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= psy1314
(275 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 = 114 bits (284), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + 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 = 114 bits (284), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 75 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 134
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + G +V++
Sbjct: 135 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 180
>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 = 113 bits (283), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 73 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 132
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + G +V++
Sbjct: 133 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 178
>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 = 113 bits (283), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 67 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 126
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + G +V++
Sbjct: 127 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 113 bits (283), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + G +V++
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 113 bits (282), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+ T + VD +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
A H + + ++PKR R + + KIFVGG+ + E +RDYF QYG I
Sbjct: 72 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 131
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
+ D+ K+GF F++FDD + ++++ + 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 = 110 bits (276), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 56/161 (34%), Positives = 95/161 (59%), Gaps = 2/161 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL+ +T E + +YF +YG V + I DP TG+SRGF F++F +VD+++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
H + K IDPKR R K KIFVGG+ ++ ++ ++FSQ+G+I + Q DK
Sbjct: 65 -QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 137 SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK 177
+GF F+++D + ++V N +++++KR +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE 164
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 49/75 (65%), Gaps = 1/75 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+F+GGL + +E ++R+YF +YG++T+ + D + +GF F+SF+ + ++V+
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 = 76.3 bits (186), Expect = 2e-14, Method: Composition-based stats.
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+GGL +T +K++ DYFS++GEV ++K DP TG+SRGF FV F ++VD ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 DHYIGNKKIDPKR 91
+H + K IDPKR
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 51.6 bits (122), Expect = 5e-07, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+GGL+ + +++D++DYFS++G + + D +GF F+ F + ++V+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 163 KQVICGKEVDVKR 175
+ + GK +D KR
Sbjct: 62 EHKLNGKVIDPKR 74
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 75.9 bits (185), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVTF Q VD +LA
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 78 GDHYIGNKKIDPK 90
H + +K IDPK
Sbjct: 87 SRHELDSKTIDPK 99
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+F+GGL+ + +++ +R+YF Q+G + E D +GF F++F DQ ++VLA
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
Query: 161 NPKQVICGKEVDVK 174
+ + K +D K
Sbjct: 86 QSRHELDSKTIDPK 99
>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 = 74.7 bits (182), Expect = 5e-14, Method: Composition-based stats.
Identities = 35/83 (42%), Positives = 53/83 (63%)
Query: 9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
A D K FVGGL +T +K++ DYF+++GEV +IK DP+TG+SRGF F+ F
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
+V+ +L +H + + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86
Score = 52.0 bits (123), Expect = 3e-07, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K FVGGL+ + S++D++DYF+++G + + D + +GF FI F D E+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 = 74.7 bits (182), Expect = 6e-14, Method: Composition-based stats.
Identities = 34/73 (46%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVTF Q VD +LA
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPK 90
H + +K IDPK
Sbjct: 62 SRHELDSKTIDPK 74
Score = 56.2 bits (134), Expect = 2e-08, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+F+GGL+ + +++ +R+YF Q+G + E D +GF F++F DQ ++VLA
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVK 174
+ + K +D K
Sbjct: 61 QSRHELDSKTIDPK 74
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 73.6 bits (179), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 49/79 (62%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T E+ + +Y+ Q+G++ + DP + +SRGF FVTF++ VD +A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 77 AGDHYIGNKKIDPKRVTKR 95
A H I + ++PKR R
Sbjct: 88 ARPHSIDGRVVEPKRAVAR 106
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ E +E+ +R+Y+ Q+G +T+ D + +GF F++F + +A
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 = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/78 (47%), Positives = 45/78 (57%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLFVGGL +T ++ + YFSQYGEV I D T QSRGF FV F V +LA+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
H + + IDPK T R
Sbjct: 78 RPHTLDGRNIDPKPCTPR 95
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL +++ +R YFSQYG + + DK+ N +GF F+ F D N VLA+
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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 71/145 (48%), Gaps = 2/145 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L +N + E+ FS GEVES + D G S G+ FV + T K + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79 DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
+ + +K I +K +++ GL ++++DV D FS++G I + D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVAEQVLAN 161
+ + +G FI FD ++ AE+ + +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITS 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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 71/145 (48%), Gaps = 2/145 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L +N + E+ FS GEVES + D G S G+ FV + T K + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79 DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
+ + +K I +K +++ GL ++++DV D FS++G I + D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVAEQVLAN 161
+ + +G FI FD ++ AE+ + +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 78/160 (48%), Gaps = 21/160 (13%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAV 71
+D K+FVG + R EK++ + F QYG V I++ D QS+G FVTF T+KA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72 DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRD 119
+ +L H I K D ++ V R K+F+G ++ + +E D+R
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
FS +G I E + + +G F++F + +A+ +
Sbjct: 115 MFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAI 153
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
++RKLF+G + + E +I FS +G++E I P G SRG AFVTFTT+
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTA 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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 21/159 (13%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND--PHTGQSRGFAFVTFTTQKAVD 72
D K+FVG + R EK++ + F QYG V I++ D + QS+G FVTF T+KA
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 73 D---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRDY 120
+ +L H I K D ++ V R K+F+G ++ + +E D+R
Sbjct: 74 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRVM 127
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
FS +G I E + + +G F++F + +A+ +
Sbjct: 128 FSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAI 165
