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= 030805
(171 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 = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/88 (38%), Positives = 53/88 (60%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
+ +LFV GLSF T+E SL F +GQ+ EV +V D+ R RGF F+ + ++++
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELR 161
A+ M+GK +DGR I V+ A ++ R
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSSDNR 96
>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 = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V L++RTS D+LR F+ +G++ +V + D+ RGFAF+R+ + ++ A++
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 138 GMHGKFLDGRVIFVEIAK 155
M G LDGR + V++A+
Sbjct: 108 AMDGAVLDGRELRVQMAR 125
>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 = 63.2 bits (152), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 48/79 (60%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+ +++ T+E LR F+ +G + +++V K + +PRG+AF+ Y E + A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 140 HGKFLDGRVIFVEIAKSRA 158
GK +DGR + V++ + R
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 62.8 bits (151), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 51/82 (62%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
+ T L V L++RTS D+LR F+ +G++ +V + D+ RGFAF+R+ + ++
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 134 RAIEGMHGKFLDGRVIFVEIAK 155
A++ M G LDGR + V++A+
Sbjct: 127 DAMDAMDGAVLDGRELRVQMAR 148
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 67 SPHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
PH+ Q LFV+ +++ T+E LR F+ +G + +++V K + +PRG+AF+
Sbjct: 90 DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
Y E + A + GK +DGR + V++ + R
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 75 RPHK-VDGRVVEPKRAVSRED 94
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 = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 73 RPHK-VDGRVVEPKRAVSRED 92
Score = 40.8 bits (94), Expect = 4e-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|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 = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 74 RPHK-VDGRVVEPKRAVSRED 93
Score = 40.8 bits (94), Expect = 4e-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|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 = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 75 RPHK-VDGRVVEPKRAVSRED 94
Score = 40.8 bits (94), Expect = 4e-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|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 76 RPHK-VDGRVVEPKRAVSRED 95
Score = 40.8 bits (94), Expect = 4e-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|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 = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+++SLR+ F+ +G L + ++ D R RGF F+ YAT EE A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
K +DGRV+ + A SR +
Sbjct: 68 RPHK-VDGRVVEPKRAVSRED 87
Score = 40.8 bits (94), Expect = 4e-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|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 47/76 (61%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V L++RTS DSLR F+ +G++ +V + + PRGFAF+R+ +++ A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 140 HGKFLDGRVIFVEIAK 155
G LDGR + V++A+
Sbjct: 76 DGAELDGRELRVQVAR 91
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++
Sbjct: 10 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
A E +G LDGR I V+ + ++
Sbjct: 70 AKERANGMELDGRRIRVDFSITK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
A E +G LDGR I V+ + ++
Sbjct: 73 AKERANGMELDGRRIRVDFSITK 95
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 57.0 bits (136), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 48/85 (56%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
RLFV LS+ +SE+ L F +G L E++ +D + +P+GFAF+ + E + +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 139 MHGKFLDGRVIFVEIAKSRAELRQA 163
+ G+ GR++ V + + E Q+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQS 94
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 56.6 bits (135), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
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 RAIEGMHGKFLDGRVIFVEIAK 155
A E M +DG + ++ AK
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAK 90
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 56.6 bits (135), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
P L V GLS T+E LR F +G + +V++V D+ + R RGFAF+ + ++++
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
A E +G LDGR I V+ + ++
Sbjct: 104 AKERANGMELDGRRIRVDFSITK 126
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 45/77 (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 AIEGMHGKFLDGRVIFV 151
A E +G LDGR I V
Sbjct: 73 AKERANGMELDGRRIRV 89
>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 = 1e-08, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 41/69 (59%)
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 GMHGKFLDG 146
++ +G
Sbjct: 150 ALNNVIPEG 158
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + ++ D G+AF+ + +E +S+RAI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
++G + + + V A+ E
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
