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= 031884
(151 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 42/69 (60%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
+ +LFV GLSF T+E SL F +GQ+ EV +V D+ R RGF F+ + ++++
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 134 RAIEGMHGK 142
A+ M+GK
Sbjct: 69 DAMMAMNGK 77
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 55.8 bits (133), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L+V+ L ++D L F +G +V+ N++ DK+ RPRG AF+RY EE++ AI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 138 GMHGKV 143
++ +
Sbjct: 150 ALNNVI 155
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + ++ D G+AF+ + +E +S+RAI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 138 GMHG 141
++G
Sbjct: 64 VLNG 67
>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 = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L+V+ L ++D L F +G +V+ N++ DK+ RPRG AF+RY EE++ AI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 138 GMHGKV 143
++ +
Sbjct: 161 ALNNVI 166
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + + D G+AF+ + +E +S+RAI+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 138 GMHG 141
++G
Sbjct: 75 VLNG 78
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 39/63 (61%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L+V+ L ++D L F +G +V+ N++ DK+ RPRG AF+RY EE++ AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 138 GMH 140
++
Sbjct: 74 ALN 76
>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 = 53.1 bits (126), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 41/67 (61%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V L++RTS D+LR F+ +G++ +V + D+ RGFAF+R+ + ++ A++
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 138 GMHGKVC 144
M G V
Sbjct: 108 AMDGAVL 114
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 41/67 (61%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V L++RTS D+LR F+ +G++ +V + D+ RGFAF+R+ + ++ A++
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 138 GMHGKVC 144
M G V
Sbjct: 131 AMDGAVL 137
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 6/72 (8%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
P P L +LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+
Sbjct: 7 PKEPEQLR------KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 125 RYATEEESRRAI 136
YAT EE A+
Sbjct: 61 TYATVEEVDAAM 72
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 6/72 (8%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
P P L +LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+
Sbjct: 5 PKEPEQLR------KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 58
Query: 125 RYATEEESRRAI 136
YAT EE A+
Sbjct: 59 TYATVEEVDAAM 70
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 40/63 (63%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
RL+V L F +ED LR F+ FG++ + L+MD R +G+ F+ ++ E +++A+E
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 139 MHG 141
++G
Sbjct: 88 LNG 90
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 38/58 (65%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 6/67 (8%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
P P L +LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+
Sbjct: 7 PKEPEQLR------KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 125 RYATEEE 131
YAT EE
Sbjct: 61 TYATVEE 67
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 6/67 (8%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
P P L +LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+
Sbjct: 6 PKEPEQLR------KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 59
Query: 125 RYATEEE 131
YAT EE
Sbjct: 60 TYATVEE 66
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 6/67 (8%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
P P L +LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+
Sbjct: 8 PKEPEQLR------KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 61
Query: 125 RYATEEE 131
YAT EE
Sbjct: 62 TYATVEE 68
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
++FV G+ T E LR+ F+ +G++ + ++ D+ + + RGFAF+ +
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
++FV GLS T E+ +R F GFG++ + L MD N+ RGF F+ + EE ++ +E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 139 MHGKV 143
+ V
Sbjct: 63 KYHNV 67
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
RLFV LS+ +SE+ L F +G L E++ +D + +P+GFAF+ + E + +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 139 MHGKV 143
+ G+V
Sbjct: 70 VDGQV 74
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA-- 135
T++FV GL + T++ SLR F+GFG + E ++ D+ + RG+ F+ A + RA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 136 -----IEGMHGKVCCCFWMAE 151
I+G V + A+
Sbjct: 78 DPNPIIDGRKANVNLAYLGAK 98
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 37/64 (57%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV GLS T E+ +R F GFG++ + L MD N+ RGF F+ + EE ++ +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 140 HGKV 143
+ V
Sbjct: 62 YHNV 65
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 36/50 (72%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT 128
+LF+ GLSF T+E+SLRN ++ +G+L + ++ D + R RGF F+ +++
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