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 76/160 (47%), Gaps = 21/160 (13%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAV 71
+D K FVG + R EK++ + F QYG V I++ D QS+G FVTF T+KA
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72 DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRD 119
+ +L H I K D ++ V R K+F+G ++ + +E D+R
Sbjct: 61 LEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDR------KLFIGXISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
FS +G I E + + +G F++F + A+ +
Sbjct: 115 XFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
++RKLF+G + + E +I FS +G++E I P G SRG AFVTFTT+
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTA 152
Query: 75 LAA 77
+ A
Sbjct: 153 IKA 155
>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 = 4e-10, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 46/74 (62%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGGL +T E++I +YF +GEVESI + D T + RGF F+TF ++ V ++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 77 AGDHYIGNKKIDPK 90
H +G K + K
Sbjct: 62 KKYHNVGLSKCEIK 75
Score = 57.8 bits (138), Expect = 6e-09, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
KIFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 46/76 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGG+ E ++R+YF ++G +TE +D K +GF FI+F+D+ +Q +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 PKQVICGKEVDVKRVK 177
I GK+V+VKR +
Sbjct: 72 HFHDIMGKKVEVKRAE 87
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 45/78 (57%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGG+ N GE E+ +YF ++G V + + D + RGF F+TF +++VD +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 78 GDHYIGNKKIDPKRVTKR 95
H I KK++ KR R
Sbjct: 72 HFHDIMGKKVEVKRAEPR 89
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
L V L +N ++E F GE+ES + D TGQS G+ FV + +KA++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 75 --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
L I P + R ++V GL ++++++ FSQYG I +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVL 159
D+ + +G FI FD + AE+ +
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
L V L +N + E F G++ES + D TGQS G+ FV ++ KA++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 75 --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
L I P + R ++V GL +S++++ FSQYG I +
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVL 159
D++ + +G FI FD + AE+ +
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAI 149
>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 = 2e-09, Method: Composition-based stats.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVGGL +T E++I +YF +GEVESI + D T + RGF F+TF ++ V ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 DHYIGNKKIDPK 90
H +G K + K
Sbjct: 62 YHNVGLSKCEIK 73
Score = 56.2 bits (134), Expect = 2e-08, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 37/57 (64%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
IFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+DE KLFVGGL +T E+ + FS+YG++ + + D T +SRGF FVTF D
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 74 LLAAGDHYIGNKKIDPKRV 92
+ A + K +D +++
Sbjct: 70 AMMA----MNGKSVDGRQI 84
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 4/78 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL+ + +EQ + FS+YG I+E D+ +GF F++F++ + A+ +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM-- 71
Query: 162 PKQVICGKEVDVKRVKFN 179
+ GK VD ++++ +
Sbjct: 72 --MAMNGKSVDGRQIRVD 87
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 57.4 bits (137), Expect = 9e-09, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
IFVGGL+ + +DV+ YF Q+G + + FDK+ N +GF F++F+ +++ E+V
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 163 KQVICGKEVDVKR 175
I K V+ K+
Sbjct: 62 FHEINNKMVECKK 74
Score = 56.2 bits (134), Expect = 2e-08, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 43/73 (58%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVGGL NT +++ YF Q+G+V+ + D T + RGF FVTF ++ V+ +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 79 DHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 62 FHEINNKMVECKK 74
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 47/166 (28%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD-- 72
L+VG LH + E + + FS G + SI + D T +S G+A+V F ++A+D
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 73 --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
D++ I + DP V IF+ L I + + D FS +G+I
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 133
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
+ D +N KG+ F+ F+ Q AE+ +L N ++V G+
Sbjct: 134 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
>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 = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/166 (28%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD-- 72
L+VG LH + E + + FS G + SI + D T +S G+A+V F ++A+D
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 73 --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
D++ I + DP V IF+ L I + + D FS +G+I
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 128
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
+ D +N KG+ F+ F+ Q AE+ +L N ++V G+
Sbjct: 129 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G+AGP R L+VG LH N E + F +G +ESI + D TG+S+G+ F+TF+
Sbjct: 22 GSAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 67 ----TQKAVDDL 74
+KA++ L
Sbjct: 77 DSECAKKALEQL 88
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+++VG L I+E +R F +G I Q D KG+ FI+F D A++ L
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 5 ANGTAGPGRNDERK--LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++G R ++ L V GL T E+++ +YFS +GEV + +K D TG S+GF F
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 63 VTFT 66
V FT
Sbjct: 62 VRFT 65
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+ V GL + +EQD+++YFS +G + Q D KGF F+ F + +V++
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ- 76
Query: 163 KQVICGKEVDVK 174
+ +I G+ D K
Sbjct: 77 RHMIDGRWCDCK 88
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV + +A L
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 78 GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++S+ D++ F +
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
G I D + KG+ FI ++ ++ +++
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ + ++ D +++
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 187 MNLFDLGGQYL---RVGKAVTP 205
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
+ +++VG + E+ E +R F+ +G I +D KGF F+ ++ A+
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 159 LANPKQVIC-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 = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI + D T + +GFAFV + +A L
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 78 GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++S+ D++ F +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
G I D + KG+ FI ++ ++ +++
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ + ++ D +++
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 172 MNLFDLGGQYL---RVGKAVTP 190
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94 KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+R + C+++VG + E+ E +R F+ +G I +D KGF F+ ++
Sbjct: 7 QRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Query: 154 VAEQVLANPKQVIC-GKEVDVKR 175
A+ L V+ G+ + V R
Sbjct: 67 AAQLALEQMNSVMLGGRNIKVGR 89
>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 = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 34/157 (21%), Positives = 71/157 (45%), Gaps = 13/157 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++VG ++ GE I F+ +G ++SI D T + +GFAFV + +A L
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 78 GDHY-IGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
+ +G + I R + + P+ +I+V + ++S+ D++ F +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
G I D + KG+ FI ++ ++ +++