>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 = 25/69 (36%), Positives = 41/69 (59%)
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 GMHGKFLDG 146
++ +G
Sbjct: 161 ALNNVIPEG 169
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 39/82 (47%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + + D G+AF+ + +E +S+RAI+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
++G + + + V A+ E
Sbjct: 75 VLNGITVRNKRLKVSYARPGGE 96
>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 = 2e-08, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 41/69 (59%)
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 GMHGKFLDG 146
++ +G
Sbjct: 74 ALNNVIPEG 82
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 47/81 (58%)
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 MHGKFLDGRVIFVEIAKSRAE 159
++G L GR + V R +
Sbjct: 88 LNGFELAGRPMKVGHVTERTD 108
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GL+ T+E L+ F G + EV L+ D+ + + RGFAF+ + +++ A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 139 MHGKFLDGRVIFVEIAK 155
M+GK L G+ I VE AK
Sbjct: 68 MNGKSLHGKAIKVEQAK 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GLSF T+E+SLRN ++ +G+L + ++ D + R RGF F+ +++ E A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 87
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
+DGRV+ + A +R E
Sbjct: 88 ARPHSIDGRVVEPKRAVAREE 108
>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 = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
+R++V + + ED++R AF FG + +++ D + + +GFAF+ Y E ++ A+E
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 138 GMHGKFLDGRVIFV 151
M+ L GR I V
Sbjct: 89 QMNSVMLGGRNIKV 102
Score = 42.0 bits (97), Expect = 2e-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 = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V + + ED++R AF FG + +++ D + + +GFAF+ Y E ++ A+E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 139 MHGKFLDGRVIFV 151
M+ L GR I V
Sbjct: 75 MNSVMLGGRNIKV 87
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 39/73 (53%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V+ + S+D +++ F+ FG++ L D + +G+ F+ Y + S+ A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 139 MHGKFLDGRVIFV 151
M+ L G+ + V
Sbjct: 172 MNLFDLGGQYLRV 184
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
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 HGKFLDGRVIFVEIAKSRAE 159
+G L+ R +FV KSR E
Sbjct: 164 NGMLLNDRKVFVGRFKSRKE 183
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 49/108 (45%), Gaps = 4/108 (3%)
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 GFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
G+A++ + ++ RA++ M+ + G+ + + ++ LR++ N
Sbjct: 58 GYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
>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 = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
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 HGKFLDGRVIFVEIAKSRAE 159
+G L+ R +FV KSR E
Sbjct: 159 NGMLLNDRKVFVGRFKSRKE 178
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 42/88 (47%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P L+V L +E L F G ++ + + D I R G+A++ + ++ RA
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQA 163
++ M+ + G+ + + ++ LR++
Sbjct: 69 LDTMNFDVIKGKPVRIMWSQRDPSLRKS 96
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T++FV GL + T++ SLR F+GFG + E ++ D+ + RG+ F+ A + RA +
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 138 GMHGKFLDGRVIFVEIA 154
+ +DGR V +A
Sbjct: 78 DPN-PIIDGRKANVNLA 93
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
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 HGKFLDGRVIFVEIAKSRAE 159
+G L+ R +FV KSR E
Sbjct: 66 NGMLLNDRKVFVGRFKSRKE 85
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%)
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 EGMHGKFLDGRVIFVEIAKSRAEL 160
++G L + I V A+ +E+
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEV 85
Score = 39.7 bits (91), Expect = 7e-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|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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%)
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 EGMHGKFLDGRVIFVEIAKSRAEL 160
++G L + I V A+ +E+
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEV 85
Score = 40.0 bits (92), Expect = 7e-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|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
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 HGKFLDGRVIFVEIAKSRAE 159
+G L+ R +FV KSR E
Sbjct: 72 NGMLLNDRKVFVGRFKSRKE 91
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+F+ GLS+ T++ L++ F FG++V+ L +D I R RGF F+ + E + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 140 HGKFLDGRVI 149
K L+G+VI
Sbjct: 62 EHK-LNGKVI 70
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%)
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 EGMHGKFLDGRVIFVEIAK 155
++G L + I V A+
Sbjct: 64 NTLNGLRLQSKTIKVSYAR 82
>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 = 23/59 (38%), Positives = 36/59 (61%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
++FV GLS T E+ +R F GFG++ + L MD N+ RGF F+ + EE ++ +E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
