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= 028972
(201 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 57.0 bits (136), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 32 DAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
+A +PG L++ GL+ L+ FG G ++E L+ D RT +S GFAF+T E
Sbjct: 3 EADHPGK-LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPAD 60
Query: 92 ADRCIKYLNRSVLEGRLITVEKAKR 116
A K +N L G+ I VE+AK+
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVEQAKK 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 45/85 (52%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V GLS LE+ F G+++E +V D T+ S GF FVT E ++ A + +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 100 NRSVLEGRLITVEKAKRSRGRTPTP 124
N ++GR I V++A +S P
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSGP 99
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V LS + DLEK F G ++E H D T++ GFAFVT E A + +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 100 NRSVLEGRLITV 111
+ V +GR++ V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 34 ANPGNN--LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
ANP N L V GLS T DL + F G + + +V D ++R S GFAFV E V+
Sbjct: 41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 92 ADRCIKYLNRSVLEGRLITVE 112
A + N L+GR I V+
Sbjct: 101 AKEAKERANGMELDGRRIRVD 121
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 36/63 (57%)
Query: 34 ANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGAD 93
+ G +++ GLS + T L ++FG G+V EC ++ DP T+ S GF FVT G D
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 94 RCI 96
+ +
Sbjct: 82 KVL 84
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V+ + R + DL + FG GK+ + ++ + R S GF FVT E ADR + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 100 NRSVLEGRLITVEKA 114
+ +V+EGR I V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
+YV+ L +TN DL + F GKV + ++ D TR+S G AF+ + A C + +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 100 NRSVLEGRLI 109
N L GR+I
Sbjct: 79 NNKQLFGRVI 88
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 45/90 (50%), Gaps = 2/90 (2%)
Query: 34 ANPGNN--LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
ANP N L V GLS T DL + F G + + +V D ++R S GFAFV E V+
Sbjct: 7 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 92 ADRCIKYLNRSVLEGRLITVEKAKRSRGRT 121
A + N L+GR I V+ + R T
Sbjct: 67 AKEAKERANGMELDGRRIRVDFSITKRPHT 96
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V+ + R + DL + FG GK+ + ++ + R S GF FVT E ADR + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 100 NRSVLEGRLITVEKA 114
+ +V+EGR I V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 34 ANPGNN--LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
ANP N L V GLS T DL + F G + + +V D ++R S GFAFV E V+
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 92 ADRCIKYLNRSVLEGRLITVE 112
A + N L+GR I V+
Sbjct: 70 AKEAKERANGMELDGRRIRVD 90
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 40/85 (47%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV GL+ V + L F G +T+ + D T + GFAFV E E A I +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 100 NRSVLEGRLITVEKAKRSRGRTPTP 124
N S L GR I V AK R + P
Sbjct: 75 NESELFGRTIRVNLAKPMRIKESGP 99
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/80 (40%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 34 ANPGNN--LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
ANP N L V GLS T DL + F G + + +V D ++R S GFAFV E V+
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 92 ADRCIKYLNRSVLEGRLITV 111
A + N L+GR I V
Sbjct: 70 AKEAKERANGMELDGRRIRV 89
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE D +
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTPG 125
V +GR++ ++A SR + PG
Sbjct: 74 RPHKV-DGRVVEPKRAV-SREDSQRPG 98
Score = 34.3 bits (77), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 93 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 153 DDHDSVDKIV 162
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 91 GADRCIKYLNRSVLEGRLITVEKAKRSRGRTPTPG 125
D + V +GR++ ++A SR + PG
Sbjct: 67 EVDAAMNARPHKV-DGRVVEPKRAV-SREDSQRPG 99
Score = 34.3 bits (77), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 154 DDHDSVDKIV 163
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE D +
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTPG 125
V +GR++ ++A SR + PG
Sbjct: 76 RPHKV-DGRVVEPKRAV-SREDSQRPG 100
Score = 34.3 bits (77), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 95 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 155 DDHDSVDKIV 164
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 91 GADRCIKYLNRSVLEGRLITVEKAKRSRGRTPTPG 125
D + V +GR++ ++A SR + PG
Sbjct: 67 EVDAAMNARPHKV-DGRVVEPKRAV-SREDSQRPG 99
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 154 DDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 91 GADRCIKYLNRSVLEGRLITVEKAKRSRGRTPTPG 125
