = 13/146 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV Y +A L
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 78 GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEITEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++++ D++ F +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFD 150
G I D + KG+ FI ++
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYE 160
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ Y ++ D +++
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 172 MNLFDLGGQYL---RVGKAVTP 190
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94 KRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+R + C+++VG + E+ E +R F+ +G I +D KGF F+ ++
Sbjct: 7 QRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Query: 154 VADQVLKNPKQVIC-GKEVDVKR 175
A L+ V+ G+ + V R
Sbjct: 67 AAQLALEQMNSVMLGGRNIKVGR 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
KIFVGGL T+ +R YF +G I E D+ +G+ F++ D+ A++ K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 162 PKQVICGKEVDV 173
P +I G++ +V
Sbjct: 79 PNPIIDGRKANV 90
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 33/55 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
K+FVGGL +T + + YF +G++E + D TG+SRG+ FVT + A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 43/66 (65%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
++G++G +D KLF+G + RN EK++ F ++G++ +++ D +TG +G AF+T
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 65 YTTQKA 70
Y +++
Sbjct: 62 YCERES 67
Score = 35.0 bits (79), Expect = 0.059, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 30/54 (55%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+F+G + + E+D++ F ++G I E D+ M KG F+++ ++ A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 66/146 (45%), Gaps = 13/146 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI D T + +GFAFV Y +A L
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 78 GDHY-IGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEITEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++++ D++ F +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFD 150
G I D + KG+ FI ++
Sbjct: 134 GKIKSCTLARDPTTGKHKGYGFIEYE 159
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ Y ++ D +++
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 171 XNLFDLGGQYL---RVGKAVTP 189
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94 KRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+R + C+++VG + E+ E +R F+ +G I +D KGF F+ ++
Sbjct: 6 QRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPE 65
Query: 154 VADQVLKNPKQV-ICGKEVDVKR 175
A L+ V + G+ + V R
Sbjct: 66 AAQLALEQXNSVXLGGRNIKVGR 88
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.2 bits (121), Expect = 8e-07, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G+AGP R L+VG LH N E + F +G +ESI + D TG+S+G+ F+T++
Sbjct: 22 GSAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 67 ----TQKAVDDL 74
+KA++ L
Sbjct: 77 DSECAKKALEQL 88
Score = 41.2 bits (95), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 29/59 (49%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+++VG L ITE +R F +G I Q D KG+ FI+F D A + L+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 5/86 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ TE+D+R+ FS+YG I + +D+ +GF F+ F +N
Sbjct: 6 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF--EN 63
Query: 154 VADQVLKNPKQVICGKEVDVKRVKFN 179
V D K K+ G E+D +R++ +
Sbjct: 64 VDDA--KEAKERANGMELDGRRIRVD 87
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV + + VDD A
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEAK 71
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 72 ERANG-MELDGRRI 84
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 5/86 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ TE+D+R+ FS+YG I + +D+ +GF F+ F +N
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF--EN 66
Query: 154 VADQVLKNPKQVICGKEVDVKRVKFN 179
V D K K+ G E+D +R++ +
Sbjct: 67 VDDA--KEAKERANGMELDGRRIRVD 90
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 51/90 (56%), Gaps = 6/90 (6%)
Query: 5 ANGTAGPGRNDERKLFVG--GLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G N + +G GL T E+++ + FS+YG + +SI D + +SRGFAF
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRV 92
V + + VDD A + G ++D +R+
Sbjct: 62 VYF---ENVDDAKEAKERANG-MELDGRRI 87
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ TE+D+R+ FS+YG I + +D+ +GF F+ F +N
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF--EN 66
Query: 154 VADQVLKNPKQVICGKEVDVKRVK 177
V D K K+ G E+D +R++
Sbjct: 67 VDDA--KEAKERANGMELDGRRIR 88
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 51/90 (56%), Gaps = 6/90 (6%)
Query: 5 ANGTAGPGRNDERKLFVG--GLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G N + +G GL T E+++ + FS+YG + +SI D + +SRGFAF
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRV 92
V + + VDD A + G ++D +R+
Sbjct: 62 VYF---ENVDDAKEAKERANG-MELDGRRI 87
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 5 ANGTAGPGRNDERK--LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G R ++ L V GL T E+++ +YFS +GEV + +K D TG S+GF F
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 63 VTYT 66
V +T
Sbjct: 62 VRFT 65
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 94 KRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
KR + V GL + TEQD+++YFS +G + Q D KGF F+ F +
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Query: 154 VADQVLKNPKQVICGKEVDVK 174
+V+ + +I G+ D K
Sbjct: 69 TQVKVMSQ-RHMIDGRWCDCK 88
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 48.5 bits (114), Expect = 5e-06, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 10 GPGRNDER-KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A V Y T
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 69 K 69
K
Sbjct: 79 K 79
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 12/53 (22%), Positives = 23/53 (43%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+FV + E E ++++ F YG I D+ KG+ + ++ A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 81
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 69 K 69
K
Sbjct: 62 K 62
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 59
>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 = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 69 K 69
K
Sbjct: 75 K 75
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
KLF+GGL+R T EK + F ++G + + + D T +SRGFAF+T+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITF 55