++F+ GL++ T+ED+LR F +G + ++ ++ D R RGF FL + ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 139 MHGKFLDGRVI 149
H LDG+VI
Sbjct: 65 QH--ILDGKVI 73
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 75 QPKT-RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
Q KT ++FV G+ F +G +++ L++DK + RGF F+ Y + +
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
R + KF+D + +EI RAE R
Sbjct: 144 RVCQ---NKFIDFKDRKIEI--KRAEPRH 167
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/99 (31%), Positives = 54/99 (54%), Gaps = 5/99 (5%)
Query: 62 ACLPPSPH--SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPR 119
+P H + + QPK RL VS + FR + LR F FG++++V ++ ++ + +
Sbjct: 13 GLVPRGSHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--K 69
Query: 120 GFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
GF F+ + ++ RA E +HG ++GR I V A +R
Sbjct: 70 GFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 41/68 (60%)
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 HGKFLDGR 147
+G L GR
Sbjct: 68 NGFELAGR 75
>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 = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 48/85 (56%), Gaps = 1/85 (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 SRRAIEGMHGKFLDGRVIFVEIAKS 156
+ +A+ M G + +I V I+ S
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAISNS 95
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 44/76 (57%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
S+ LFV L+ +++LRNAF+ F + +++ D RG+ F+ + ++++
Sbjct: 82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 132 SRRAIEGMHGKFLDGR 147
++ A++ M G+ L+GR
Sbjct: 142 AQNAMDSMQGQDLNGR 157
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V L +ED L+ FQ G + + +++DK N+ +AF+ Y ++ A++ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 140 HGKFLDGRVIFVEIA 154
+GK ++ ++ + A
Sbjct: 62 NGKQIENNIVKINWA 76
>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 = 4e-07, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
+FV GLS T E+ +R F GFG++ + L MD N+ RGF F+ + EE ++ +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 42/78 (53%)
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 GMHGKFLDGRVIFVEIAK 155
++G L + I V A+
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>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 = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 44/84 (52%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
S K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E+
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 132 SRRAIEGMHGKFLDGRVIFVEIAK 155
+ AI+ M+ L GR I V +AK
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLAK 85
>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 = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
R++V + + ED++R AF FG + ++ D + + +GFAF+ Y E ++ A+E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 139 MHGKFLDGRVIFV 151
+ L GR I V
Sbjct: 74 XNSVXLGGRNIKV 86
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 32/58 (55%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
R++V+ + S+D +++ F+ FG++ L D + +G+ F+ Y + S+ A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>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 = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 45/75 (60%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV L+ +++LRNAF+ F + +++ D RG+ F+ + ++++++ A++ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 140 HGKFLDGRVIFVEIA 154
G+ L+GR + + A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 45/89 (50%)
Query: 67 SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
S S K L+V GL+ + L AF FG + ++ + +D + RGFAF+ +
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAK 155
E++ AI+ M+ L GR I V +AK
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 49.7 bits (117), Expect = 7e-07, 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|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
++FV G+ E LR F+ FG + EV ++ D RPRGF F+ + E+ +A+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNP 168
MH + G+ + V+ RAE R + + P
Sbjct: 71 MHFHDIMGKKVEVK----RAEPRDSKSSGP 96
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 3/85 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV + + +E+ L++ F G +V LV D+ +P+G+ F Y +E + A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 140 HGKFLDGRVIFVEIA---KSRAELR 161
+G+ GR + V+ A K++ EL+
Sbjct: 71 NGREFSGRALRVDNAASEKNKEELK 95
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 72 NGQDLMGQPISVD 84
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 41/74 (55%)
Query: 82 VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
V+ LS T E L+ F+ FG + + L DK + +GFAF+ + E++ RAI G+ G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 142 KFLDGRVIFVEIAK 155
D ++ VE AK
Sbjct: 80 FGYDHLILNVEWAK 93
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 86 NGQDLMGQPISVD 98
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 43/79 (54%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 137 EGMHGKFLDGRVIFVEIAK 155
+ M+ L GR I V +AK
Sbjct: 65 DNMNESELFGRTIRVNLAK 83
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
RL VS + FR + LR F FG++++V ++ ++ + +GF F+ + ++ RA E
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREK 74