D + V +GR++ ++A SR + PG
Sbjct: 65 EVDAAMNARPHKV-DGRVVEPKRAV-SREDSQRPG 97
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 92 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 152 DDHDSVDKIV 161
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/86 (36%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L++ GLS T+ L F G +T+C ++ DP T+ S GF FVT TVE D +
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 100 NRSVLEGRLITVEKAKRSRGRTPTPG 125
V +GR++ ++A SR + PG
Sbjct: 69 PHKV-DGRVVEPKRAV-SREDSQRPG 92
Score = 33.9 bits (76), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 32 DAANPGNNL-----YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
D+ PG +L +V G+ L +F GK+ ++TD + + GFAFVT
Sbjct: 87 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Query: 87 ETVEGADRCI 96
+ + D+ +
Sbjct: 147 DDHDSVDKIV 156
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
++V GL T+A L K+F G G + E ++TD +T +S G+ FVTM A+R K
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 100 NRSVLEGRLITVEKA 114
N +++GR V A
Sbjct: 80 N-PIIDGRKANVNLA 93
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 34/58 (58%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI 96
+++ GLS + T L ++FG G+V EC ++ DP T+ S GF FVT G D+ +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+++ GL+ T +L ++FG G VT+ ++ DP T S GF F++ E D +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 99 LNRSVLEGRLITVEKA 114
+ +L+G++I ++A
Sbjct: 64 -TQHILDGKVIDPKRA 78
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 32 DAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEG 91
D + ++V G+ V + E+FF G + + L+ D T +S GF FVT ++ +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 92 ADRCIKYLNRSV-LEGRLITVEKAK 115
DR + N+ + + R I +++A+
Sbjct: 142 VDRVCQ--NKFIDFKDRKIEIKRAE 164
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T + + FG G + C LV D T +S G+ FV AD+ I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 99 LNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 66 LNGLKLQTKTIKVSYARPS 84
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYV+GL ++ ++E+ F G++ ++ D T S G F+ + A+ IK
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 99 LN 100
LN
Sbjct: 152 LN 153
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T + + FG G + C LV D T +S G+ FV AD+ I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 99 LNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 66 LNGLKLQTKTIKVSYARPS 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 37/76 (48%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV GL+ V + L F G +T+ + D T + GFAFV E E A I +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 100 NRSVLEGRLITVEKAK 115
N S L GR I V AK
Sbjct: 68 NESELFGRTIRVNLAK 83
>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 = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 37/76 (48%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV GL+ V + L F G +T+ + D T + GFAFV E E A I +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 100 NRSVLEGRLITVEKAK 115
N S L GR I V AK
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 3/89 (3%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
L++ GLS T L ++ GK+T+C ++ DP ++ S GF FVT ++ D +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 99 LNRSVLEGRLITVEK--AKRSRGRTPTPG 125
S+ +GR++ ++ A+ G P+ G
Sbjct: 89 RPHSI-DGRVVEPKRAVAREESGSGPSSG 116
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+L V L+ R + L + F G+V + ++ D T+ES GFAFV A+ +
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTPGH 126
++ +VL+GR + V+ A+ GR P H
Sbjct: 109 MDGAVLDGRELRVQMAR--YGRPPDSHH 134
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
+++ GLS T DL+ +F G+V +C L DP T S GF FV + E D+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 100 NRSVLEGRLITVEKA 114
L G++I ++A
Sbjct: 62 EHK-LNGKVIDPKRA 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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV GL+ V + L F G +T+ + D T + GFAFV E E A I +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 100 NRSVLEGRLITVEKA 114
N S L GR I V A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+L V L+ R + L + F G+V + ++ D T+ES GFAFV A+ +
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTPGH 126
++ +VL+GR + V+ A+ GR P H
Sbjct: 132 MDGAVLDGRELRVQMAR--YGRPPDSHH 157
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 44/92 (47%)
Query: 34 ANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGAD 93
A+ + VT LS DL++ F G ++ +L D T +S GFAF++ E A
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 94 RCIKYLNRSVLEGRLITVEKAKRSRGRTPTPG 125
R I ++ + ++ VE AK S P+ G
Sbjct: 72 RAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%)
Query: 36 PGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRC 95
P +LYV L VT A L + F G + + D TR S G+A+V + A+R