>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 = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 67 SPHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
PH+ Q LFV+ +++ T+E LR F+ +G + +++V K + +PRG+AF+
Sbjct: 90 DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 125 RYATEEESRRAIEGMHGK 142
Y E + A + GK
Sbjct: 150 EYEHERDMHSAYKHADGK 167
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
QP LFV GLS T+E++L+ +F G V +V D+ +GF F+ + +EE+++
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 134 RAIEGMH 140
A E M
Sbjct: 69 AAKEAME 75
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 35/48 (72%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
+LFV GL + T++++LR+ F +G++V+ ++ DK N+ RGF F+++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V L F +ED LR F+ FG++ + L+ D R +G+ F+ ++ E +RRA+E +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 140 HG 141
+G
Sbjct: 68 NG 69
>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 = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 67 SPHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
PH+ Q LFV+ +++ T+E LR F+ +G + +++V K + +PRG+AF+
Sbjct: 90 DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 125 RYATEEESRRAIEGMHGK 142
Y E + A + GK
Sbjct: 150 EYEHERDMHSAYKHADGK 167
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
+R++V + + ED++R AF FG + +++ D + + +GFAF+ Y E ++ A+E
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 138 GMH 140
M+
Sbjct: 89 QMN 91
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V+ + S+D +++ F+ FG++ L D + +G+ F+ Y + S+ A+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 139 MH 140
M+
Sbjct: 187 MN 188
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V + + ED++R AF FG + +++ D + + +GFAF+ Y E ++ A+E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 139 MH 140
M+
Sbjct: 75 MN 76
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V+ + S+D +++ F+ FG++ L D + +G+ F+ Y + S+ A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 139 MH 140
M+
Sbjct: 172 MN 173
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE-- 137
+F+ GLS+ T++ L++ F FG++V+ L +D I R RGF F+ + E + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 138 --GMHGKVC 144
++GKV
Sbjct: 62 EHKLNGKVI 70
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 70 SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
S + P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ +
Sbjct: 5 SRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 130 EESRRAIEGMHG 141
++++ A E +G
Sbjct: 65 DDAKEAKERANG 76
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+T L V+ L ++D LR+ F G++ L+ DK+A G+ F+ Y T +++ RAI
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 137 EGMHG 141
++G
Sbjct: 64 NTLNG 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 = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 135 AIEGMHG 141
A E +G
Sbjct: 73 AKERANG 79
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
+FV GLS T+ + +++ F+ FG++ + L+ DK NR RGF F+ + +E+ + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+T L V+ L ++D LR+ F G++ L+ DK+A G+ F+ Y T +++ RAI
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 137 EGMHG 141
++G
Sbjct: 62 NTLNG 66
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L++SGL ++ + + F FG+++ +++D+ RG AF+R+ E+ AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 140 HG 141
+G
Sbjct: 151 NG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+T L V+ L ++D LR+ F G++ L+ DK+A G+ F+ Y T +++ RAI
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 137 EGMHG 141
++G
Sbjct: 62 NTLNG 66
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L++SGL ++ + + F FG+++ +++D+ RG AF+R+ E+ AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 140 HG 141
+G
Sbjct: 151 NG 152
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 135 AIEGMHG 141
A E +G
Sbjct: 73 AKERANG 79
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++D LR+ F G++ L+ DK+A G+ F+ Y T +++ RAI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 138 GMHG 141
++G
Sbjct: 80 TLNG 83
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++ A E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 140 HG 141
+G
Sbjct: 109 NG 110
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
++FV G+ E LR F+ FG + EV ++ D RPRGF F+ + E+ +A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 138 GMH 140
MH
Sbjct: 70 NMH 72
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 37/62 (59%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V L++RTS DSLR F+ +G++ +V + + PRGFAF+R+ +++ A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 140 HG 141
G
Sbjct: 76 DG 77
>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 = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGK 142
+G+
Sbjct: 70 NGQ 72
>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 = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGK 142
+G+
Sbjct: 70 NGQ 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 = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 140 HGK 142
+G+
Sbjct: 72 NGQ 74
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGK 142
+G+
Sbjct: 70 NGQ 72
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