Query: 139 MHGKFLDGRVIFVEIAKSRA 158
+HG ++GR I V A +R
Sbjct: 75 LHGTVVEGRKIEVNNATARV 94
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 137 EGMHGKFLDGRVIFVEIA 154
+ M+ L GR I V +A
Sbjct: 123 DNMNESELFGRTIRVNLA 140
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 2/94 (2%)
Query: 68 PHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
P +ST P + +LF+ GL ++D ++ FG L NLV D +G+AF
Sbjct: 103 PGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 162
Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
Y + +AI G++G L + + V+ A A+
Sbjct: 163 YVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+G+ +E+ + + F +G++ ++L +D+ +G+ + Y T +E++ A+EG+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 140 HGKFLDGRVIFVE 152
+G+ L G+ I V+
Sbjct: 85 NGQDLMGQPISVD 97
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K+ ++VS L F + + L F +G++V+V ++ DK + +G AF+ + ++ ++
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 137 EGMHGKFLDGRVIFVEIA 154
++ K L GRVI IA
Sbjct: 76 RAINNKQLFGRVIKASIA 93
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 10/84 (11%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV GLS T+ + +++ F+ FG++ + L+ DK NR RGF F+ + +E+ + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-- 59
Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
+ F EI E ++A
Sbjct: 60 --------IHFHEINNKMVECKKA 75
>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 = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
K L+V GL+ + L AF FG + ++ + +D + RGFAF+ + E++ AI
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 137 EGMHGKFLDGRVIFVEIA 154
+ M+ L GR I V +A
Sbjct: 62 DNMNESELFGRTIRVNLA 79
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V L ++ LR AF FG + ++M+ R +GF F+ +++ EE+ +A+ M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
+G+ + + ++V +A+ R E RQ+
Sbjct: 76 NGRIVATKPLYVALAQ-RKEERQS 98
>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 = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+ FV GLS+ TS+ L++ F FG++V+ + D R RGF F+ + + ++
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 139 MHGKFLDGRVI 149
+ LDGRVI
Sbjct: 73 KEHR-LDGRVI 82
>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 = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%)
Query: 68 PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
PH +LF+ GL ++D ++ FG L NLV D +G+AF Y
Sbjct: 87 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 146
Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIA 154
+ +AI G++G L + + V+ A
Sbjct: 147 DINVTDQAIAGLNGMQLGDKKLLVQRA 173
>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 = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 50/93 (53%), Gaps = 1/93 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV LS + + ++ AF FG++ + +V D + +G+ F+ + + ++ AI+ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 140 HGKFLDGRVIFVEIAKSRAEL-RQAFKNNPRQN 171
G++L GR I A + + +++N +Q+
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%)
Query: 68 PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
PH +LF+ GL ++D ++ FG L NLV D +G+AF Y
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144
Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIA 154
+ +AI G++G L + + V+ A
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQRA 171
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 46.2 bits (108), 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|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+FV LS + + +++AF FG++ + +V D + +G+ F+ + + ++ AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 139 MHGKFLDGRVIFVEIA 154
M G++L GR I A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+LF+ GL ++D ++ FG L NLV D +G+AF Y + +AI G
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
++G L + + V+ A A+
Sbjct: 63 LNGMQLGDKKLLVQRASVGAK 83
>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 = 3e-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|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 44.3 bits (103), Expect = 3e-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|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR----- 134
+F+ LSF + E++L Q FG L V +V+ +G AF ++ T+E +++
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 135 AIEGMHGKF-LDGRVIFVEIAKSRAE 159
++E G LDGR + V++A +R E
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLAVTRDE 103
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V LSF T+E+ + F G + ++ + +DK+ GF F+ Y + ++ A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 140 HGKFLDGRVIFVEIAKSRAELRQ 162
+G LD R+I + E RQ
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQ 124
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
Q + L V GL ++T+E L+ F FG+++ V + D +GF F+R+ E +
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
+ H +DGR ++ S+
Sbjct: 73 VMSQRH--MIDGRWCDCKLPNSK 93
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.9 bits (102), 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: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 1/78 (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 EGMHGKFLDGRVIFVEIA 154
E M+G++L R I V A
Sbjct: 66 EAMNGQYLCNRPITVSYA 83