Sbjct: 134 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++V +H++ + +I F +G+++S ++ DP TG+ +G+ F+ + ++ D +++
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 78 GDHY-IGNKKIDPKRVTKRVNP 98
+ + +G + + RV K V P
Sbjct: 171 XNLFDLGGQYL---RVGKAVTP 189
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94 KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+R + C+++VG + E+ E +R F+ +G I +D KGF F+ ++
Sbjct: 6 QRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPE 65
Query: 154 VAEQVLANPKQV-ICGKEVDVKR 175
A+ L V + G+ + V R
Sbjct: 66 AAQLALEQXNSVXLGGRNIKVGR 88
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 17/171 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ F T
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 67 TQ-KAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG 125
TQ A D ++ G + D + + P K+F+GGL +++ V++ + +G
Sbjct: 67 TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 121
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-KEVDVKR 175
+ F D + + KG+ F + D NV +Q +A + G K++ V+R
Sbjct: 122 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL ++ +R YF +G I E D+ +G+ F++ D+ AE+ +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 162 PKQVICGKEVDV 173
P +I G++ +V
Sbjct: 79 PNPIIDGRKANV 90
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 33/55 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
K+FVGGL +T + + YF +G++E + D TG+SRG+ FVT + A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 51/91 (56%), Gaps = 5/91 (5%)
Query: 90 KRVTKRVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
+ V R NP C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKRVKFN 179
F++ + A++ K+ G E+D +R++ +
Sbjct: 95 FENVDDAKEA----KERANGMELDGRRIRVD 121
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV F VDD A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 105
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 106 ERANG-MELDGRRI 118
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 17/171 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ F T
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67 TQ-KAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG 125
TQ A D ++ G + D + + P K+F+GGL +++ V++ + +G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-KEVDVKR 175
+ F D + + KG+ F + D NV +Q +A + G K++ V+R
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
KLF+GGL+R T EK + F ++G + + + D T +SRGFAF+TF
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITF 55
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 8/80 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAEQ 157
K+F+GGL E +E+ ++ F ++G I+E D++ + +GF FI+F D +N A+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKNAAKD 67
Query: 158 VLANPKQVICGKEVDVKRVK 177
+ + + GK + V++ K
Sbjct: 68 MNG---KSLHGKAIKVEQAK 84
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 42/66 (63%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
++G++G +D KLF+G + RN EK++ F ++G++ +++ D TG +G AF+T
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 65 FTTQKA 70
+ +++
Sbjct: 62 YCERES 67
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+F+G + + E+D++ F ++G I E D+ M KG F+++ ++ A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
>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 = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 44/186 (23%), Positives = 81/186 (43%), Gaps = 27/186 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
R+L+VG + E+ + D+F+ + ++ +P Q + FAF+ F T
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67 TQ-KAVDDLLAAGDHYIGNKKID---------------PKRVTKRVNPLKCKIFVGGLTT 110
TQ A D ++ G + D P V+ V K+F+GGL
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-K 169
+++ V++ + +G + F D + + KG+ F + D NV +Q +A + G K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 170 EVDVKR 175
++ V+R
Sbjct: 185 KLLVQR 190
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ +
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 154 VAEQVLANPKQVICGKEVDVKRVK 177
A++ K+ G E+D +R++
Sbjct: 69 DAKEA----KERANGMELDGRRIR 88
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV F VDD A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 74
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 75 ERANG-MELDGRRI 87
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A V + T
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 69 K 69
K
Sbjct: 79 K 79
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV + E E ++++ F YG I D+ KG+ + ++ Q LA
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK---QALA-A 84
Query: 163 KQVICGKEV 171
K+ + G E+
Sbjct: 85 KEALNGAEI 93
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 69 K 69
K
Sbjct: 75 K 75
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
>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 = 7e-06, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDER-KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 69 K 69
K
Sbjct: 62 K 62
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 29/57 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++ A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ +
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
A++ K+ G E+D +R++ +
Sbjct: 69 DAKEA----KERANGMELDGRRIRVD 90
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV F + VDD A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEAK 74
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 75 ERANG-MELDGRRI 87
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ +
Sbjct: 6 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
A++ K+ G E+D +R++ +
Sbjct: 66 DAKEA----KERANGMELDGRRIRVD 87
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV F + VDD A
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEAK 71
Query: 79 DHYIGNKKIDPKRV 92
+ G ++D +R+
Sbjct: 72 ERANG-MELDGRRI 84
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
GP R+ E LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 69 K 69
K
Sbjct: 76 K 76
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 8/153 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
L V L ++ ++E+ F G + + I D TG S G+AFV FT +Q+A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
+ NK++ +K ++V L I++ + F +YGSI +
Sbjct: 66 ---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
DK +G F+ ++ + A++ ++ VI
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 37.7 bits (86), Expect = 0.007, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 29/57 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 37.7 bits (86), Expect = 0.007, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 29/57 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
GP R+ E LFV +H E EI + F YGE+++I + D TG S+G+A V + T
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 69 K 69
K
Sbjct: 125 K 125
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV + E E ++++ F YG I D+ KG+ + ++ +Q LA
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE---THKQALA-A 130
Query: 163 KQVICGKEV 171
K+ + G E+
Sbjct: 131 KEALNGAEI 139
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
LFV G+H E++I+D F++YGE+++I + D TG +G+ V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FV G+ E +E+D+ D F++YG I D+ KG+ + ++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
G G G+ +FVGG+ E EI +F++YG V+ + I D TG S+G+ FV+F
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 59
Query: 67 TQKAVDDLLAAGDHYIGNK-KIDP 89
V ++ + ++ G K K+ P
Sbjct: 60 NDVDVQKIVESQINFHGKKLKLGP 83
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF D Q + E
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 69
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 5 ANGTAGPGR--NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++GP R +D + V L +T E ++ + F +G + I + D TGQS+GFAF
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 63 VTF 65
++F
Sbjct: 62 ISF 64
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
I V L+ + E D+++ F +GSI+ DK+ KGF FISF + A + +A