ST K +LF+SGL F +++ L + G + ++ LV ++ A +P+G A++ Y E +
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70
Query: 132 SRRAIEGMHG 141
+ +A+ M G
Sbjct: 71 ASQAVMKMDG 80
>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 = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
++F+ GL++ T+ED+LR F +G + ++ ++ D R RGF FL + ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 139 MH---GKVC 144
H GKV
Sbjct: 65 QHILDGKVI 73
Score = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 75 QPKT-RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
Q KT ++FV G+ F +G +++ L++DK + RGF F+ Y + +
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Query: 134 RA 135
R
Sbjct: 144 RV 145
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 140 HGK 142
+G+
Sbjct: 86 NGQ 88
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
R++V + + ED++R AF FG + ++ D + + +GFAF+ Y E ++ A+E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
R++V+ + S+D +++ F+ FG++ L D + +G+ F+ Y + S+ A+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LFV L+ + SED +R F+ FG + E ++ N +G AF++Y++ E++ AI
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS-KGCAFVKYSSHAEAQAAINA 75
Query: 139 MHG 141
+HG
Sbjct: 76 LHG 78
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 40/63 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 140 HGK 142
+G+
Sbjct: 85 NGQ 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 62 ACLPPSPH--SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPR 119
+P H + + QPK RL VS + FR + LR F FG++++V ++ ++ + +
Sbjct: 13 GLVPRGSHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--K 69
Query: 120 GFAFLRYATEEESRRAIEGMHGKVC 144
GF F+ + ++ RA E +HG V
Sbjct: 70 GFGFVTFENSADADRAREKLHGTVV 94
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 40/71 (56%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
S+ LFV L+ +++LRNAF+ F + +++ D RG+ F+ + ++++
Sbjct: 82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 132 SRRAIEGMHGK 142
++ A++ M G+
Sbjct: 142 AQNAMDSMQGQ 152
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V L +ED L+ FQ G + + +++DK N+ +AF+ Y ++ A++ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 140 HGK 142
+GK
Sbjct: 62 NGK 64
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 68 PHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
P +ST P + +LF+ GL ++D ++ FG L NLV D +G+AF
Sbjct: 103 PGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 162
Query: 126 YATEEESRRAIEGMHG 141
Y + +AI G++G
Sbjct: 163 YVDINVTDQAIAGLNG 178
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 38/63 (60%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV L+ +++LRNAF+ F + +++ D RG+ F+ + ++++++ A++ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 140 HGK 142
G+
Sbjct: 64 QGQ 66
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 37/63 (58%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+VSGL ++ L F +G+++ +++D++ RG F+R+ E+ AI+G+
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 140 HGK 142
+G+
Sbjct: 151 NGQ 153
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GL+ T+E L+ F G + EV L+ D+ + + RGFAF+ + +++ A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 139 MHGK 142
M+GK
Sbjct: 68 MNGK 71
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 82 VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
V+ LS T E L+ F+ FG + + L DK + +GFAF+ + E++ RAI G+ G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 68 PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
PH +LF+ GL ++D ++ FG L NLV D +G+AF Y
Sbjct: 87 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 146
Query: 128 TEEESRRAIEGMHG 141
+ +AI G++G
Sbjct: 147 DINVTDQAIAGLNG 160
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 68 PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
PH +LF+ GL ++D ++ FG L NLV D +G+AF Y
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144
Query: 128 TEEESRRAIEGMHG 141
+ +AI G++G
Sbjct: 145 DINVTDQAIAGLNG 158
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 33/51 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
++F+ GLS++T+++ LR F FG++ E ++ D + R RGF F+ + +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
Q + L V GL ++T+E L+ F FG+++ V + D +GF F+R+ E
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Query: 134 RAIEGMH---GKVCCC 146
+ + H G+ C C
Sbjct: 72 KVMSQRHMIDGRWCDC 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+VSGL S+ + F +G+++ +++D+ RG F+R+ E+ AI+G+
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 140 HGK 142
+G+
Sbjct: 153 NGQ 155
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
S K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E+
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 132 SRRAIEGMH 140
+ AI+ M+
Sbjct: 62 AAAAIDNMN 70
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 33/51 (64%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
++F+ GLS++T+++ LR F FG++ E ++ D + R RGF F+ + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>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 = 6e-05, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+VSGL S+ + F +G+++ +++D+ RG F+R+ E+ AI+G+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 140 HGK 142
+G+