>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 = 7e-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|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 = 8e-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|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+ + ED ++ F +G++ ++L +D+ +G+A + Y T +++ A E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 140 HGKFLDGRVIFVE 152
+G + G+ I V+
Sbjct: 89 NGAEIMGQTIQVD 101
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
++ G++ ++ +R F FGQ++E+ + +K G++F+R++T E + AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 140 HGKFLDGRVIFVEIAKSRAEL 160
+G ++G V+ K ++
Sbjct: 82 NGTTIEGHVVKCYWGKESPDM 102
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV+ + ED ++ F +G++ ++L +D+ +G+A + Y T +++ A E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 140 HGKFLDGRVIFVE 152
+G + G+ I V+
Sbjct: 135 NGAEIMGQTIQVD 147
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-----RGFAFLRYATEEESRR 134
LF+ L+F T+E++L+ F G + + + K N+ GF F+ Y E++++
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIK--SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 135 AIEGMHGKFLDGRVIFVEIAK 155
A++ + G +DG + V I++
Sbjct: 66 ALKQLQGHTVDGHKLEVRISE 86
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L+V LSF T+E+ + F G + ++ + +DK+ GF F+ Y + ++ A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRYI 79
Query: 140 HGKFLDGRVI 149
+G LD R+I
Sbjct: 80 NGTRLDDRII 89
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 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|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 39.7 bits (91), Expect = 9e-04, 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 = 39.7 bits (91), Expect = 0.001, 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|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 = 0.001, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
++V L + + + ++ F FG++ V L+ D+ +P+GF F+ EE AI +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 140 HGKFLDGRVIFVEIAKSRAELR 161
GR I V A + L
Sbjct: 63 DNTDFMGRTIRVTEANPKKSLE 84
>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 = 39.3 bits (90), Expect = 0.001, 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|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.3 bits (90), Expect = 0.001, 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|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
++FV +S + LR+ F+ G+++E ++V D +AF+ E +++ AI
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 139 MHGKFLDGRVIFVEIA 154
++GK + G+ I VE++
Sbjct: 63 LNGKEVKGKRINVELS 78
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/118 (23%), Positives = 50/118 (42%), Gaps = 21/118 (17%)
Query: 42 DFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTR----------LFVSGLSFRTSE 91
DF+S L + L L + + +PK R L LSF +E
Sbjct: 60 DFESAEDLEK------ALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITE 113
Query: 92 DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI 149
D L+ F+ +E+ LV + +G A++ + +E ++ + +E G +DGR +
Sbjct: 114 DELKEVFE---DALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LFV L+ +E+ L AF FG+L V + D +AF+ + + + +A+E M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 140 HGKFLDGRVIFVEIAK 155
+GK L+G I + AK
Sbjct: 66 NGKDLEGENIEIVFAK 81
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)
Query: 65 PPSPHSLSTCQP--KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFA 122
PP P S + K ++V + + ++ L F G + + ++ DK + P+G+A
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 123 FLRYATEEESRRAIEGMHGKFLDGRVIFV 151
++ +A E S A M GR I V
Sbjct: 82 YIEFA-ERNSVDAAVAMDETVFRGRTIKV 109
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 38.9 bits (89), Expect = 0.001, 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|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
++V GL + SE L F G +V ++ D++ + +G+ F+ + +EE++ AI+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 140 HGKFLDGRVIFVEIAKSR 157
L G+ I V A +
Sbjct: 78 DMIKLYGKPIRVNKASAH 95
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L LSF +ED L+ F+ +E+ LV + +G A++ + +E ++ + +E
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLEEK 73
Query: 140 HGKFLDGRVI 149
G +DGR +
Sbjct: 74 QGAEIDGRSV 83
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGFAFLRYATEEESRRAI 136
+LF+ +S + +E+ +R F FGQ+ E ++ D ++ RG AF+ + T ++ AI
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS---RGCAFVTFTTRAMAQTAI 165
Query: 137 EGMH 140
+ MH
Sbjct: 166 KAMH 169
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 3/91 (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 EGMHG-KFLDGRVIFVEIAKSRAELRQAFKN 166
+H K L G +++ + +E A ++
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVED 107
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.7 bits (86), Expect = 0.003, 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|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGFAFLRYATEEESRRAI 136
+LF+ +S + +E+ +R F FGQ+ E ++ D ++ RG AF+ + T ++ AI
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS---RGCAFVTFTTRAMAQTAI 153
Query: 137 EGMH 140
+ MH
Sbjct: 154 KAMH 157
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
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-KFLDG 146
+H K L G
Sbjct: 65 NALHNMKVLPG 75