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 5/76 (6%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K+F+GGL E E+ ++ F ++G I+E D++ + +GF FI+F +N AD KN
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITF--ENPADA--KN 63
Query: 162 PKQVICGKEVDVKRVK 177
+ + GK + K +K
Sbjct: 64 AAKDMNGKSLHGKAIK 79
>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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++ A ++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 69 K 69
K
Sbjct: 76 K 76
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
LFV +H E EI + F YGE+++I + D TG S+G+A V Y T K
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV + E E ++++ F YG I D+ KG+ + ++
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/171 (23%), Positives = 78/171 (45%), Gaps = 17/171 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPYTG----QSRGFAFVTY-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ + T
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 67 TQK-AVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYG 125
TQ A D ++ G + D + + P K+F+GGL + + V++ + +G
Sbjct: 67 TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 121
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICG-KEVDVKR 175
+ F D + + KG+ F + D NV DQ + + G K++ V+R
Sbjct: 122 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF Y D +A
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 78 GDHY-IGNKKIDPKRVT 93
+ +G+KK+ +R +
Sbjct: 158 LNGMQLGDKKLLVQRAS 174
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V Y T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E TE+D+ D F++YG I D+ KG+ + ++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/171 (23%), Positives = 78/171 (45%), Gaps = 17/171 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPYTG----QSRGFAFVTY-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ + T
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67 TQK-AVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYG 125
TQ A D ++ G + D + + P K+F+GGL + + V++ + +G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICG-KEVDVKR 175
+ F D + + KG+ F + D NV DQ + + G K++ V+R
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF Y D +A
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 78 GDHY-IGNKKIDPKRVT 93
+ +G+KK+ +R +
Sbjct: 156 LNGMQLGDKKLLVQRAS 172
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 5 ANGTAGPGR--NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++GP R +D + V L +T E ++ + F +G + I + D TGQS+GFAF
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 63 VTY 65
+++
Sbjct: 62 ISF 64
Score = 36.6 bits (83), Expect = 0.023, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
I V L+ + E D+++ F +GSI+ DK+ KGF FISF
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+FVG + E TE+ ++D FS+ G + F+ +D+ KG+ F + DQ A ++N
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
R +FVG + E+++ D FS+ G V S + D TG+ +G+ F Y Q+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTG--QSRGFAFVTYTTQKA 70
+D K+FVG + R EK++ + F QYG V I++ D QS+G FVT+ T+KA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISF 149
K+FVG + +E+D+R+ F QYG++ E D+S+N KG CF++F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/186 (23%), Positives = 79/186 (42%), Gaps = 27/186 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPYTG----QSRGFAFVTY-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ + T
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67 TQK-AVDDLLAAGDHYIGNKKID---------------PKRVTKRVNPLKCKIFVGGLTT 110
TQ A D ++ G + D P V+ V K+F+GGL
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 111 EITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICG-K 169
+ + V++ + +G + F D + + KG+ F + D NV DQ + + G K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 170 EVDVKR 175
++ V+R
Sbjct: 185 KLLVQR 190
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF Y D +A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 78 GDHY-IGNKKIDPKRVT 93
+ +G+KK+ +R +
Sbjct: 176 LNGMQLGDKKLLVQRAS 192
>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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 25/60 (41%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
GPGR + L V L +N + E+ FS GEVES + D G S G+ FV Y T K
Sbjct: 1 GPGRTN---LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK 57
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+C++FVG L T+ITE+D + F +YG +P + N +GF FI + + +A+
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYG------EPSEVFINRDRGFGFIRLESRTLAE 72
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 10/110 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+LFVG L + E++ F +YGE + I D RGF F+ ++ + A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE 77
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSI 127
D I + P R+ R + V L+ ++ + + FSQ+G +
Sbjct: 78 LDGTILKSR--PLRI--RFATHGAALTVKNLSPVVSNELLEQAFSQFGPV 123
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 17/76 (22%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FVG T ++TE ++R++FSQYG + + +PF + F F++F D +A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-------RAFAFVTFADDQIA----- 55
Query: 161 NPKQVICGKEVDVKRV 176
Q +CG+++ +K +
Sbjct: 56 ---QSLCGEDLIIKGI 68
Score = 35.8 bits (81), Expect = 0.033, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
G + +FVG + E E+ ++FSQYG+V + I P+ R FAFVT+ +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-PF----RAFAFVTFADDQIA 55
Query: 72 DDL 74
L
Sbjct: 56 QSL 58
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G G G+ +FVGG+ E EI +F++YG V+ + I D TG S+G+ FV++
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 59
Query: 67 TQKAVDDLLAAGDHYIGNK-KIDP 89
V ++ + ++ G K K+ P
Sbjct: 60 NDVDVQKIVESQINFHGKKLKLGP 83
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSF 58
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D+R ++VG + + +++ +FS G + I+I D ++G +G+A++ + + +VD
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
+A + + I K + KR N
Sbjct: 95 VAMDETVFRGRTI--KVLPKRTN 115
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K ++VG + T QD+ +FS GSI DK KG+ +I F ++N D +
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 160 KNPKQVICGKEVDV 173
+ V G+ + V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYT 66
G + L+VG LH N E + F +G++++I + D TG+S+G+ F+T++
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFS 55
Score = 35.4 bits (80), Expect = 0.046, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