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 8/153 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
L V L ++ ++E+ F G + + I D TG S G+AFV FT +Q+A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
+ NK++ +K ++V L I++ + F +YGSI +
Sbjct: 77 NGIT---VRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 133
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
DK +G F+ ++ + A++ ++ VI
Sbjct: 134 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
>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: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND--PHTGQSRGFAFVTFTTQKA 70
+D K+FVG + R EK++ + F QYG V I++ D + QS+G FVTF T+KA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Score = 44.3 bits (103), Expect = 7e-05, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISFDDQNVA 155
K+FVG + SE+D+R+ F QYG++ E D+S+N KG CF++F + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKA 70
G + +F+G L EK + D FS +G + ++ I DP TG S+G+AF+ F + A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 71 VDDLLAAGD-HYIGNKKI 87
D + A + Y+ N+ I
Sbjct: 61 SDAAIEAMNGQYLCNRPI 78
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G + L+VG LH N E + F +G++++I + D TG+S+G+ F+TF+ +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 72 DDLLAAGDHY-IGNKKIDPKRVTKRVN 97
L + + + + + VT+R++
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLD 87
Score = 34.7 bits (78), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++VG L I+E +R F +G I D KG+ FI+F D A + L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+C++FVG L T+I+E+D + F +YG +P + N +GF FI + + +AE
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYG------EPSEVFINRDRGFGFIRLESRTLAE 72
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 10/110 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+LFVG L + E++ F +YGE + I D RGF F+ ++ + A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE 77
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
D I + P R+ R + V L+ +S + + FSQ+G +
Sbjct: 78 LDGTILKSR--PLRI--RFATHGAALTVKNLSPVVSNELLEQAFSQFGPV 123
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
++G++GP + L V L T + F +YG V + I +PHT RGFAFV
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 65 FTTQKAVDDLLAAGD 79
F ++ D AA D
Sbjct: 62 FHDRRDAQDAEAAMD 76
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
V LT S +R F +YG + + P + +GF F+ F D+ A+ A
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA---- 73
Query: 165 VICGKEVDVKRVKFN 179
+ G E+D + ++
Sbjct: 74 AMDGAELDGRELRVQ 88
>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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVGG+ E EI +F++YG V+ + I D TG S+G+ FV+F V ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 79 DHYIGNK-KIDP 89
++ G K K+ P
Sbjct: 71 INFHGKKLKLGP 82
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF D Q + E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68
>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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVGG+ E EI +F++YG V+ + I D TG S+G+ FV+F 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 = 4e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF D Q + E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG + E +E+ ++D FS+ G + F+ +D+ KG+ F + DQ A + N
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
R +FVG + E+++ D FS+ G V S + D TG+ +G+ F + Q+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D+R ++VG + + +++ +FS G + I+I D +G +G+A++ F + +VD
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
+A + + I K + KR N
Sbjct: 95 VAMDETVFRGRTI--KVLPKRTN 115
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K ++VG + + QD+ +FS GSI DK KG+ +I F ++N + +
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 160 ANPKQVICGKEVDV 173
A + V G+ + V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ F
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V GL +S++++ FSQYG I + D++ + +G FI FD + AE+ +
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 17/77 (22%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FVG T +++E ++R++FSQYG + + +PF + F F++F D +A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-------RAFAFVTFADDQIA----- 55
Query: 161 NPKQVICGKEVDVKRVK 177
Q +CG+++ +K +
Sbjct: 56 ---QSLCGEDLIIKGIS 69
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G + +FVG + E E+ ++FSQYG+V + I P R FAFVTF +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-PF----RAFAFVTFADDQIA 55
Query: 72 DDLLA 76
L
Sbjct: 56 QSLCG 60
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
++FV L+ SE+D+ FS YG ++E P D KGF F++F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+LFV L + E+++ FS YG + + D T + +GFAFVTF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R L V + E ++ F +YG +ES+ I D T QSRG+ FV F + + +A
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 77 AGDHY-IGNKKI 87
+ + I NK++
Sbjct: 103 GLNGFNILNKRL 114
Score = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 87 IDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCF 146
I P ++ + L+ + V + T + E +R F +YG I + D+ +G+ F
Sbjct: 30 IPPTQMNPEPDVLR-NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88
Query: 147 ISFDDQNVAEQVLA 160
+ F + A+Q +A
Sbjct: 89 VKFQSGSSAQQAIA 102
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 33/59 (55%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+F+GGL +++ V++ + +G + F D + + KG+ F + D NV +Q +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLF+GGL + ++ + + +G +++ ++ D TG S+G+AF + D +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 78 -GDHYIGNKKIDPKRVT 93
+G+KK+ +R +
Sbjct: 63 LNGMQLGDKKLLVQRAS 79
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D +G +GFA++ F+ +++V
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
LA + ++I K + KR N
Sbjct: 64 LALDESLFRGRQI--KVIPKRTN 84
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 33/71 (46%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
I+VG + + +++ +F GS+ DK KGF +I F D+ LA
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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D R ++VG + +E+ +F G V ++I D +G +GFA++ F+ +++V
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
LA + ++I K + KR N
Sbjct: 65 LALDESLFRGRQI--KVIPKRTN 85
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 33/71 (46%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
I+VG + + +++ +F GS+ DK KGF +I F D+ LA
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 163 KQVICGKEVDV 173
+ + G+++ V
Sbjct: 69 ESLFRGRQIKV 79
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 11 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 153 NVAEQVLANPKQV-ICGKEVDVKRVK 177
A + N + + G+ + V K
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNLAK 90
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK----AV 71
+R L+VGGL +K ++ F +G++ I I D T + RGFAFV F + A+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 72 DDL 74
D++
Sbjct: 72 DNM 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 41.6 bits (96), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
G +R L+VGGL +K ++ F +G++ I I D T + RGFAFV F +
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELA 57
Query: 72 DDLLAAGDH 80
+D AA D+
Sbjct: 58 EDAAAAIDN 66
Score = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 4 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 55
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG--FCFISFDDQNVAEQV 158
C+I+VG L +I +D+ D F +YG+I + KN + G F F+ F+D AE
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-----KNRRGGPPFAFVEFEDPRDAEDA 77
Query: 159 L 159
+
Sbjct: 78 V 78
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG---FAFVTFT 66
GP N++ +++VG L + K+I D F +YG + I +KN RG FAFV F
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN------RRGGPPFAFVEFE 69
Query: 67 TQKAVDDLLAAGDHY 81
+ +D + D Y
Sbjct: 70 DPRDAEDAVYGRDGY 84
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN 139
H+ G+ + K + K C ++VG L+ +E+ + + FS+ G I + DK K