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/73 (19%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFLRYATEEESRRAI 136
T++ + L+ ++D + F +G++ +++ ++++ + +G+A++ + +E+ +A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 137 EGMHGKFLDGRVI 149
+ M G +DG+ I
Sbjct: 65 KHMDGGQIDGQEI 77
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 78 TRLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
+R+F+ L + + + F +G++V ++ +GFAF++Y E +R A+
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAV 67
Query: 137 EGMHGKFLDGRVIFVEIA 154
G G+ + G+V+ + +A
Sbjct: 68 AGEDGRMIAGQVLDINLA 85
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+++V L + L AF +G L V IA P GFAF+ + ++ A+ G
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 139 MHGKFLDGRVIFVEIA 154
+ GK + G + VE++
Sbjct: 57 LDGKVICGSRVRVELS 72
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 76 PKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
PK+RLF+ L + S++ L F +G ++++N+ F F+++ + R
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRD 60
Query: 135 AIEGMHGKFLDGRVIFVEIAKSRA 158
AIE + G+ + +E++ S A
Sbjct: 61 AIECESQEMNFGKKLILEVSSSNA 84
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
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-KFLDG 146
+H K L G
Sbjct: 65 NALHNMKVLPG 75
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.007, 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|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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 29/49 (59%)
Query: 101 FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI 149
FG++ + +V D + +G+ F+ + + ++ AI+ M G++L GR I
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
L+V L TSE+ + F G + V + R +AF+ ++ E++ A++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMK 69
Query: 138 GMHGKFLDGRVIFVEIAK 155
++GK LDG I V +AK
Sbjct: 70 ALNGKVLDGSPIEVTLAK 87
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGFAFLRYATEEESRRAI 136
+LF+ +S + +E+ +R F FGQ+ E ++ D ++ RG AF+ + T ++ AI
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLS---RGCAFVTFTTRAXAQTAI 153
Query: 137 EGMH 140
+ H
Sbjct: 154 KAXH 157
Score = 35.0 bits (79), Expect = 0.022, 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|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 76 PKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
PK+RLF+ L + S++ L F +G ++++N+ F F+++ + R
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRD 52
Query: 135 AIEGMHGKFLDGRVIFVEIAKSRA 158
AIE + G+ + +E++ S A
Sbjct: 53 AIECESQEMNFGKKLILEVSSSNA 76
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 46/90 (51%)
Query: 70 SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
S + +P L++ LS R +E L + F F + + + R RG AF+ + +
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77
Query: 130 EESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
E + +A+ ++G L G+++ +E K++ +
Sbjct: 78 EIAWQALHLVNGYKLYGKILVIEFGKNKKQ 107
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 10/89 (11%)
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 EEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
++ A+E GK G + V +A+ +
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
P TRL+V GL TS +L F FG + ++ V + FA+++Y + + ++
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQ 67
Query: 134 RAIEGMHGKFLDG--RVIFVEIAKS 156
A M G L G R + V+ AKS
Sbjct: 68 AACAKMRGFPLGGPDRRLRVDFAKS 92
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L +S LS+ +E++L+ F+ ++V + + +G+AF+ +A+ E+++ A+
Sbjct: 18 LVLSNLSYSATEETLQEVFEK-ATFIKVPQNQN---GKSKGYAFIEFASFEDAKEALNSC 73
Query: 140 HGKFLDGRVIFVEIAKSRA 158
+ + ++GR I +E+ R
Sbjct: 74 NKREIEGRAIRLELQGPRG 92
>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 = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 31/55 (56%)
Query: 91 EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD 145
+ +L + F G++V + +D+ + +GF F+ + ++++ I+ HGK LD
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 93 SLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD 145
+L + F G++V + +D+ + +GF F+ + ++++ I+ HGK LD
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>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 = 0.032, 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|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 34.3 bits (77), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 14/74 (18%), Positives = 36/74 (48%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 136 IEGMHGKFLDGRVI 149
+ ++G L R +
Sbjct: 63 VRNLNGYQLGSRFL 76
>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 = 34.3 bits (77), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 40/84 (47%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
LF+ L + L F FG +V + +DK N + F F+ Y ++ AI+
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 138 GMHGKFLDGRVIFVEIAKSRAELR 161
M+G + + + V++ +S+ + +
Sbjct: 86 SMNGFQIGMKRLKVQLKRSKNDSK 109
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 34.3 bits (77), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 88 RTSEDSLRNAFQGFGQLV--EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF-- 143
T DS+ A + L + L+ DK + RGFAF++ ++ ++ + ++ +
Sbjct: 20 HTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPP 79
Query: 144 --LDGRVIFVEIAKS 156
+DG+ I V+ AKS