++VG L ITE +R F +G I D KG+ FI+F D A + L+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 67/153 (43%), Gaps = 8/153 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
L V L ++ ++E+ F G + + I D TG S G+AFV +T+ Q+A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
+ NK++ +K ++V L IT+ + F +YGSI +
Sbjct: 66 ---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 134 FDKSKNMKKGFCFISFDDQNVADQVLKNPKQVI 166
DK +G F+ ++ + A + + VI
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D ++G +GFA++ ++ +++V
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
LA + ++I K + KR N
Sbjct: 64 LALDESLFRGRQI--KVIPKRTN 84
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 32/71 (45%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
I+VG + T +++ +F GS+ DK KGF +I F D+ L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 163 KQVICGKEVDV 173
+ + G+++ V
Sbjct: 68 ESLFRGRQIKV 78
>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 = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D ++G +GFA++ ++ +++V
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
LA + ++I K + KR N
Sbjct: 65 LALDESLFRGRQI--KVIPKRTN 85
Score = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 32/71 (45%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
I+VG + T +++ +F GS+ DK KGF +I F D+ L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 163 KQVICGKEVDV 173
+ + G+++ V
Sbjct: 69 ESLFRGRQIKV 79
>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 = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
+FVGG+ E EI +F++YG V+ + I D TG S+G+ FV++ V ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 79 DHYIGNK-KIDP 89
++ G K K+ P
Sbjct: 71 INFHGKKLKLGP 82
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSF 57
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
+FVGG+ E EI +F++YG V+ + I D TG S+G+ FV++ V ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 79 DHYIGNK-KIDP 89
++ G K K+ P
Sbjct: 71 INFHGKKLKLGP 82
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSF 57
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 17/77 (22%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K+FVG T ++T ++++ +F QYG + + +PF + F F++F D VA
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-------RAFAFVTFADDKVA---- 61
Query: 160 KNPKQVICGKEVDVKRV 176
Q +CG+++ +K +
Sbjct: 62 ----QSLCGEDLIIKGI 74
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
K+FVG + +E+ +F QYGEV + I P+ R FAFVT+ K L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-PF----RAFAFVTFADDKVAQSL 64
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 67/153 (43%), Gaps = 8/153 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----QKAVDDL 74
L V L ++ ++E+ F G + + I D TG S G+AFV +T+ Q+A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
+ NK++ +K ++V L IT+ + F +YGSI +
Sbjct: 77 NGI---TVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 133
Query: 134 FDKSKNMKKGFCFISFDDQNVADQVLKNPKQVI 166
DK +G F+ ++ + A + + VI
Sbjct: 134 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF Y D +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 78 -GDHYIGNKKIDPKRVT 93
+G+KK+ +R +
Sbjct: 63 LNGMQLGDKKLLVQRAS 79
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K+F+GGL + + V++ + +G + F D + + KG+ F + D NV DQ +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
I+VG L T + V++ FSQ+G + + +D+ KGF F+ +++V++ + K
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 163 KQVICGKEVDVKRVKFNPE 181
G+ + V NP+
Sbjct: 64 NTDFMGRTIRVTEA--NPK 80
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R ++VG L + +++ + FSQ+G+V ++ + D T + +GF FV +++V + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 77 AGDH 80
D+
Sbjct: 61 KLDN 64
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 5 ANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G R RKLFVG L++ E ++ F +G +E +I P G S+G AF
Sbjct: 2 SSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAF 60
Query: 63 VTYTTQ 68
V Y++
Sbjct: 61 VKYSSH 66
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 95 RVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITE 129
R P K+FVG L + +E DVR F +G+I E
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEE 44
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPYTGQSRGFAFVTYTTQKA 70
G + +F+G L EK + D FS +G + ++ I DP TG S+G+AF+ + + A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 71 VDDLLAAGD-HYIGNKKI 87
D + A + Y+ N+ I
Sbjct: 61 SDAAIEAMNGQYLCNRPI 78
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 8/60 (13%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
K+F+G L E TEQ++R F QYG + E ++ K + F+ +D+ A+ ++N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHIEDKTAAEDAIRN 61
Score = 36.2 bits (82), Expect = 0.031, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
KLF+G L R E+EI F QYG+V E IKN + FV + A +D +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN---------YGFVHIEDKTAAEDAIR 60
Query: 77 AGDHY 81
HY
Sbjct: 61 NLHHY 65
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF-DDQNVADQVLKN 161
+FVG L+ EIT +D++ F+ +G I++ + D + KG+ F+SF + + + ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 162 PKQVICGKEV 171
Q + G+++
Sbjct: 78 GGQWLGGRQI 87
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT-YTTQKAVDDLLAA 77
+FVG L ++I F+ +G++ + D TG+S+G+ FV+ Y A + ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P C +F+ L E T+ D+ F +G++ + DK ++ K F F+SFD+ + A
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 158 VLKNPKQVICGKEVDVKRVK 177
+K + G +V KR+K
Sbjct: 98 AIK----AMNGFQVGTKRLK 113
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
++FV L+ +E+D+ FS YG ++E P D KGF F++F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
+LFV L + E+++ FS YG + + D T + +GFAFVT+
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
+ LFV ++ +T E ++ F YG ++ I + +G+ RG+AF+ Y ++ D+ +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER---DMHS 159
Query: 77 AGDHYIGNKKIDPKRV 92
A H G KKID +RV
Sbjct: 160 AYKHADG-KKIDGRRV 174
Score = 34.7 bits (78), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+FV + + TE +R F YG I + K +G+ FI ++ + K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH- 163
Query: 163 KQVICGKEVDVKRV 176
GK++D +RV
Sbjct: 164 ---ADGKKIDGRRV 174
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 4 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 55
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAV 71
G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV + +
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELA 57
Query: 72 DDLLAAGDH 80
+D AA D+
Sbjct: 58 EDAAAAIDN 66