Sbjct: 24 HFRGDNEEQEKLLKK-----SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78
Query: 140 MKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK 177
GFCF+ + + AE N + I G +D + ++
Sbjct: 79 TACGFCFVEYYSRADAE----NAMRYINGTRLDDRIIR 112
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+VG L T E++I + FS+ G+++ I + D + GF FV + ++ ++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM--- 98
Query: 79 DHYIGNKKIDPK 90
YI ++D +
Sbjct: 99 -RYINGTRLDDR 109
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
RN + ++VGGL E + + F Q G V + + D TGQ +G+ FV F +++ D
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
++VGGL ++SE + + F Q G + P D+ +G+ F+ F
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
+FVG L+ EI+ +D++ F+ +G I++ + D + KG+ F+SF ++ AE + +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 162 PKQVICGKEV 171
Q + G+++
Sbjct: 78 GGQWLGGRQI 87
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ-KAVDDLLAA 77
+FVG L ++I F+ +G++ + D TG+S+G+ FV+F + A + ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FVG L+ EI+ +D++ F+ +G I++ + D + KG+ F+SF ++ AE +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI--- 74
Query: 163 KQVICGKEVDVKRVKFNPET 182
Q + G+ + ++++ N T
Sbjct: 75 -QQMGGQWLGGRQIRTNWAT 93
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT-FTTQKAVDDLLAA 77
+FVG L ++I F+ +G + + D TG+S+G+ FV+ F A + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 5 ANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++G R RKLFVG L++ E ++ F +G +E +I P G S+G AF
Sbjct: 2 SSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAF 60
Query: 63 VTFTT----QKAVDDL 74
V +++ Q A++ L
Sbjct: 61 VKYSSHAEAQAAINAL 76
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE 129
R P K+FVG L + SE DVR F +G+I E
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEE 44
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 62 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R L+VGGL +K ++ F +G++ I I D T + RGFAFV F
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----Q 68
R ++RKLFVG L + ++++ F +G ++ ++ P G S+G AFV F T Q
Sbjct: 9 RGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQ 67
Query: 69 KAVDDL 74
A++ L
Sbjct: 68 AAINTL 73
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K+FVG L + +++DVR F +G+I E KG F+ F A+ +
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAI 70
>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 = 40.8 bits (94), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
TKRV ++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 6 TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 57
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+R L+VGGL +K ++ F +G++ I I D T + RGFAFV F + +D
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAA 63
Query: 76 AAGDH 80
AA D+
Sbjct: 64 AAIDN 68
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL- 159
+ V LT S +R F +YG + + P D+ +GF F+ F D+ AE +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 160 ANPKQVICGKEVDVKRVKF 178
A V+ G+E+ V+ ++
Sbjct: 108 AMDGAVLDGRELRVQMARY 126
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L T + F +YG V + I D +T +SRGFAFV F ++ +D + A
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 79 D 79
D
Sbjct: 110 D 110
>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 = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+R L+VGGL +K ++ F +G++ I I D T + RGFAFV F + +D
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAA 58
Query: 76 AAGDH 80
AA D+
Sbjct: 59 AAIDN 63
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
++VGGL E+ ++ + F +G IT+ Q P D +GF F+ F+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 52
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+D KLFVG + R E+++ F ++G + +++ D TG +G AF+T+ +
Sbjct: 13 HDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCAR 67
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+FVG + + EQD++ F ++G I E D+ + KG F+++ ++ A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
+++ P +F+ L E +QD+ F +G++ + DK N+ K F F+S+D+
Sbjct: 18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 153 NVAEQVLANPKQVICGKEVDVKRVK 177
A+ + Q + G ++ +KR+K
Sbjct: 78 VSAQAAI----QSMNGFQIGMKRLK 98
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+D LFVG L+ N ++ + + F + S + D TG SRG+ FV+FT+Q DD
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ---DD 141
Query: 74 LLAAGDHYIG 83
A D G
Sbjct: 142 AQNAMDSMQG 151
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 35/176 (19%), Positives = 74/176 (42%), Gaps = 27/176 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R L+VG L + E + YF G + +I I D + ++ +AFV +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQ--------- 50
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLKC-------------KIFVGGLTTEISEQDVRDYFSQ 123
+ D I + ++ K++ + + +FVG L + ++ +R+ F
Sbjct: 51 SHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN 179
+ S +D +G+ F+SF Q+ A+ N + G++++ + ++ N
Sbjct: 111 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ----NAMDSMQGQDLNGRPLRIN 162
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L+ N ++ + + F + S + D TG SRG+ FV+FT+Q DD A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ---DDAQNAM 60
Query: 79 DHYIG 83
D G
Sbjct: 61 DSMQG 65
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 28/57 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FVG L + ++ +R+ F + S +D +G+ F+SF Q+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P C +F+ L E ++ D+ F +G++ + DK ++ K F F+SFD+ + A+
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 158 VLANPKQVICGKEVDVKRVK 177
+ + + G +V KR+K
Sbjct: 98 AI----KAMNGFQVGTKRLK 113
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ LFV ++ +T E ++ F YG ++ I + +G+ RG+AF+ + ++ D+ +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER---DMHS 159
Query: 77 AGDHYIGNKKIDPKRV 92
A H G KKID +RV
Sbjct: 160 AYKHADG-KKIDGRRV 174
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV + + +E +R F YG I + K +G+ FI ++ E+ + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE----HERDMHSA 160
Query: 163 KQVICGKEVDVKRV 176
+ GK++D +RV
Sbjct: 161 YKHADGKKIDGRRV 174
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ +F+ L ++ E+ + + Q+G+++ + + P T S+G AF F TQ+A LA
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 77 AGDHYI--GNKKIDPKRV 92
A G K+D +++
Sbjct: 76 AASLEAEGGGLKLDGRQL 93
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 5 ANGTAG--PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPHTGQSRGFA 61
++G++G P + K+ V + ++EI + FS +GE++++ + K TG RGF
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 62 FVTFTTQ---KAVDDLLAAGDHYIGNKKI 87
FV F T+ K + L H G + +
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLV 90
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 8/60 (13%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+G L E +EQ++R F QYG + E ++ K + F+ +D+ AE + N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHIEDKTAAEDAIRN 61
Score = 35.4 bits (80), Expect = 0.034, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 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|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL- 159
+ V LT S +R F +YG + + P D+ +GF F+ F D+ AE +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 160 ANPKQVICGKEVDVKRVKF 178
A V+ G+E+ V+ ++
Sbjct: 131 AMDGAVLDGRELRVQMARY 149
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L T + F +YG V + I D +T +SRGFAFV F ++ +D + A
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 79 D 79
D
Sbjct: 133 D 133
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ F
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 27/59 (45%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+++G + + +E+ + D S G + + FD KG+ FI F D + + N
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 10/67 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQS------RGFAFVTFTTQKA 70