Sbjct: 80 LKIDGKTIGVDFAKS 94
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.9 bits (76), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 6/90 (6%)
Query: 67 SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
S S CQ +FV L F + L++ F G ++ ++ M+ + +G +++
Sbjct: 2 SSGSSGACQ----IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVKF 55
Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKS 156
+ E + RA M+G L GR I V I ++
Sbjct: 56 ESPEVAERACRMMNGMKLSGREIDVRIDRN 85
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.9 bits (76), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 6/89 (6%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
T + RLFV L +E+ + F+ +G+ EV + NR RGF F+R +
Sbjct: 17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTL 70
Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAEL 160
+ A + G L R + + A A L
Sbjct: 71 AEIAKAELDGTILKSRPLRIRFATHGAAL 99
Score = 27.7 bits (60), Expect = 3.5, 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|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.9 bits (76), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 25/36 (69%)
Query: 119 RGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA 154
+G+AF++Y+ E +R A+ G +G+ L G+ + + +A
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 33.9 bits (76), Expect = 0.047, 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|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 33.5 bits (75), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 5/81 (6%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNL--VMDKIANRPRGFAFLRYATEEESR--RA 135
+ + L+ ++ DS+ A + L N+ + DK RGFAF++ +T E ++ +
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQI 85
Query: 136 IEGMHGKF-LDGRVIFVEIAK 155
++ +H +DG+ I VE AK
Sbjct: 86 LQALHPPLTIDGKTINVEFAK 106
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.5 bits (75), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 14/74 (18%), Positives = 36/74 (48%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 136 IEGMHGKFLDGRVI 149
+ ++G L R +
Sbjct: 61 VRNLNGYQLGSRFL 74
>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 = 33.5 bits (75), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
++V S+ T++ L + G +VE+ ++ + +G+A + A+E + +E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQ 162
+ GK L+G + V A +R L Q
Sbjct: 118 LLPGKVLNGEKVDVRPA-TRQNLSQ 141
>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 = 33.1 bits (74), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 14/74 (18%), Positives = 36/74 (48%)
Query: 76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
P +++ + + +E+ + + G ++ + ++ D R +G+AF+ + E S A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 136 IEGMHGKFLDGRVI 149
+ ++G L R +
Sbjct: 62 VRNLNGYQLGSRFL 75
>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 = 33.1 bits (74), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 94 LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI 153
LR AF FG ++++++ + PR AF+ Y E + +A+ ++G ++ + V I
Sbjct: 54 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Query: 154 AKSRAELRQA 163
A+ + L A
Sbjct: 108 ARKQPMLDAA 117
>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 = 0.087, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 77 KTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
K+RLF+ L + S++ L F +G ++++N+ F F+++ + R A
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDA 73
Query: 136 IEGMHGKFLDGRVIFVEIAKSRA 158
IE + G+ + +E++ S A
Sbjct: 74 IECESQEMNFGKKLILEVSSSNA 96
>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 = 0.088, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 77 KTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
K+RLF+ L + S++ L F +G ++++N+ F F+++ + R A
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDA 73
Query: 136 IEGMHGKFLDGRVIFVEIAKSRA 158
IE + G+ + +E++ S A
Sbjct: 74 IEXESQEMNFGKKLILEVSSSNA 96
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 33.1 bits (74), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRG-FAF 123
P S H LS+ + +L+V E RNAF G LVE+NL + +++ P F
Sbjct: 235 PGSFHGLSSLK---KLWVMNSQVSLIE---RNAFDGLASLVELNLAHNNLSSLPHDLFTP 288
Query: 124 LRYATE 129
LRY E
Sbjct: 289 LRYLVE 294
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.7 bits (73), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV L R E+ L F G L +V + D+ +P+ F F+ + E AI +
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77
Query: 140 HGKFLDGRVIFV 151
+G L GR I V
Sbjct: 78 NGIRLYGRPINV 89
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 32/62 (51%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
LF+ L ++ L + F FG ++ + +DK + + F F+ + + ++ AI+ M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 140 HG 141
+G
Sbjct: 103 NG 104
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
+C +++V L ++ L AF +G L V +A P GFAF+ + +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRD 122
Query: 132 SRRAIEGMHGKFLDGRVIFVEIA 154
+ A+ + G+ L G + VE++
Sbjct: 123 AADAVRDLDGRTLCGCRVRVELS 145
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
+FV L F + L++ F G ++ ++ M+ + +G +++ + E + RA M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVKFESPEVAERACRMM 65
Query: 140 HGKFLDGRVIFVEIAKS 156
+G L GR I V I ++