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 96 IKYLNRSVLEGRLITVEKAKR 116
+ +N V++G+ + + ++R
Sbjct: 74 LDTMNFDVIKGKPVRIMWSQR 94
>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 = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
N +YV + +++ D++ F GK+ C L DP T + G+ F+ E + + +
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 98 YLNRSVLEGRLITVEKA 114
+N L G+ + V KA
Sbjct: 171 SMNLFDLGGQYLRVGKA 187
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%)
Query: 36 PGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRC 95
P +LYV L VT A L + F G + + D TR S G+A+V + A+R
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 96 IKYLNRSVLEGRLITVEKAKR 116
+ +N V++G+ + + ++R
Sbjct: 69 LDTMNFDVIKGKPVRIMWSQR 89
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 38/79 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T + FG G++ C LV D T +S G+ FV + A++ I
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 99 LNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 64 LNGLRLQTKTIKVSYARPS 82
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYV+GL +T +LE+ F G++ ++ D T S G F+ + A+ IK
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 99 LN 100
LN
Sbjct: 150 LN 151
>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 = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 33/68 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYVT L +T+ L+ FG G + + +++ D T G AFV E A I
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 99 LNRSVLEG 106
LN + EG
Sbjct: 75 LNNVIPEG 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 36/75 (48%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV GL+ V + L F G +T+ + D T + GFAFV E E A I +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 100 NRSVLEGRLITVEKA 114
N S L GR I V A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+++V LS +T D++ F GK+++ +V D T +S G+ FV+ A+ I +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTP 124
+ L GR I A R + P P
Sbjct: 77 MGGQWLGGRQIRTNWATR---KPPAP 99
>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 = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 37/77 (48%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
N +YV + +++ D++ F GK+ C L DP T + G+ F+ E + + +
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 98 YLNRSVLEGRLITVEKA 114
N L G+ + V KA
Sbjct: 170 SXNLFDLGGQYLRVGKA 186
>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 = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 36 PG-NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADR 94
PG NL V L +T +L F G+V L+ D S G+ FV T + A+R
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 95 CIKYLNRSVLEGRLITVEKAKRS 117
I LN L+ + I V A+ S
Sbjct: 62 AINTLNGLRLQSKTIKVSYARPS 84
>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 = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 36/81 (44%)
Query: 37 GNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI 96
G NL V L T +L F G+V L+ D S G+ FV T + A+R I
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 97 KYLNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 79 NTLNGLRLQSKTIKVSYARPS 99
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 33/68 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYVT L +T+ L+ FG G + + +++ D T G AFV E A I
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 99 LNRSVLEG 106
LN + EG
Sbjct: 162 LNNVIPEG 169
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 2/85 (2%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P A+N NL V L T+ +L F G + C + D +T S G+AFV +
Sbjct: 10 PRASN--TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX 67
Query: 91 GADRCIKYLNRSVLEGRLITVEKAK 115
+ R IK LN + + + V A+
Sbjct: 68 DSQRAIKVLNGITVRNKRLKVSYAR 92
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 41 YVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYLN 100
+V GLS + DL+ +F G+V +C + DP T S GF F+ + ++ +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 101 RSVLEGRLITVEKA 114
L+GR+I +KA
Sbjct: 75 HR-LDGRVIDPKKA 87
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 33/68 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYVT L +T+ L+ FG G + + +++ D T G AFV E A I
Sbjct: 91 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Query: 99 LNRSVLEG 106
LN + EG
Sbjct: 151 LNNVIPEG 158
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T+ +L F G + C ++ D +T S G+AFV + + R IK
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 99 LNRSVLEGRLITVEKAK 115
LN + + + V A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 3/96 (3%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+++V LS +T D++ F G++++ +V D T +S G+ FV+ A+ I+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 99 LNRSVLEGRLITVEKAKRSRGRTPTPGHYHGLREKQ 134
+ L GR I A R + P P + KQ
Sbjct: 77 MGGQWLGGRQIRTNWATR---KPPAPKSTYESNTKQ 109