RK+FVGGL + E EI F ++G + + + PH +S +G+AF+ F + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQEESS 64
Query: 71 VDDLLAA 77
V L+ A
Sbjct: 65 VQALIDA 71
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF---DKSKNMKKGFCFISFDDQNVAEQV 158
K+FVGGL +I E ++ F ++G + P KS KG+ F+ F +++ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 159 L 159
+
Sbjct: 69 I 69
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 32/56 (57%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
I+VG L + + V++ FSQ+G + + +D+ KGF F+ +++V+E +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAI 59
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R ++VG L + +++ + FSQ+G+V ++ + D T + +GF FV +++V + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 77 AGDH 80
D+
Sbjct: 61 KLDN 64
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ F
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 27/59 (45%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+++G + + +E+ + D S G + + FD KG+ FI F D + + N
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+RKLFVG L++ E+++ F +G ++ ++ P G S+G AFV F++
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE---FQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
K+FVG L + SE+DV F +G I E + P S KG F+ F A+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS----KGCAFVKFSSHTEAQAA 72
Query: 159 L 159
+
Sbjct: 73 I 73
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 17/77 (22%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K+FVG T +++ ++++ +F QYG + + +PF + F F++F D VA
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-------RAFAFVTFADDKVA---- 61
Query: 160 ANPKQVICGKEVDVKRV 176
Q +CG+++ +K +
Sbjct: 62 ----QSLCGEDLIIKGI 74
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
K+FVG + +E+ +F QYGEV + I P R FAFVTF K L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-PF----RAFAFVTFADDKVAQSL 64
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
P D R +F L +++ D+FS G+V + I +D ++ +S+G A+V F ++
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 71 V 71
V
Sbjct: 80 V 80
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+F L I +D+ D+FS G + + + D++ KG ++ F
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ LFV ++ +T E ++ F YG ++ I + +G+ RG+AF+ + ++ D+ +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER---DMHS 159
Query: 77 AGDHYIGNKKIDPKRV 92
A H G KKID +RV
Sbjct: 160 AYKHADG-KKIDGRRV 174
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV + + +E +R F YG I + K +G+ FI ++ E+ + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE----HERDMHSA 160
Query: 163 KQVICGKEVDVKRV 176
+ GK++D +RV
Sbjct: 161 YKHADGKKIDGRRV 174
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+V L R + +++ F +YG + +I D TG+ RG AFV + ++ + ++A
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 79 DHYI 82
++ I
Sbjct: 76 NNVI 79
>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 = 37.7 bits (86), Expect = 0.007, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R +++G + + E++I D S G V ++ + DP TG+S+G+AF+ F
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 29/65 (44%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
NP +++G + + +E+ + D S G + + FD KG+ FI F D +
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 157 QVLAN 161
+ N
Sbjct: 61 SAVRN 65
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 9/91 (9%)
Query: 5 ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
++G++GP + + LFV GL +T E+ + + F G V + I D TG S+GF F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRA-RIVTDRETGSSKGFGF 58
Query: 63 VTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT 93
V F +++ A + + +ID +VT
Sbjct: 59 VDFNSEEDA----KAAKEAMEDGEIDGNKVT 85
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D L++ L + E+E+ + +G+V S I D +G SRG F + + + +
Sbjct: 24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAV 82
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLKCK 102
+ H+ G P V+ PL CK
Sbjct: 83 IG---HFNGKFIKTPPGVSAPTEPLLCK 107
>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 = 0.016, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 8/68 (11%)
Query: 7 GTAGPGRNDER--KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
G++G D+ L+VGGL E ++ ++F Q+GE+ +I++ Q + AF+
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQ 54
Query: 65 FTTQKAVD 72
F T++A +
Sbjct: 55 FATRQAAE 62
Score = 32.7 bits (73), Expect = 0.21, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++VGGL I+E D+R++F Q+G I + ++ FI F + AE
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTI------TVVQRQQCAFIQFATRQAAEVAAEKS 68
Query: 163 --KQVICGKEVDVK 174
K ++ G+ ++VK
Sbjct: 69 FNKLIVNGRRLNVK 82
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+++ GL ++QD+ YG I + DK+ N KG+ F+ FD + A++ +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Score = 34.3 bits (77), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
G + L++ GL T ++++ YG++ S D T + +G+ FV F +
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 68 QKAVDDLLAAG 78
QKAV L A+G
Sbjct: 61 QKAVTALKASG 71
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 85 KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKG 143
K++ + V + +P C ++ GG+ + +++Q +R FS +G I E + P +KG
Sbjct: 10 KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-------EKG 62
Query: 144 FCFISFDDQNVAEQVLAN 161
+ F+ F A + +
Sbjct: 63 YSFVRFSTHESAAHAIVS 80
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
L V L +N + E F G++ES + D TGQS G+ FV ++ KA++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
>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 = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 80 HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN 139
H+ G+ + K + K C ++VG L+ +E+ + + FS+ G I + DK K
Sbjct: 3 HFRGDNEEQEKLLKK-----SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT 57
Query: 140 MKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK 177
GFCF+ + + AE N + I G +D + ++
Sbjct: 58 -ACGFCFVEYYSRADAE----NAMRYINGTRLDDRIIR 90
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+VG L T E++I + FS+ G+++ I + D GF FV + ++ ++ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAM--- 76
Query: 79 DHYIGNKKIDPKRV 92
YI ++D + +
Sbjct: 77 -RYINGTRLDDRII 89
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K++VG L G+ E+ FS YG + ++ I +P GFAFV F + +D +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 78 GD 79
D
Sbjct: 57 LD 58
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ-VLA 160
K++VG L T + ++ FS YG + ++N GF F+ F+D AE V
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI----ARN-PPGFAFVEFEDPRDAEDAVRG 56
Query: 161 NPKQVICGKEVDVK 174
+VICG V V+
Sbjct: 57 LDGKVICGSRVRVE 70
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 17/90 (18%)
Query: 86 KIDPKRVTKRVNPLKCKIFVGGLTTEISEQ-DVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
K DP+ + RV F+G L T + ++ DV FS+YG I ++ KGF
Sbjct: 8 KTDPRSMNSRV-------FIGNLNTLVVKKSDVEAIFSKYGKIVGC--------SVHKGF 52
Query: 145 CFISF-DDQNVAEQVLANPKQVICGKEVDV 173
F+ + +++N V ++I G+ +D+
Sbjct: 53 AFVQYVNERNARAAVAGEDGRMIAGQVLDI 82
>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 = 0.034, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ ++FVG L +I+E+++R F +YG E D KGF FI + + +AE
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 65
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 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 = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
A RAN P N R L++ L +E+ D F +YG + I + N P T RG A
Sbjct: 6 AKRANIRLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTA 60
Query: 62 FVTFTTQKAVDDLLAAGDHYIG 83
+V + + + D A DH G
Sbjct: 61 YVVY---EDIFDAKNACDHLSG 79
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ ++FVG L +I+E+++R F +YG E D KGF FI + + +AE
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 72
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 47/110 (42%), Gaps = 10/110 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+LFVG L + E+E+ F +YG+ + I D +GF F+ T+ L