Sbjct: 66 NGMKLSGREIDVRIDRN 82
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L+V GL +E LRN F FG++ + +V + AF+++AT + + A E
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
Query: 138 GMHGKFL-DGRVIFVEIAK 155
K + +GR + V+ +
Sbjct: 67 KSFNKLIVNGRRLNVKWGR 85
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 94 LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI 153
LR AF FG ++++++ + PR AF+ Y E + +A+ ++G ++ + V I
Sbjct: 30 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 154 AKSRAEL 160
A+ + L
Sbjct: 84 ARKQPML 90
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
+L++ LS + D LR F G +L V+ K G+AF+ Y + + RAIE
Sbjct: 10 KLYIGNLSPAVTADDLRQLF-GDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIET 63
Query: 139 MHGKF-LDGRVIFVEIAKSR 157
+ GK L G+++ V+ + S+
Sbjct: 64 LSGKVELHGKIMEVDYSVSK 83
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
+C +++V L ++ L AF +G L V +A P GFAF+ + +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRD 122
Query: 132 SRRAIEGMHGKFLDGRVIFVEIA 154
+ A+ + G+ L G + VE++
Sbjct: 123 AADAVRELDGRTLCGCRVRVELS 145
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 105 VEVNLVMDKIANRPRGF--AFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
V+ N V + N +G A +++ E+++R++ E +H K L+GR FV + + ++R+
Sbjct: 41 VDENAVHVLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFVHVV-TLEDMRE 98
Query: 163 AFKNNPRQ 170
KN P Q
Sbjct: 99 IEKNPPAQ 106
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.8 bits (68), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLV-EVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
L++ L E+ + AF G+ V V ++ +++ P G+ F+ +A + + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 139 MHGKFLDG 146
++GK L G
Sbjct: 72 INGKPLPG 79
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 30.8 bits (68), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR------PRGFAFLRYATEE 130
K +FV GLS R ++ + + FG+ +++ V+ + P A++ Y E
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSR 157
++ RAI+ ++ +DGR + + ++
Sbjct: 75 DALRAIQCVNNVVVDGRTLKASLGTTK 101
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
T L V+ L ++ L F+ G + ++ D G+AF+ + +E +S+RAI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
++G + + + V A+ E
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.4 bits (67), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V+ L ++ + FG L LV + + +G+ F Y ++ + RA +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 140 HGKFLDGRVIFV 151
GK L R ++V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.0 bits (66), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLV--EVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
++FV GL ED + +F+ FG LV + K P+G+AFL + E + I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 137 EG 138
+
Sbjct: 70 DA 71
>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 = 30.0 bits (66), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V+ L ++ + FG L LV + + +G+ F Y ++ + RA +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 140 HGKFLDGRVIFV 151
GK L R ++V
Sbjct: 156 LGKPLGPRTLYV 167
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.0 bits (66), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%)
Query: 80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
L V+ L ++ + FG L LV + + +G+ F Y ++ + RA +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 140 HGKFLDGRVIFV 151
GK L R ++V
Sbjct: 158 LGKPLGPRTLYV 169
>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 = 0.70, 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|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 0.76, 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|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 = 1.4, 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|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRG--FAFLRYATEEESRRAI 136
R++V L + + F +G + +++L NR G FAF+ + ++ A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-----KNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 137 EGMHGKFLDGRVIFVEIAKS 156
G G DG + VE +S
Sbjct: 79 YGRDGYDYDGYRLRVEFPRS 98
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 28.1 bits (61), Expect = 2.7, 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|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 = 27.7 bits (60), Expect = 3.0, 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 = 27.7 bits (60), Expect = 3.0, 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|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 27.7 bits (60), Expect = 3.6, 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|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-RGFAFLRYATEE 130
+ +FV + +ED LR F +G VMD +P R FAF+ +A ++
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGD------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
0.325 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,774,630
Number of Sequences: 62578
Number of extensions: 177962
Number of successful extensions: 643
Number of sequences better than 100.0: 160
Number of HSP's better than 100.0 without gapping: 133
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 460
Number of HSP's gapped (non-prelim): 185
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)