Sbjct: 64 NGQ 66
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 137 EGMH 140
+ M+
Sbjct: 123 DNMN 126
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%)
Query: 67 SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
S S K L+V GL+ + L AF FG + ++ + +D + RGFAF+ +
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 127 ATEEESRRAIEGMH 140
E++ AI+ M+
Sbjct: 62 ELAEDAAAAIDNMN 75
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 35/63 (55%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV + + +E+ L++ F G +V LV D+ +P+G+ F Y +E + A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 140 HGK 142
+G+
Sbjct: 71 NGR 73
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
RL VS + FR + LR F FG++++V ++ ++ + +GF F+ + ++ RA E
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREK 74
Query: 139 MHGKVC 144
+HG V
Sbjct: 75 LHGTVV 80
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 137 EGMH 140
+ M+
Sbjct: 62 DNMN 65
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 137 EGMH 140
+ M+
Sbjct: 65 DNMN 68
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GL ++D ++ FG L NLV D +G+AF Y + +AI G
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 139 MHG 141
++G
Sbjct: 63 LNG 65
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+F+ L +L + F FG ++ +V D+ N +G+ F+ + T+E + RAIE M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 140 HG 141
+G
Sbjct: 159 NG 160
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P L+V L +E L F G ++ + + D I R G+A++ + ++ RA
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 136 IEGMH-----GKVCCCFW 148
++ M+ GK W
Sbjct: 69 LDTMNFDVIKGKPVRIMW 86
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+F+ L +L + F FG ++ +V D+ N +G+ F+ + T+E + RAIE M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 140 HG 141
+G
Sbjct: 164 NG 165
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 60 PLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPR 119
PL + PS S P L+V L +E L F G ++ + + D I R
Sbjct: 2 PLGSMNPSAPSY----PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL 57
Query: 120 GFAFLRYATEEESRRAIEGMH-----GKVCCCFW 148
G+A++ + ++ RA++ M+ GK W
Sbjct: 58 GYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM-DKIANRPRGFAFLRYATEEESRRAI 136
+ +F+ L E L + F FG +++ +M D +G+AF+ +A+ + S AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 137 EGMHGKVCC 145
E M+G+ C
Sbjct: 66 EAMNGQYLC 74
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V L ++ LR AF FG + ++M+ R +GF F+ +++ EE+ +A+ M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 140 HGKVCCC 146
+G++
Sbjct: 76 NGRIVAT 82
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
+ FV GLS+ TS+ L++ F FG++V+ + D R RGF F+
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFI 58
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+F+ L +L + F FG ++ +V D+ N +G+ F+ + T+E + RAIE M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 140 HG 141
+G
Sbjct: 66 NG 67
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+F+ L +L + F FG ++ +V D+ N +G+ F+ + T+E + RAIE M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 140 HG 141
+G
Sbjct: 72 NG 73
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
TRLFV E L F FG + EV KI N GFAF+ + E + +AIE
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEV-----KILN---GFAFVEFEEAESAAKAIE 56
Query: 138 GMHGK 142
+HGK
Sbjct: 57 EVHGK 61
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 11/77 (14%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
++ G++ ++ +R F FGQ++E+ + +K G++F+R++T E + AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 140 H-----GKVCCCFWMAE 151
+ G V C+W E
Sbjct: 82 NGTTIEGHVVKCYWGKE 98
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
TRLFV E L F FG + EV KI N GFAF+ + E + +AIE
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEV-----KILN---GFAFVEFEEAESAAKAIE 83
Query: 138 GMHGK 142
+HGK
Sbjct: 84 EVHGK 88
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+ + ED ++ F +G++ ++L +D+ +G+A + Y T +++ A E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 140 HG 141
+G
Sbjct: 89 NG 90
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 34/61 (55%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L++ GL T++ L Q +G++V ++DK N+ +G+ F+ + + +++A+ +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 140 H 140
Sbjct: 68 K 68
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 32/57 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
++V + + + + L F G G + V ++ DK + P+GFA++ ++ +E R ++
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>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 = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 32/57 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
++V + + + + L F G G + V ++ DK + P+GFA++ ++ +E R ++
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ + E L+ F+ FG++ E+ ++ D+ +G AFL Y E + +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 139 MH 140
+H
Sbjct: 75 LH 76
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+ + ED ++ F +G++ ++L +D+ +G+A + Y T +++ A E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 140 HG 141
+G
Sbjct: 135 NG 136