>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 = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 6 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 57
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
+R L+VGGL +K ++ F +G++ I I D T + RGFAFV + + +D
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAA 63
Query: 76 AAGDH 80
AA D+
Sbjct: 64 AAIDN 68
>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 = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKN 139
H+ G+ + K + K C ++VG L+ TE+ + + FS+ G I + DK K
Sbjct: 24 HFRGDNEEQEKLLKK-----SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78
Query: 140 MKKGFCFISFDDQNVADQVLK 160
GFCF+ + + A+ ++
Sbjct: 79 TACGFCFVEYYSRADAENAMR 99
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L+VG L T E++I + FS+ G+++ I + D + GF FV Y ++ ++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM--- 98
Query: 79 DHYIGNKKIDPK 90
YI ++D +
Sbjct: 99 -RYINGTRLDDR 109
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 5 ANGTAG-PGRN-DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++G P ++ D KLFVG + R E+++ F ++G + +++ D TG +G AF
Sbjct: 2 SSGSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAF 61
Query: 63 VTYTTQKA 70
+TY + +
Sbjct: 62 LTYCARDS 69
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
K+FVG + + EQD++ F ++G I E D+ + KG F+++
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+FVG L+ EIT +D++ F+ +G I++ + D + KG+ F+SF ++ A+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI--- 74
Query: 163 KQVICGKEVDVKRVKFNPET 182
Q + G+ + ++++ N T
Sbjct: 75 -QQMGGQWLGGRQIRTNWAT 93
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ-KAVDDLLAA 77
+FVG L ++I F+ +G + + D TG+S+G+ FV++ + A + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V L T + F +YG V + I D YT +SRGFAFV + ++ +D + A
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 79 D 79
D
Sbjct: 110 D 110
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+ V LT + +R F +YG + + P D+ +GF F+ F D+ A+ +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 161 N-PKQVICGKEVDVKRVKFN 179
V+ G+E+ V+ ++
Sbjct: 108 AMDGAVLDGRELRVQMARYG 127
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 11 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
++G++G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV
Sbjct: 2 SSGSSGMA-TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 65 YTTQKAVDDLLAAGDH 80
+ + +D AA D+
Sbjct: 61 F---ELAEDAAAAIDN 73
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R L V + E ++ F +YG +ES+ I D T QSRG+ FV + + + +A
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 77 AGDHY-IGNKKI 87
+ + I NK++
Sbjct: 103 GLNGFNILNKRL 114
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 87 IDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCF 146
I P ++ + L+ + V + T + E +R F +YG I + D+ +G+ F
Sbjct: 30 IPPTQMNPEPDVLR-NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88
Query: 147 ISFDDQNVADQVL 159
+ F + A Q +
Sbjct: 89 VKFQSGSSAQQAI 101
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 26/51 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQK 69
L V L +N + E+ FS GEVES + D G S G+ FV Y T K
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK 72
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 52
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
+R L+VGGL +K ++ F +G++ I I D T + RGFAFV + + +D
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAA 58
Query: 76 AAGDH 80
AA D+
Sbjct: 59 AAIDN 63
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 62 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R L+VGGL +K ++ F +G++ I I D T + RGFAFV + + +D A
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 120
Query: 77 AGDH 80
A D+
Sbjct: 121 AIDN 124
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
++V GL ++++++ FSQYG I + D++ + +G FI FD + A++ +K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
RN + ++VGGL E + + F Q G V + + D TGQ +G+ FV + +++ D
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
++G++GP + L V L T + F +YG V + I +P+T RGFAFV
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 65 YTTQKAVDDLLAAGD 79
+ ++ D AA D
Sbjct: 62 FHDRRDAQDAEAAMD 76
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 105 VGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQ 164
V LT + +R F +YG + + P + +GF F+ F D+ A ++ +
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA----QDAEA 73
Query: 165 VICGKEVDVKRVK 177
+ G E+D + ++
Sbjct: 74 AMDGAELDGRELR 86
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L V L T + F +YG V + I D YT +SRGFAFV + ++ +D + A
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 79 D 79
D
Sbjct: 133 D 133
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 105 VGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN-PK 163
V LT + +R F +YG + + P D+ +GF F+ F D+ A+ +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 164 QVICGKEVDVKRVKF 178
V+ G+E+ V+ ++
Sbjct: 135 AVLDGRELRVQMARY 149
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
+ LFV ++ +T E ++ F YG ++ I + +G+ RG+AF+ Y ++ D+ +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER---DMHS 159
Query: 77 AGDHYIGNKKIDPKRV 92
A H G KKID +RV
Sbjct: 160 AYKHADG-KKIDGRRV 174
Score = 34.7 bits (78), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+FV + + TE +R F YG I + K +G+ FI ++ + K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH- 163
Query: 163 KQVICGKEVDVKRV 176
GK++D +RV
Sbjct: 164 ---ADGKKIDGRRV 174
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT----Q 68
R ++RKLFVG L + ++++ F +G ++ ++ P G S+G AFV + T Q
Sbjct: 9 RGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQ 67
Query: 69 KAVDDL 74
A++ L
Sbjct: 68 AAINTL 73
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITE 129
K+FVG L + T++DVR F +G+I E
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDE 41
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
+ L+V L R + +++ F +YG + +I D TG+ RG AFV Y ++ + +
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 76 AAGDHYI 82
+A ++ I
Sbjct: 73 SALNNVI 79
Score = 28.9 bits (63), Expect = 3.9, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
++V L IT+ + F +YGSI + DK +G F+ ++ + A + +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 163 KQVI 166
VI
Sbjct: 76 NNVI 79
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 5 ANGTAG--PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPYTGQSRGFA 61
++G++G P + K+ V + ++EI + FS +GE++++ + K TG RGF
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 62 FVTYTTQK 69