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 36/79 (45%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T +L F G+V L+ D S G+ FV T + A+R I
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 99 LNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 64 LNGLRLQSKTIKVSYARPS 82
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLY++GL +T D+E F G++ ++ D T S G AF+ + A+ I
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
Query: 99 LN 100
N
Sbjct: 150 FN 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 36/79 (45%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T +L F G+V L+ D S G+ FV T + A+R I
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 99 LNRSVLEGRLITVEKAKRS 117
LN L+ + I V A+ S
Sbjct: 64 LNGLRLQSKTIKVSYARPS 82
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLY++GL +T D+E F G++ ++ D T S G AF+ + A+ I
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
Query: 99 LN 100
N
Sbjct: 150 FN 151
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
N +YV + +++ D++ F GK+ L DP T + G+ F+ E + + +
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 98 YLNRSVLEGRLITVEKA 114
+N L G+ + V KA
Sbjct: 186 SMNLFDLGGQYLRVGKA 202
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 5/92 (5%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV LS T + + F G + + + D + +CGF FV + A+ ++Y+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 100 NRSVLEGRLITVE-----KAKRSRGRTPTPGH 126
N + L+ R+I + K R GR + G
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQ 133
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 77 EAQAAMEGLNGQDLMGQPISVD 98
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 3 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 62
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 63 EAQAAMEGLNGQDLMGQPISVD 84
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVD 82
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVD 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 31 PDA-ANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETV 89
P+A + P L+V GLS T L++ F G +VTD T S GF FV +
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSE 64
Query: 90 EGADRCIKYLNRSVLEGRLITVEKAK 115
E A + + ++G +T++ AK
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVTLDWAK 90
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 76 EAQAAMEGLNGQDLMGQPISVD 97
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VTG+ T D+ F G++ HL D RT G+ V ET +
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A ++ LN L G+ I+V+
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVD 82
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
N+YV L T+ +++ F GKV L+ D T++ GF FV M+ E I
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 99 LNRSVLEGRLITVEKA 114
L+ + GR I V +A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 9/87 (10%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
++V +S T+ +L F G+V EC +V D +AFV ME A I L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 100 NRSVLEGRLITVEKAKRSRGRT-PTPG 125
N ++G+ I VE + + + ++ P+ G
Sbjct: 64 NGKEVKGKRINVELSTKGQKKSGPSSG 90
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 3/89 (3%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTEC-HLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
+++ L + L F G + + ++ DP T S G+AF+ + + +D I+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 99 LNRSVLEGRLITVEKA--KRSRGRTPTPG 125
+N L R ITV A K S+G P+ G
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKGSGPSSG 96
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
++ L+ R+ DLE FF GKV + +++D +R S G A+V ++ I
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 87
Query: 100 NRSVLEGRLITVEKAKRSRGRTPTPGH 126
+ +L G I V+ ++ + R P
Sbjct: 88 GQRLL-GVPIIVQASQAEKNRLSGPSS 113
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL V L +T+ +L F G + C ++ D +T S G+AFV + + R IK
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 99 LNRSVLEGRLITVEKAK 115
LN + + + V A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
N ++V G+ +L ++F G VTE ++ D + GF F+T E + D+ +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 98 YLNRSVLEGRLITVEKAKRSRGRTPTP 124
++ G+ + V++A+ ++ P
Sbjct: 71 MHFHDIM-GKKVEVKRAEPRDSKSSGP 96
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 4/95 (4%)
Query: 33 AANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGA 92
A ++L V GL + T DL+++F G+V + D +T S GF FV E
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 93 DRCIKYLNRSVLEGRL--ITVEKAKRSRGRTPTPG 125
+ + R +++GR + +K+S+ P+ G
Sbjct: 71 VKVMS--QRHMIDGRWCDCKLPNSKQSQDSGPSSG 103
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLYV+GL ++ ++E+ F G++ ++ D T S G F+ + A+ IK
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 99 LN 100
LN
Sbjct: 63 LN 64
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 33/72 (45%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV L +T L F G++ L+ D T S G+ F+T E A + ++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 100 NRSVLEGRLITV 111