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR----TLAEI 73
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
+ N + K++ R + V L +S + + + FS +G +
Sbjct: 74 AKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQV 123
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 12/88 (13%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 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|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P K ++V L ++ D+ FS+YG + + DK KG FI F D++ A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Score = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
++V L + ++ FS+YG+V ++I D T +S+G AF+ F
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
>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 = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ----- 157
IF+ L I + + D FS +G+I + D +N KG+ F+ F+ Q AE+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 158 --VLANPKQVICGK 169
+L N ++V G+
Sbjct: 66 NGMLLNDRKVFVGR 79
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+F+ L ++ K + D FS +G + S + D + S+G+ FV F TQ+A +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 59
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
A RAN P N R L + L +E+ D F +YG + I + N P T RG A
Sbjct: 6 AKRANIRLPPEVN--RILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTA 60
Query: 62 FVTFTTQKAVDDLLAAGDHYIG 83
+V + + + D A DH G
Sbjct: 61 YVVY---EDIFDAKNACDHLSG 79
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYG---SITEFQQPFDKSKNMKKGFCFISFDD-QN 153
PL CK++VG L ++ ++ F YG S+ + P GF F+ F+D ++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRD 122
Query: 154 VAEQVLANPKQVICGKEVDVK 174
A+ V + +CG V V+
Sbjct: 123 AADAVRELDGRTLCGCRVRVE 143
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
K++VG L N + E+ F YG + S+ + +P GFAFV F
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEF 117
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ----- 157
IF+ L I + + D FS +G+I + D +N KG+ F+ F+ Q AE+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 71
Query: 158 --VLANPKQVICGK 169
+L N ++V G+
Sbjct: 72 NGMLLNDRKVFVGR 85
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+F+ L ++ K + D FS +G + S + D + S+G+ FV F TQ+A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 65
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYG---SITEFQQPFDKSKNMKKGFCFISFDD-QN 153
PL CK++VG L ++ ++ F YG S+ + P GF F+ F+D ++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRD 122
Query: 154 VAEQVLANPKQVICGKEVDVK 174
A+ V + +CG V V+
Sbjct: 123 AADAVRDLDGRTLCGCRVRVE 143
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
K++VG L N + E+ F YG + S+ + +P GFAFV F
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEF 117
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 33.9 bits (76), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 24 LHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
L+ N E + D +YGEVE + I P T + G A V FT+ + +
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
RAN P N R L++ L +E+ D F +YG + I + N P T RG A+V
Sbjct: 2 RANIRLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYV 56
Query: 64 TFTTQKAVDDLLAAGDHYIG 83
+ + + D A DH G
Sbjct: 57 VY---EDIFDAKNACDHLSG 73
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
L V L ++ ++E+ F G + + I D TG S G+AFV FT++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSE 55
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT----FTTQKAVD 72
R L++ L +E+ D F +YG + I + N P T RG A+V F + AVD
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65
Query: 73 DL 74
L
Sbjct: 66 HL 67
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 7 GTAGPGRNDERKLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
G G + + +LF+G L +N ++++ FS YG + I+IKN F F+ F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQF 64
Query: 66 TTQKAVDD 73
++V D
Sbjct: 65 DNPQSVRD 72
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.1 bits (74), Expect = 0.15, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPHTGQSRGFAFVTFTTQKAVDDL 74
K+ +G L RN + I + FS YG+++ I + + PH S+G+A+V F +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHL--SKGYAYVEFENPDEAEKA 63
Query: 75 LAAGDHYIGNKKIDPKRVT 93
L ++ +ID + +T
Sbjct: 64 L----KHMDGGQIDGQEIT 78
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/109 (22%), Positives = 50/109 (45%), Gaps = 17/109 (15%)
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
L+ G H K PKR + V + + D+R F Q+G I + +
Sbjct: 14 LVPRGSHMNTENKSQPKR-----------LHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPET 182
F++ + KGF F++F++ A++ ++ + G V+ ++++ N T
Sbjct: 63 FNERGS--KGFGFVTFENSADADRA----REKLHGTVVEGRKIEVNNAT 105
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 7 GTAGPGRNDERKLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
G G + + +LF+G L +N ++++ FS YG + I+IKN F F+ F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQF 64
Query: 66 TTQKAVDD 73
++V D
Sbjct: 65 DNPQSVRD 72
>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 = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTF 65
D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V+F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ---QPF-----DKSKNMKKGFCFISFDD 151
IFV GL ++ + V DYF Q G I + QP D+ KG +SFDD
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTF 65
+D +FV GL N + + DYF Q G +++ I++ D TG+ +G A V+F
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ---QPF-----DKSKNMKKGFCFISFDD 151
IFV GL ++ + V DYF Q G I + QP D+ KG +SFDD
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 18 KLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+LF+G L +N ++++ FS YG + I+IKN F F+ F ++V D +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 62
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 25/141 (17%), Positives = 60/141 (42%), Gaps = 11/141 (7%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ RK+ + GL + +E++D S Y E++ + + +G AFVT + +
Sbjct: 19 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAE-- 69
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF 134
A + ++ + ++ ++ P + V L +++Q + +GS+ +
Sbjct: 70 --AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 127
Query: 135 DKSKNMKKGFCFISFDDQNVA 155
+ KG+ F + ++ A
Sbjct: 128 SERTGQSKGYGFAEYMKKDSA 148
>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 = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD 135
K V +NP++ + F LT E++V+ F+Q+ E PFD
Sbjct: 279 KLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWLERHGPFD 324
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 25/141 (17%), Positives = 60/141 (42%), Gaps = 11/141 (7%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ RK+ + GL + +E++D S Y E++ + + +G AFVT + +
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAE-- 71
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF 134
A + ++ + ++ ++ P + V L +++Q + +GS+ +
Sbjct: 72 --AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 135 DKSKNMKKGFCFISFDDQNVA 155
+ KG+ F + ++ A
Sbjct: 130 SERTGQSKGYGFAEYMKKDSA 150
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 32.0 bits (71), Expect = 0.36, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 18 KLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+LF+G L +N ++++ FS YG + I+IKN F F+ F ++V D +
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 54
>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 = 0.38, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 90 KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD 135
K V +NP++ + F LT E++V+ F+Q+ E PFD
Sbjct: 279 KLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWLERHGPFD 324
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 29/157 (18%), Positives = 66/157 (42%), Gaps = 15/157 (9%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ RK+ + GL + +E++D S Y E++ + + +G AFVT + +
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAE-- 71