FV + T++
Sbjct: 62 FVDFITKQ 69
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRG---FAFVTYT 66
GP N++ +++VG L + K+I D F +YG + I +KN RG FAFV +
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN------RRGGPPFAFVEFE 69
Query: 67 TQKAVDDLLAAGDHY 81
+ +D + D Y
Sbjct: 70 DPRDAEDAVYGRDGY 84
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKG--FCFISFDDQNVADQV 158
C+I+VG L +I +D+ D F +YG+I + KN + G F F+ F+D A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-----KNRRGGPPFAFVEFEDPRDAEDA 77
Query: 159 L 159
+
Sbjct: 78 V 78
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 93 TKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
+++ P +F+ L E +QD+ F +G++ + DK N+ K F F+S+D+
Sbjct: 18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 153 NVADQVLKNPKQVICGKEVDVKRVK 177
A + Q + G ++ +KR+K
Sbjct: 78 VSAQAAI----QSMNGFQIGMKRLK 98
Score = 28.1 bits (61), Expect = 6.9, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 1 MSYRANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSR 58
++ ++ G AG + + LF+ L + G++++ F +G V S + D T S+
Sbjct: 8 LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
Query: 59 GFAFVTY 65
F FV+Y
Sbjct: 68 CFGFVSY 74
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+ + L V L +N + E F G++ES + D TGQS G+ FV Y+ D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 27/60 (45%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
K + V L +T+ + + F G I + DK G+ F+++ D N AD+ +
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 36/176 (20%), Positives = 73/176 (41%), Gaps = 27/176 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R L+VG L + E + YF G + +I I D ++ +AFV Y
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQ--------- 50
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLKC-------------KIFVGGLTTEITEQDVRDYFSQ 123
+ D I + ++ K++ + + +FVG L + ++ +R+ F
Sbjct: 51 SHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFN 179
+ S +D +G+ F+SF Q+ A +N + G++++ + ++ N
Sbjct: 111 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA----QNAMDSMQGQDLNGRPLRIN 162
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+D LFVG L+ N ++ + + F + S + D TG SRG+ FV++T+Q DD
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ---DD 141
Query: 74 LLAAGDHYIG 83
A D G
Sbjct: 142 AQNAMDSMQG 151
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQ 157
P K ++V L +T D+ FS+YG + + DK KG FI F D++ A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 158 VLK--NPKQV 165
+ N KQ+
Sbjct: 74 CTRAINNKQL 83
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
++V L + ++ FS+YG+V ++I D T +S+G AF+ + + + + A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA- 77
Query: 79 DHYIGNKKI 87
I NK++
Sbjct: 78 ---INNKQL 83
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
+ +F+ L ++ E+ + + Q+G+++ + + P T S+G AF + TQ+A LA
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 77 AG 78
A
Sbjct: 76 AA 77
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKN 139
H+ G+ + K + K C ++VG L+ TE+ + + FS+ G I + DK K
Sbjct: 3 HFRGDNEEQEKLLKK-----SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT 57
Query: 140 MKKGFCFISFDDQNVADQVLK 160
GFCF+ + + A+ ++
Sbjct: 58 -ACGFCFVEYYSRADAENAMR 77
Score = 31.2 bits (69), Expect = 0.79, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
L+VG L T E++I + FS+ G+++ I + D + GF FV Y ++ ++ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAM--- 76
Query: 79 DHYIGNKKIDPK 90
YI ++D +
Sbjct: 77 -RYINGTRLDDR 87
>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 = 0.010, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAG 78
LFVG L+ N ++ + + F + S + D TG SRG+ FV++T+Q DD A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ---DDAQNAM 60
Query: 79 DHYIG 83
D G
Sbjct: 61 DSMQG 65
Score = 31.6 bits (70), Expect = 0.65, Method: Composition-based stats.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
+FVG L + ++ +R+ F + S +D +G+ F+SF Q+ A +N
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA----QNA 59
Query: 163 KQVICGKEVDVKRVKFN 179
+ G++++ + ++ N
Sbjct: 60 MDSMQGQDLNGRPLRIN 76
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 9/91 (9%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAF 62
++G++GP + + LFV GL +T E+ + + F G V + I D TG S+GF F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRA-RIVTDRETGSSKGFGF 58
Query: 63 VTYTTQKAVDDLLAAGDHYIGNKKIDPKRVT 93
V + +++ A + + +ID +VT
Sbjct: 59 VDFNSEEDAK----AAKEAMEDGEIDGNKVT 85
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 95 RVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
R P K +FV GL+ + TE+ +++ F GS+ + D+ KGF F+ F+ +
Sbjct: 11 RSQPSK-TLFVKGLSEDTTEETLKESFD--GSVRA-RIVTDRETGSSKGFGFVDFNSEED 66
Query: 155 ADQVLKNPKQVICGKEVDVKRVKFN 179
A K K+ + E+D +V +
Sbjct: 67 A----KAAKEAMEDGEIDGNKVTLD 87
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
+RKLFVG L++ E+++ F +G ++ ++ P G S+G AFV +++
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYG---SITEFQQPFDKSKNMKKGFCFISFDD-QN 153
PL CK++VG L + ++ F YG S+ + P GF F+ F+D ++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRD 122
Query: 154 VADQVLKNPKQVICGKEVDVK 174
AD V + + +CG V V+
Sbjct: 123 AADAVRELDGRTLCGCRVRVE 143
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
K++VG L N + E+ F YG + S+ + +P GFAFV +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF 117
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+++G + + TE+ + D S G + + FD KG+ FI F D + ++N
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
>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 = 0.022, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+++ GL T+QD+ YG I + DK+ N KG+ F+ FD + A + +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTT---- 67
G + L++ GL T ++++ YG++ S D T + +G+ FV + +
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 68 QKAVDDLLAAG 78
QKAV L A+G
Sbjct: 61 QKAVTALKASG 71
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 8/68 (11%)
Query: 7 GTAGPGRNDER--KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVT 64
G++G D+ L+VGGL E ++ ++F Q+GE+ +I++ Q + AF+
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQ 54
Query: 65 YTTQKAVD 72
+ T++A +
Sbjct: 55 FATRQAAE 62
Score = 34.7 bits (78), Expect = 0.086, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNP 162
++VGGL ITE D+R++F Q+G I + ++ FI F + A+ +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTI------TVVQRQQCAFIQFATRQAAEVAAEKS 68
Query: 163 --KQVICGKEVDVK 174
K ++ G+ ++VK
Sbjct: 69 FNKLIVNGRRLNVK 82