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 35/63 (55%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV LS + + ++ AF FG++ + +V D + +G+ F+ + + ++ AI+ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 140 HGK 142
G+
Sbjct: 78 GGQ 80
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+++V L + L AF +G L V IA P GFAF+ + ++ A+ G
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 139 MHGKVCC 145
+ GKV C
Sbjct: 57 LDGKVIC 63
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 35/63 (55%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV LS + + +++AF FG++ + +V D + +G+ F+ + + ++ AI M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 140 HGK 142
G+
Sbjct: 78 GGQ 80
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 64 LPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGF 121
+ P+ + +LF+ +S + +E+ +R F FGQ+ E ++ D ++ RG
Sbjct: 82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS---RGC 138
Query: 122 AFLRYATEEESRRAIEGMH 140
AF+ + T ++ AI+ MH
Sbjct: 139 AFVTFTTRAMAQTAIKAMH 157
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRAI 136
++FV + SE LR F+ +G + E+N++ D+ N P +G F+ + T + + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 137 EGMH 140
+H
Sbjct: 65 NALH 68
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 64 LPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGF 121
+ P+ + +LF+ +S + +E+ +R F FGQ+ E ++ D ++ RG
Sbjct: 94 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS---RGC 150
Query: 122 AFLRYATEEESRRAIEGMH 140
AF+ + T ++ AI+ MH
Sbjct: 151 AFVTFTTRAMAQTAIKAMH 169
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRAI 136
++FV + SE LR F+ +G + E+N++ D+ N P +G F+ + T + + A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 137 EGMH 140
+H
Sbjct: 77 NALH 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 36/69 (52%)
Query: 71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
+S ++V GL + SE L F G +V ++ D++ + +G+ F+ + +EE
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 131 ESRRAIEGM 139
++ AI+ M
Sbjct: 69 DADYAIKIM 77
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LFV + E L+ F+ FG++ E+ ++ D++ +G AFL Y + + +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 139 MH 140
+H
Sbjct: 77 LH 78
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
++V L + + + ++ F FG++ V L+ D+ +P+GF F+ E
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE 53
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
+F+ LSF + E++L Q FG L V +V+ +G AF ++ T+E +++
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
>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 = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRAI 136
++FV + SE LR F+ +G + E+N++ D+ N P +G F+ + T + + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 137 EGMHG 141
+H
Sbjct: 65 NALHN 69
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LFV L+ + SE+ + FQ FG + E V+ +G AF+++++ E++ AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECT-VLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 139 MHG 141
+HG
Sbjct: 76 LHG 78
>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 = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 56 GACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DK 113
G P+ P + + + +LF+ +S + +E+ +R F FGQ+ E ++ D
Sbjct: 75 GXHHPIQXKPADSEKNNAVEDR-KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDG 133
Query: 114 IANRPRGFAFLRYATEEESRRAIEGMH 140
++ RG AF+ + T ++ AI+ H
Sbjct: 134 LS---RGCAFVTFTTRAXAQTAIKAXH 157
Score = 34.3 bits (77), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRAI 136
+ FV + SE LR F+ +G + E+N++ D+ N P +G F+ + T + + A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 137 EGMH 140
+H
Sbjct: 65 NALH 68
>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 = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 65 PPSPHSLSTCQP--KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFA 122
PP P S + K ++V + + ++ L F G + + ++ DK + P+G+A
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 123 FLRYA 127
++ +A
Sbjct: 82 YIEFA 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-----RGFAFLRYATEEESRR 134
LF+ L+F T+E++L+ F G + + + K N+ GF F+ Y E++++
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAI--KSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 135 AIEGMHG 141
A++ + G
Sbjct: 66 ALKQLQG 72
>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 = 34.7 bits (78), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V LSF T+E+ + F G + ++ + +DK+ GF F+ Y + ++ A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 140 HG 141
+G
Sbjct: 102 NG 103
>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 = 34.3 bits (77), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 89 TSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+ED +R Q G Q EV L+ +K + + RGFAF+ ++ +++ R +E
Sbjct: 13 ATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 34.3 bits (77), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 42 DFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGF 101
+ L L + G FP P S H LS+ + +L+V E RNAF G
Sbjct: 213 NLTPLVGLEELEMSGNHFP-EIRPGSFHGLSSLK---KLWVMNSQVSLIE---RNAFDGL 265
Query: 102 GQLVEVNLVMDKIANRPRG-FAFLRYATE 129
LVE+NL + +++ P F LRY E
Sbjct: 266 ASLVELNLAHNNLSSLPHDLFTPLRYLVE 294