Query: 75 LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF 134
A + ++ + ++ ++ P + V L +++Q + +GS+ +
Sbjct: 72 --AAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 135 DKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEV 171
+ KG+ F + ++ A A K + GK +
Sbjct: 130 SERTGQSKGYGFAEYMKKDSA----ARAKSDLLGKPL 162
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 11/91 (12%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPHTGQSRGFAFVTFT-- 66
G + LF+ L+ +T E+ + FS+ G ++S +I KN S GF FV +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 67 --TQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
QKA+ L H + K++ R+++R
Sbjct: 61 EQAQKALKQLQG---HTVDGHKLEV-RISER 87
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+++G L+ ++ D+R F + + P +K G+ F+ + DQN A
Sbjct: 10 KLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWA 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 = 31.2 bits (69), Expect = 0.70, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ-KAVDDLLAA 77
+FVG L I F+ +G + + D TG+S+G+ FV+F + A + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 78 GDHYIGNKKIDPKRVTKR 95
G ++G ++I T++
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
>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 = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEV 171
+ ++ + FS+ G + + P D++ KGF F+ N A++++ + GK +
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS----FHGKRL 79
Query: 172 DVKRVKF 178
D+K F
Sbjct: 80 DLKHRLF 86
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+K + FS+ G+V ++ D TG+++GF FV
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ V + + D+R F Q+G I + + F++ + KGF F++F++ A++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRA--- 71
Query: 162 PKQVICGKEVDVKRVKFNPET 182
++ + G V+ ++++ N T
Sbjct: 72 -REKLHGTVVEGRKIEVNNAT 91
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.8 bits (68), Expect = 0.84, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF 178
FS+ G + + P D++ KGF F+ N A++++ + GK +D+K F
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS----FHGKRLDLKHRLF 86
Score = 27.7 bits (60), Expect = 6.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
+K + FS+ G+V ++ D TG+++GF FV
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 12/61 (19%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDD 73
+LFV + E E+N+ F +G ++ + I N GFAFV F + KA+++
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84
Query: 74 L 74
+
Sbjct: 85 V 85
>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 = 30.4 bits (67), Expect = 1.0, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 30 EKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH 80
E +I +G + + + + +GQSRGFAFV F+ + + A H
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQH 66
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++ GL K + D+F + VE SI I P G++ G FV F + L
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRNEADYKAALCR 86
Query: 78 GDHYIGNKKIDPKRVTKR 95
Y+GN+ I +TK+
Sbjct: 87 HKQYMGNRFIQVHPITKK 104
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 14/68 (20%)
Query: 5 ANGTAGPGRND--ERKLFVGGLHRNTGEKEINDYFSQYGEVESISI-----KNDPHTGQS 57
++G++G +D R L+VG L R+ E I FSQ G +S + NDP
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP----- 56
Query: 58 RGFAFVTF 65
+ FV F
Sbjct: 57 --YCFVEF 62
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF-DDQNVAEQVLAN 161
++VG L+ +++E + FSQ G + + + N +CF+ F + ++ A + A
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 75
Query: 162 PKQVICGKEVDV 173
+ I GKEV V
Sbjct: 76 NGRKILGKEVKV 87
>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 = 2.8, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 75 LAAGDHYIGNKKIDPKRV-TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
+A G+ KKIDP T ++ PL V L ++S ++++QY SI + +
Sbjct: 77 IAGGNTLACTKKIDPDLSKTTKIYPLPHMYVVKDLVPDLS-----NFYAQYKSIEPYLKK 131
Query: 134 FDKSKNMKKGFCFISFDDQN 153
D+SK K+ + S +D+
Sbjct: 132 KDESKQGKEQY-LQSIEDRQ 150
>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 = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIK--NDPHTGQSRGFAFVTFTTQKA 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|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FV L T ++E+ + FS++G + ++ D + F+ F+D+ A + +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAM 66
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L++ L E+++ F+++ E + I+ TG+ RG AF+TF ++ L
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 79 DHY 81
+ Y
Sbjct: 88 NGY 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.5 bits (62), Expect = 3.8, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 12/61 (19%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDD 73
+LFV + E E+N+ F +G ++ + I N GFAFV F + KA+++
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 57
Query: 74 L 74
+
Sbjct: 58 V 58
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQY--GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+LF+GG+ + +EI + ++ G ++ I + ++RGFAFV + + +A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA---- 65
Query: 76 AAGDHYIGNKKIDPKRV 92
+ +K+ P R+
Sbjct: 66 -----AMARRKLMPGRI 77
>pdb|2J8A|A Chain A, X-Ray Structure Of The N-Terminus Rrm Domain Of Set1
Length = 136
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 99 LKCKIFV----GGLTTEISEQDVRDYFSQYGSITEFQ 131
+ C+I V TT I + +++YF +YG I+ F+
Sbjct: 1 MSCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFE 37
>pdb|2NTS|A Chain A, Crystal Structure Of Sek-Hvb5.1
pdb|2NTT|A Chain A, Crystal Structure Of Sek
pdb|2NTT|B Chain B, Crystal Structure Of Sek
Length = 217
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
YG +T + DKS+N+ +I+ + + ++ ++ K+ + +E+DVK K+ E
Sbjct: 79 YGGVTATNEYLDKSRNIPIN-IWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQE 135
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 43 VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV 92
V +I + D T Q+RGFAFV ++ LL KID K +
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI 87
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+VG L + D+ F SI + DK + KGFC++ FD+ + ++ L
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFV 63
++G++GP E LFVG L + + + ++F + Y + D TG S+G+ FV
Sbjct: 2 SSGSSGP----EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFV 56
Query: 64 TFTTQ 68
FT +
Sbjct: 57 KFTDE 61
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FV L ++E+ + FSQ+G + ++ D + FI FD+++ A + +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAM 62
>pdb|3EA6|A Chain A, Atomic Resolution Of Crystal Structure Of Sek
Length = 219
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
YG +T + DKS+N+ +I+ + + ++ ++ K+ + +E+DVK K+ E
Sbjct: 79 YGGVTATNEYLDKSRNIPIN-IWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQE 135
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+ V L +S+ D+++ F+++G++ + +D+S G + F+ + A + +
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 147
Query: 161 NPKQV-ICGKEVDVKRV 176
K V + G+ +D++ V
Sbjct: 148 QYKGVPLDGRPMDIQLV 164
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ---QP-----FDKSKNMKKGFCFISFDDQNV 154
I+V GL ++ D+ D+F Q G + + QP DK KG +S++D
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 155 AEQVL 159
A+ +
Sbjct: 78 AKAAV 82
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L+V L ++ + FS +G + S + + G+S+GF FV F++ KAV ++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKND 51
N +L+VGGL NT + F ++G + +I +K D
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
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
0.317 0.134 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,505,717
Number of Sequences: 62578
Number of extensions: 275474
Number of successful extensions: 1088
Number of sequences better than 100.0: 176
Number of HSP's better than 100.0 without gapping: 130
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 778
Number of HSP's gapped (non-prelim): 318
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)