>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 = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 30/65 (46%)
Query: 97 NPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
NP +++G + + TE+ + D S G + + FD KG+ FI F D +
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 157 QVLKN 161
++N
Sbjct: 61 SAVRN 65
Score = 36.2 bits (82), Expect = 0.028, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ +
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 98 PLKCKIFVGGLTTEITEQDVRDYFSQYG---SITEFQQPFDKSKNMKKGFCFISFDD-QN 153
PL CK++VG L + ++ F YG S+ + P GF F+ F+D ++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRD 122
Query: 154 VADQVLKNPKQVICGKEVDVK 174
AD V + +CG V V+
Sbjct: 123 AADAVRDLDGRTLCGCRVRVE 143
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
K++VG L N + E+ F YG + S+ + +P GFAFV +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF 117
>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 = 36.2 bits (82), Expect = 0.030, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ +
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
Score = 34.7 bits (78), Expect = 0.081, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
+++G + + TE+ + D S G + + FD KG+ FI F D + ++N
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.2 bits (82), Expect = 0.031, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
P D R +F L +++ D+FS G+V + I +D + +S+G A+V + ++
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 71 V 71
V
Sbjct: 80 V 80
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+F L I +D+ D+FS G + + + D++ KG ++ F
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.8 bits (81), Expect = 0.033, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKG 143
K++ + V + +P C ++ GG+ + +T+Q +R FS +G I E + P +KG
Sbjct: 10 KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-------EKG 62
Query: 144 FCFISFDDQNVADQVL 159
+ F+ F A +
Sbjct: 63 YSFVRFSTHESAAHAI 78
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 26/109 (23%), Positives = 50/109 (45%), Gaps = 17/109 (15%)
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
L+ G H K PKR + V + + D+R F Q+G I + +
Sbjct: 14 LVPRGSHMNTENKSQPKR-----------LHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62
Query: 134 FDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKFNPET 182
F++ + KGF F++F++ AD+ ++ + G V+ ++++ N T
Sbjct: 63 FNERGS--KGFGFVTFENSADADRA----REKLHGTVVEGRKIEVNNAT 105
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ ++FVG L +ITE+++R F +YG E D KGF FI + + +A+
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 72
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 47/110 (42%), Gaps = 10/110 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+LFVG L + E+E+ F +YG+ + I D +GF F+ T+ L
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR----TLAEI 73
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSI 127
+ N + K++ R + V L ++ + + + FS +G +
Sbjct: 74 AKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQV 123
>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 = 35.4 bits (80), Expect = 0.044, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAD 156
+ ++FVG L +ITE+++R F +YG E D KGF FI + + +A+
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 65
Score = 31.6 bits (70), Expect = 0.67, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ 68
+LFVG L + E+E+ F +YG+ + I D +GF F+ T+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR 61
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
RAN P N R L++ L +E+ D F +YG + I + N P ++RG A+V
Sbjct: 8 RANIRLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYV 62
Query: 64 TYTTQKAVDDLLAAGDHYIG 83
Y + + D A DH G
Sbjct: 63 VY---EDIFDAKNACDHLSG 79
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 34.3 bits (77), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 28/142 (19%), Positives = 61/142 (42%), Gaps = 11/142 (7%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ RK+ + GL + +E++D S Y E++ + D Y +G AFVT + +
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV--DKY----KGTAFVTLLNGEQAE- 71
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
A + ++ + ++ ++ P + V L +T+Q + +GS+
Sbjct: 72 ---AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Query: 134 FDKSKNMKKGFCFISFDDQNVA 155
+ + KG+ F + ++ A
Sbjct: 129 YSERTGQSKGYGFAEYMKKDSA 150
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 87 IDPKRVTKRVNPL------KCKIFVGGLTTEITEQDVRDYFSQY 124
+DP+ + KR+ + KI + GL ++T Q+V D S Y
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY 46
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 34.3 bits (77), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 28/142 (19%), Positives = 61/142 (42%), Gaps = 11/142 (7%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ RK+ + GL + +E++D S Y E++ + D Y +G AFVT + +
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV--DKY----KGTAFVTLLNGEQAE- 71
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
A + ++ + ++ ++ P + V L +T+Q + +GS+
Sbjct: 72 ---AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Query: 134 FDKSKNMKKGFCFISFDDQNVA 155
+ + KG+ F + ++ A
Sbjct: 129 YSERTGQSKGYGFAEYMKKDSA 150
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 87 IDPKRVTKRVNPL------KCKIFVGGLTTEITEQDVRDYFSQY 124
+DP+ + KR+ + KI + GL ++T Q+V D S Y
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY 46
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
K++VG L G+ E+ FS YG + ++ I +P GFAFV + + +D +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 78 GD 79
D
Sbjct: 57 LD 58
Score = 31.2 bits (69), Expect = 0.87, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD-QNVADQVLK 160
K++VG L T + ++ FS YG + ++N GF F+ F+D ++ D V
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVW----IARN-PPGFAFVEFEDPRDAEDAVRG 56
Query: 161 NPKQVICGKEVDVK 174
+VICG V V+
Sbjct: 57 LDGKVICGSRVRVE 70
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
D L++ L + E+E+ + +G+V S I D +G SRG F + + + +
Sbjct: 24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAV 82
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLKCK 102
+ H+ G P V+ PL CK
Sbjct: 83 IG---HFNGKFIKTPPGVSAPTEPLLCK 107
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
RAN P N R L + L +E+ D F +YG + I + N P ++RG A+V
Sbjct: 8 RANIRLPPEVN--RILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYV 62
Query: 64 TYTTQKAVDDLLAAGDHYIG 83
Y + + D A DH G
Sbjct: 63 VY---EDIFDAKNACDHLSG 79