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 33.1 bits (74), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 21/110 (19%)
Query: 42 DFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTR----------LFVSGLSFRTSE 91
DF+S L + L L + + +PK R L LSF +E
Sbjct: 60 DFESAEDLEK------ALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITE 113
Query: 92 DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
D L+ F+ +E+ LV + +G A++ + +E ++ + +E G
Sbjct: 114 DELKEVFE---DALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLEEKQG 158
>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 = 33.1 bits (74), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V LSF T+E+ + F G + ++ + +DK+ GF F+ Y + ++ A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRYI 79
Query: 140 HG 141
+G
Sbjct: 80 NG 81
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.1 bits (74), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV L+ +E+ L AF FG+L V + D +AF+ + + + +A+E M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 140 HGK 142
+GK
Sbjct: 66 NGK 68
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 33.1 bits (74), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 33/66 (50%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 136 IEGMHG 141
+ ++G
Sbjct: 63 VRNLNG 68
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.7 bits (73), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LFV L + +++ +R F+ FG + E V+ +G AF+++ T E++ AI
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECT-VLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 139 MH 140
+H
Sbjct: 73 LH 74
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 32/63 (50%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
LF+ L ++ L + F FG ++ + +DK + + F F+ + + ++ AI+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 139 MHG 141
M+G
Sbjct: 102 MNG 104
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 33/66 (50%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 136 IEGMHG 141
+ ++G
Sbjct: 61 VRNLNG 66
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 33/66 (50%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 136 IEGMHG 141
+ ++G
Sbjct: 62 VRNLNG 67
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 29/52 (55%)
Query: 91 EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK 142
+ +L + F G++V + +D+ + +GF F+ + ++++ I+ HGK
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
P TRL+V GL TS +L F FG + ++ V + FA+++Y + + ++
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQ 67
Query: 134 RAIEGMHG 141
A M G
Sbjct: 68 AACAKMRG 75
>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 = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
LF+ L + L F FG +V + +DK N + F F+ Y ++ AI+
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 138 GMHG 141
M+G
Sbjct: 86 SMNG 89
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L LSF +ED L+ F+ +E+ LV + +G A++ + +E ++ + +E
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLEEK 73
Query: 140 HG 141
G
Sbjct: 74 QG 75
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT 128
T + RLFV L +E+ + F+ +G+ EV + NR RGF F+R +
Sbjct: 17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLES 67
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
L V LS S + L AF FG + + +V+D R G F+ +A + +R+A+E
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALE 155
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLV--EVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
++FV GL ED + +F+ FG LV + K P+G+AFL + E + I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 137 EG---MHGKVCCC 146
+ GK+ C
Sbjct: 70 DACLEEDGKLYLC 82
>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 = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 93 SLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK 142
+L + F G++V + +D+ + +GF F+ + ++++ I+ HGK
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
+C +++V L ++ L AF +G L V +A P GFAF+ + +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRD 122
Query: 132 SRRAIEGMHGKVCC 145
+ A+ + G+ C
Sbjct: 123 AADAVRDLDGRTLC 136
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L+V GL +E LRN F FG++ + +V + AF+++AT + + A E
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
+C +++V L ++ L AF +G L V +A P GFAF+ + +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRD 122
Query: 132 SRRAIEGMHGKVCC 145
+ A+ + G+ C
Sbjct: 123 AADAVRELDGRTLC 136
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV L+ +E+ L +F FG+L V + D +AF+ + + +A++ M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 140 HGK 142
+GK
Sbjct: 70 NGK 72
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 30.0 bits (66), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P LF++ L T+E L F F EV LV ++ AF+ + TE +S A
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAA 61
Query: 136 IEGMHG 141
E + G
Sbjct: 62 KEALQG 67
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 78 TRLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+R+F+ L + + + F +G++V ++ +GFAF++Y E +R A+
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAV 67
Query: 137 EGMHGKVCC 145
G G++
Sbjct: 68 AGEDGRMIA 76
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 10/74 (13%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVN---------LVMDKIANRPRGFAFLRYAT 128