N L GR + V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 32 DAANPGNNLYVTGLSTRVTNADLEKFFG----GEGKVTECHLVTDPRTRESCGFAFVTME 87
+ P LY+ LS RVT DL F +G + ++T R R G AF+T
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTG-RMR---GQAFITFP 75
Query: 88 TVEGADRCIKYLNRSVLEGRLITVEKAKRSRGRTPTP 124
E A + + +N L G+++ +E K + R+ P
Sbjct: 76 NKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGP 112
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
+ LYV L +T L F GK+ L+ D T S G+ F+T E A R ++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 98 YLNRSVLEGRLITV 111
LN L GR + V
Sbjct: 66 QLNGFELAGRPMRV 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L V L+ R + L + F G+V + ++ +P T+ GFAFV A +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 100 NRSVLEGRLITVEKAKRSR 118
+ + L+GR + V+ A+ R
Sbjct: 76 DGAELDGRELRVQVARYGR 94
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 33/71 (46%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
+ LY+ GL T+ DL K GK+ + D T + G+ FV ++ A + +
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 98 YLNRSVLEGRL 108
L S ++ ++
Sbjct: 66 ALKASGVQAQM 76
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VT + ++++ F G++ HL D RT S G+A V ET +
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A + LN + + G+ I V+
Sbjct: 80 QALAAKEALNGAEIMGQTIQVD 101
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
P + G L+VT + ++++ F G++ HL D RT S G+A V ET +
Sbjct: 66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
Query: 91 GADRCIKYLNRSVLEGRLITVE 112
A + LN + + G+ I V+
Sbjct: 126 QALAAKEALNGAEIMGQTIQVD 147
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LYV LS T + + F G + + + D + + +CGF FV + A+ ++Y+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRYI 79
Query: 100 NRSVLEGRLI 109
N + L+ R+I
Sbjct: 80 NGTRLDDRII 89
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
P+ N ++V G+ R+ ++ FF G V E ++TD RT S G+ FV+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMET 88
++V GLS T D++ +F GKV + L+ D T GF FVT E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTME 87
L+V GL T L +F G+V +C ++ D T +S GF FV +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
P+ N ++V G+ R+ ++ FF G V E ++TD RT S G+ FV+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L++ L T ++ F GKV EC ++ + + FV +E A+ I+ L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 100 NRSVLEGRLITVEKAKRSRGRTPTP 124
+ L G I VE +K + P
Sbjct: 63 HHYKLHGVNINVEASKNKSKASSGP 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTM 86
N ++V G+ R+ ++ FF G V E ++TD RT S G+ FV+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 58
>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 = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI--K 97
++V GLS + ++FGG G+V L D +T + GF F+T + E + + K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 98 YLN 100
Y N
Sbjct: 64 YHN 66
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI--K 97
++V GLS + ++FGG G+V L D +T + GF F+T + E + + K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 98 YLN 100
Y N
Sbjct: 62 YHN 64
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
N LY+ LS VT DL + FG + L + G+AFV A R I+
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62
Query: 98 YLNRSV-LEGRLITVEK--AKRSRGRTPTPG 125
L+ V L G+++ V+ +K+ R P+ G
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93
>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 = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V ++ T + L + F G + H+V R+ + G+AF+ E K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 100 NRSVLEGR--LITVEKAKRSRG 119
+ ++GR L+ VE+ + +G
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKG 186
>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 = 34.3 bits (77), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V ++ T + L + F G + H+V R+ + G+AF+ E K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 100 NRSVLEGR--LITVEKAKRSRG 119
+ ++GR L+ VE+ + +G
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKG 186
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 31 PDAANPGNNLYVTGLSTRVTNADLEKFFGGEGKV--------TECHLVTDPRTRESCGFA 82
PD + + +YV GL+ VT DL FF G V H+ D T + G A
Sbjct: 9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 83 FVTMETVEGADRCIKYLNRSVLEGRLITVEKAKR 116
V+ E A +++ + +G + V A++
Sbjct: 69 TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.5 bits (75), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
L+V L+ VT LEK F GK+ + D +AF+ + +GA + ++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 100 NRSVLEGRLITVEKAK 115
N LEG I + AK
Sbjct: 66 NGKDLEGENIEIVFAK 81
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 62 GKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYLNRSVLEGRLI 109
G+V E ++ PRTR+ G A V + GA +K L+ + + G +I