>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 = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 28/142 (19%), Positives = 61/142 (42%), Gaps = 11/142 (7%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
+ RK+ + GL + +E++D S Y E++ + D Y +G AFVT + +
Sbjct: 18 RNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV--DKY----KGTAFVTLLNGEQAE- 69
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
A + ++ + ++ ++ P + V L +T+Q + +GS+
Sbjct: 70 ---AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 126
Query: 134 FDKSKNMKKGFCFISFDDQNVA 155
+ + KG+ F + ++ A
Sbjct: 127 YSERTGQSKGYGFAEYMKKDSA 148
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 87 IDPKRVTKRVNPL------KCKIFVGGLTTEITEQDVRDYFSQY 124
+DP+ + KR+ + KI + GL ++T Q+V D S Y
Sbjct: 1 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY 44
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 19/81 (23%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKN 161
++ V + + D+R F Q+G I + + F++ + KGF F++F++ AD+
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRA--- 71
Query: 162 PKQVICGKEVDVKRVKFNPET 182
++ + G V+ ++++ N T
Sbjct: 72 -REKLHGTVVEGRKIEVNNAT 91
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 10/67 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQS------RGFAFVTYTTQKA 70
RK+FVGGL + E EI F ++G + + + P+ +S +G+AF+ + + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQEESS 64
Query: 71 VDDLLAA 77
V L+ A
Sbjct: 65 VQALIDA 71
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEF--QQPFDKSKNMKKGFCFISFDDQN 153
K+FVGGL +I E ++ F ++G + + KS KG+ F+ F +++
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK-- 160
IF+ L I + + D FS +G+I + D +N KG+ F+ F+ Q A++ ++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 71
Query: 161 -----NPKQVICGK 169
N ++V G+
Sbjct: 72 NGMLLNDRKVFVGR 85
Score = 32.7 bits (73), Expect = 0.33, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+F+ L ++ K + D FS +G + S + D S+G+ FV + TQ+A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 65
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.7 bits (73), Expect = 0.31, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
RAN P N R L++ L +E+ D F +YG + I + N P ++RG A+V
Sbjct: 2 RANIRLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYV 56
Query: 64 TYTTQKAVDDLLAAGDHYIG 83
Y + + D A DH G
Sbjct: 57 VY---EDIFDAKNACDHLSG 73
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 112 ITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEV 171
+ ++ + FS+ G + + P D++ KGF F+ N A +++K+ GK +
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS----FHGKRL 79
Query: 172 DVKRVKF 178
D+K F
Sbjct: 80 DLKHRLF 86
Score = 28.1 bits (61), Expect = 8.4, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 30 EKEINDYFSQYGEVESISIKNDPYTGQSRGFAFV 63
+K + FS+ G+V ++ D TG+++GF FV
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.3 bits (72), Expect = 0.35, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 12 GRNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
G + + +LF+G L +N ++++ FS YG + I+IKN F F+ + ++
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQS 69
Query: 71 VDDLL 75
V D +
Sbjct: 70 VRDAI 74
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 12 GRNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKA 70
G + + +LF+G L +N ++++ FS YG + I+IKN F F+ + ++
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQS 69
Query: 71 VDDLL 75
V D +
Sbjct: 70 VRDAI 74
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFD 135
K V +NP++ + F LT E++V+ F+Q+ E PFD
Sbjct: 279 KLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWLERHGPFD 324
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLKNPKQVICGKEVDVKRVKF 178
FS+ G + + P D++ KGF F+ N A +++K+ GK +D+K F
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS----FHGKRLDLKHRLF 86
>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 = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK-- 160
IF+ L I + + D FS +G+I + D +N KG+ F+ F+ Q A++ ++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 161 -----NPKQVICGK 169
N ++V G+
Sbjct: 66 NGMLLNDRKVFVGR 79
Score = 32.0 bits (71), Expect = 0.46, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVD 72
+F+ L ++ K + D FS +G + S + D S+G+ FV + TQ+A +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 59
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R L++ L +E+ D F +YG + I + N P ++RG A+V Y + + D
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVY---EDIFDAKN 62
Query: 77 AGDHYIG 83
A DH G
Sbjct: 63 AVDHLSG 69
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFD 135
K V +NP++ + F LT E++V+ F+Q+ E PFD
Sbjct: 279 KLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWLERHGPFD 324
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 32.0 bits (71), Expect = 0.51, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 12/88 (13%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLA 76
R +FV G R ++++YF +G V S+ + D FA V A + +L+
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLS 63
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLKCKIF 104
H +G ++ RV P + K F
Sbjct: 64 QSQHSLGGHRL-------RVRPREQKEF 84
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.6 bits (70), Expect = 0.68, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 18 KLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
+LF+G L +N ++++ FS YG + I+IKN F F+ + ++V D +
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 54
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.6 bits (70), Expect = 0.69, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 10/94 (10%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPYTGQSRGFAFVTY--- 65
G + LF+ L+ +T E+ + FS+ G ++S +I KN S GF FV Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 66 -TTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNP 98
QKA+ L H + K++ + + P
Sbjct: 61 EQAQKALKQLQG---HTVDGHKLEVRISERATKP 91
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQ---QPF-----DKSKNMKKGFCFISFDD 151
IFV GL +T + V DYF Q G I + QP D+ KG +SFDD
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPYTGQSRGFAFVTY 65
D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V++
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQ---QPF-----DKSKNMKKGFCFISFDD 151
IFV GL +T + V DYF Q G I + QP D+ KG +SFDD
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPYTGQSRGFAFVTY 65
+D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V++
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 102 KIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+++G L+ +T D+R F + + P +K G+ F+ + DQN A