+ ++V GL+ + D L + F+ G +V++N + +DK +P+G A + Y
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCG-VVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 129 EEESRRAIEGMHGK 142
++ A+E GK
Sbjct: 75 PPTAKAAVEWFDGK 88
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.6 bits (65), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + ++ D G+AF+ + +E +S+RAI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 138 GMHG 141
++G
Sbjct: 64 VLNG 67
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 29.6 bits (65), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
+L++ LS + D LR F G +L V+ K G+AF+ Y + + RAIE
Sbjct: 9 NKLYIGNLSPAVTADDLRQLF-GDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIE 62
Query: 138 GMHGKV 143
+ GKV
Sbjct: 63 TLSGKV 68
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 29.3 bits (64), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 119 RGFAFLRYATEEESRRAIEGMHGKVCC 145
+G+AF++Y+ E +R A+ G +G+V
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLA 88
>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 = 29.3 bits (64), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 10/42 (23%), Positives = 24/42 (57%)
Query: 101 FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK 142
FG++ + +V D + +G+ F+ + + ++ AI+ M G+
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ 71
>pdb|3UZU|A Chain A, The Structure Of The Ribosomal Rna Small Subunit
Methyltransferase A From Burkholderia Pseudomallei
Length = 279
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 3/76 (3%)
Query: 63 CLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFA 122
+P +PH L P V +F LRN G+ LV+ + + +A R
Sbjct: 202 MIPHAPHELPAVDPAVLGEVVTAAFSQRRKMLRNTLGGYRDLVDFDALGFDLARRAEDIG 261
Query: 123 ---FLRYATEEESRRA 135
++R A S RA
Sbjct: 262 VDEYVRVAQAVASARA 277
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLV-EVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
L++ L E+ + AF G+ V V ++ +++ P G+ F+ +A + + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 139 MHGK 142
++GK
Sbjct: 72 INGK 75
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 94 LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
LR AF FG ++++++ + PR AF+ Y E + +A+ ++G
Sbjct: 30 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNG 71
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 116 NRPRGFAFLRYATEEESRRAIEGMHGK 142
N+P ++F RY T EES+RA ++GK
Sbjct: 62 NKP--YSFARYRTTEESKRAYVTLNGK 86
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 94 LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
LR AF FG ++++++ + PR AF+ Y E + +A+ ++G
Sbjct: 54 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNG 95
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
++V S+ T++ L + G +VE+ ++ + +G+A + A+E + +E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 138 GMHGKV 143
+ GKV
Sbjct: 118 LLPGKV 123
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 116 NRPRGFAFLRYATEEESRRAIEGMHGK 142
N+P ++F RY T EES+RA ++GK
Sbjct: 55 NKP--YSFARYRTTEESKRAYVTLNGK 79
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 116 NRPRGFAFLRYATEEESRRAIEGMHGK 142
N+P ++F RY T EES+RA ++GK
Sbjct: 55 NKP--YSFARYRTTEESKRAYVTLNGK 79
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
L+V L TSE+ + F G + V + R +AF+ ++ E++ A++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMK 69
Query: 138 GMHGKV 143
++GKV
Sbjct: 70 ALNGKV 75
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 36/89 (40%), Gaps = 8/89 (8%)
Query: 56 GACFPLACLP---PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMD 112
GA P +P P LS P LF++ L T+E L F F EV LV
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242
Query: 113 KIANRPRGFAFLRYATEEESRRAIEGMHG 141
+ AF+ + E ++ A + + G
Sbjct: 243 R-----HDIAFVEFDNEVQAGAARDALQG 266
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 89 TSEDSLRNAFQGFGQLV--EVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T DS+ A + L + L+ DK + RGFAF++ ++ ++ + ++
Sbjct: 21 TVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
L +S LS+ +E++L+ F+ ++V + + +G+AF+ +A+ E+++ A+
Sbjct: 18 LVLSNLSYSATEETLQEVFEK-ATFIKVPQNQN---GKSKGYAFIEFASFEDAKEAL 70
>pdb|2QKD|A Chain A, Crystal Structure Of Tandem Zpr1 Domains
Length = 404
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 92 DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR--YATEEESRRAIE 137
+ L+ Q GQ++E + I N P G ++L+ YA E++ +E
Sbjct: 346 EKLQEFSQKLGQIIEGKMKAHFIMNDPAGNSYLQNVYAPEDDPEMKVE 393
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-RGFAFLRYATEE 130
+ +FV + +ED LR F +G VMD +P R FAF+ +A ++
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGD------VMDVFIPKPFRAFAFVTFADDQ 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
0.327 0.139 0.444
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,290,823
Number of Sequences: 62578
Number of extensions: 156061
Number of successful extensions: 549
Number of sequences better than 100.0: 146
Number of HSP's better than 100.0 without gapping: 124
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 382
Number of HSP's gapped (non-prelim): 170
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)