Sbjct: 10 KLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWA 57
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 9/61 (14%)
Query: 16 ERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDL 74
+ +LF+G L +N ++++ FS YG + I+IKN F F+ + ++V D
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDA 61
Query: 75 L 75
+
Sbjct: 62 I 62
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPYTGQSRGFAFVTYTTQKAVDDL 74
K+ +G L RN + I + FS YG+++ I + + P+ S+G+A+V + +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHL--SKGYAYVEFENPDEAEKA 63
Query: 75 LAAGD 79
L D
Sbjct: 64 LKHMD 68
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 24 LHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDD 73
L+ N E + D +YGEVE + I P T + G A V +T+ + +
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 5 ANGTAGPGRND--ERKLFVGGLHRNTGEKEINDYFSQYGEVESISI-----KNDPY 53
++G++G +D R L+VG L R+ E I FSQ G +S + NDPY
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPY 57
>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 = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQ-KAVDDLLAA 77
+FVG L I F+ +G + + D TG+S+G+ FV++ + A + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPYTGQSRGFAFVT 64
G++G N +LF+GG+ + +EI + ++ E ++ I + ++RGFAFV
Sbjct: 1 GSSGSSGN--CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVE 58
Query: 65 YTTQKA 70
Y + +A
Sbjct: 59 YESHRA 64
>pdb|1YQ3|B Chain B, Avian Respiratory Complex Ii With Oxaloacetate And
Ubiquinone
pdb|1YQ4|B Chain B, Avian Respiratory Complex Ii With 3-Nitropropionate And
Ubiquinone
pdb|2FBW|B Chain B, Avian Respiratory Complex Ii With Carboxin Bound
pdb|2FBW|O Chain O, Avian Respiratory Complex Ii With Carboxin Bound
pdb|2H88|B Chain B, Avian Mitochondrial Respiratory Complex Ii At 1.8 Angstrom
Resolution
pdb|2H88|O Chain O, Avian Mitochondrial Respiratory Complex Ii At 1.8 Angstrom
Resolution
pdb|2H89|B Chain B, Avian Respiratory Complex Ii With Malonate Bound
pdb|2WQY|B Chain B, Remodelling Of Carboxin Binding To The Q-Site Of Avian
Respiratory Complex Ii
pdb|2WQY|O Chain O, Remodelling Of Carboxin Binding To The Q-Site Of Avian
Respiratory Complex Ii
Length = 252
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 75 LAAGDHYIGNKKIDPK-RVTKRVNPLKCKIFVGGLTTEITEQDVRDYFSQYGSITEFQQP 133
+A G+ KKIDP T ++ PL V L D+ ++++QY SI + +
Sbjct: 77 IAGGNTLACTKKIDPDLSKTTKIYPLPHMYVVKDLVP-----DLSNFYAQYKSIEPYLKK 131
Query: 134 FDKSKNMKKGFCFISFDDQNVAD 156
D+SK K+ + S +D+ D
Sbjct: 132 KDESKQGKEQY-LQSIEDRQKLD 153
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 30 EKEINDYFSQYG-EVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAAGDH 80
E +I +G + + + + +GQSRGFAFV ++ + + A H
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQH 66
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPYTGQSRGFAFVTYTTQKAVDDLLAA 77
+++ GL K + D+F + VE SI I P G++ G FV + + L
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRNEADYKAALCR 86
Query: 78 GDHYIGNKKIDPKRVTKR 95
Y+GN+ I +TK+
Sbjct: 87 HKQYMGNRFIQVHPITKK 104
>pdb|2J8A|A Chain A, X-Ray Structure Of The N-Terminus Rrm Domain Of Set1
Length = 136
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 99 LKCKIFV----GGLTTEITEQDVRDYFSQYGSITEFQ 131
+ C+I V TT I + +++YF +YG I+ F+
Sbjct: 1 MSCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFE 37
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.5 bits (62), Expect = 6.3, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 12/61 (19%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY----TTQKAVDD 73
+LFV + E E+N+ F +G ++ + I N GFAFV + + KA+++
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 57
Query: 74 L 74
+
Sbjct: 58 V 58
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 101 CKIFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
K+ V L +++ D+++ F+++G++ + +D+S G + F+ + A + +K
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 147
Query: 161 NPKQV-ICGKEVDVKRV 176
K V + G+ +D++ V
Sbjct: 148 QYKGVPLDGRPMDIQLV 164
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIK--NDPYTGQSRGFAFVTYTTQKA 70
RN ++VG T ++++ G + + +K + GQS+G+A V ++ +
Sbjct: 52 RNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENS 111
Query: 71 VDDLLAAGDHYIGN-KKIDPKRVTKR 95
V LL + N +K+D + T++
Sbjct: 112 VHKLLELLPGKVLNGEKVDVRPATRQ 137
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVLK 160
+FV L +TE+ + FSQ+G + ++ K +K + FI FD+++ A + ++
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKL-------ERVKKLKD-YAFIHFDERDGAVKAME 63
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQ---QP-----FDKSKNMKKGFCFISFDDQNV 154
I+V GL +T D+ D+F Q G + + QP DK KG +S++D
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 155 A 155
A
Sbjct: 78 A 78
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.1 bits (61), Expect = 7.0, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 8/53 (15%)
Query: 103 IFVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
+FV L T +TE+ + FS++G + ++ K +K + F+ F+D+ A
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKL-------ERVKKLKD-YAFVHFEDRGAA 62
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.1 bits (61), Expect = 7.2, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPYTGQSRGFAFVTYTTQKAVDDLL 75
+FV GL + + E+ +YF ++G++ + I N S+G + Y T +D L
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 76 AA 77
A
Sbjct: 78 RA 79
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.1 bits (61), Expect = 8.5, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPYTGQSRGFAFVTY----TT 67
G +LFV + E E+N+ F +G ++ + I N GFAFV + +
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78
Query: 68 QKAVDDL 74
KA++++
Sbjct: 79 AKAIEEV 85
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 27.7 bits (60), Expect = 9.1, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 104 FVGGLTTEITEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVADQVL 159
+VG L + D+ F SI + DK + KGFC++ FD+ + + L
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
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 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,824,879
Number of Sequences: 62578
Number of extensions: 387533
Number of successful extensions: 1320
Number of sequences better than 100.0: 167
Number of HSP's better than 100.0 without gapping: 124
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 1002
Number of HSP's gapped (non-prelim): 308
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
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: 52 (24.6 bits)