Sbjct: 31 GEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNII 78
>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 = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 34/78 (43%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL+V L+ V + L F H++ D +T S G+ FV+ + + A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 99 LNRSVLEGRLITVEKAKR 116
+ L GR + + A +
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 32 DAANPGN-NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVE 90
+ ++P N +Y G+++ +T+ + + F G++ E + + G++FV T E
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHE 72
Query: 91 GADRCIKYLNRSVLEGRLITVEKAKRSRGRTPTP 124
A I +N + +EG ++ K S T P
Sbjct: 73 SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 65 TECHLVTDPRTRESCGFAFVTMETVEGAD--RCIKYLNRSV-LEGRLITVEKAKRSR 118
+ ++ D +T+ + GFAF+ + T+E A + ++ L+ + ++G+ I VE AK S+
Sbjct: 53 SNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAKGSK 109
>pdb|3TAC|A Chain A, Crystal Structure Of The Liprin-AlphaCASK COMPLEX
Length = 361
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 43 TGLSTRVTNADLEKFFGGEGKVTE--------CHLVTDPRTRE------SCGFAFVTMET 88
TG V D+ KF G TE CH++ P E S G ++ E
Sbjct: 50 TGQQFAVKIVDVAKFTSSPGLSTEDLKREASICHMLKHPHIVELLETYSSDGMLYMVFEF 109
Query: 89 VEGADRCIKYLNRS 102
++GAD C + + R+
Sbjct: 110 MDGADLCFEIVKRA 123
>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 = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 37 GNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI 96
GN LYV G +T L F G + + L DP +C AFVT E +E AD+ +
Sbjct: 39 GNTLYVYG--EDMTPTLLRGAFSPFGNIID--LSMDPP--RNC--AFVTYEKMESADQAV 90
Query: 97 KYLNRSVLEGRLITVEKAKR 116
LN + +E + V A++
Sbjct: 91 AELNGTQVESVQLKVNIARK 110
>pdb|3C0G|A Chain A, Cask Cam-kinase Domain- 3'-amp Complex, P1 Form
pdb|3C0G|B Chain B, Cask Cam-kinase Domain- 3'-amp Complex, P1 Form
pdb|3C0H|A Chain A, Cask Cam-Kinase Domain- Amppnp Complex, P1 Form
pdb|3C0H|B Chain B, Cask Cam-Kinase Domain- Amppnp Complex, P1 Form
pdb|3C0I|A Chain A, Cask Cam-Kinase Domain- 3'-Amp Complex, P212121 Form
Length = 351
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 43 TGLSTRVTNADLEKFFGGEGKVTE--------CHLVTDPRTRE------SCGFAFVTMET 88
TG V D+ KF G TE CH++ P E S G ++ E
Sbjct: 48 TGQQFAVKIVDVAKFTSSPGLSTEDLKREASICHMLKHPHIVELLETYSSDGMLYMVFEF 107
Query: 89 VEGADRCIKYLNRS 102
++GAD C + + R+
Sbjct: 108 MDGADLCFEIVKRA 121
>pdb|3MFR|A Chain A, Cask-4m Cam Kinase Domain, Native
pdb|3MFS|A Chain A, Cask-4m Cam Kinase Domain, Amppnp
pdb|3MFT|A Chain A, Cask-4m Cam Kinase Domain, Mn2+
pdb|3MFU|A Chain A, Cask-4m Cam Kinase Domain, Amppnp-Mn2+
Length = 351
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 43 TGLSTRVTNADLEKFFGGEGKVTE--------CHLVTDPRTRE------SCGFAFVTMET 88
TG V D+ KF G TE CH++ P E S G ++ E
Sbjct: 48 TGQQFAVKIVDVAKFTSSPGLSTEDLKREASICHMLKHPHIVELLETYSSDGMLYMVFEF 107
Query: 89 VEGADRCIKYLNRS 102
++GAD C + + R+
Sbjct: 108 MDGADLCFEIVKRA 121
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LY+ L ++T ++ FG G + + + P TR G A+V E + A + +L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDHL 67
Query: 100 NRSVLEGRLITV 111
+ + R + V
Sbjct: 68 SGFNVSNRYLVV 79
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 37 GNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCI 96
GN LYV G +T L F G + + L DP +C AFVT E +E AD+ +
Sbjct: 15 GNTLYVYG--EDMTPTLLRGAFSPFGNIID--LSMDPP--RNC--AFVTYEKMESADQAV 66
Query: 97 KYLNRSVLEGRLITVEKAKR 116
LN + +E + V A++
Sbjct: 67 AELNGTQVESVQLKVNIARK 86
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 34/78 (43%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NL+V L+ V + L F H++ D +T S G+ FV+ + + A +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 99 LNRSVLEGRLITVEKAKR 116
+ L GR + + A +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 62 GKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYLNRSVLEGRLITVEKAKR 116
G++++ +V D T +S G+ FV+ A+ I+ + L GR I A R
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 38 NNLYVTGLSTRVTNADLEK---FFGGEGKVTECHLVTDPRTRESCG---FAFVTMETVEG 91
N ++V GLS R+ + ++ K +FG GK+ + + S G A+VT E
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 92 ADRCIKYLNRSVLEGRLI 109
A R I+ +N V++GR +
Sbjct: 76 ALRAIQCVNNVVVDGRTL 93
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 31/74 (41%)
Query: 36 PGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRC 95
P +Y+ + T + G V ++ DP+T S G+AF+ +E +
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 96 IKYLNRSVLEGRLI 109
++ LN L R +
Sbjct: 63 VRNLNGYQLGSRFL 76
>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 = 30.8 bits (68), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
+ L+++GL T +LE+ G V + LVT+ R + G A+V E A + +
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVM 76
Query: 98 YLNRSVLEGRLITV 111
++ ++ +I V
Sbjct: 77 KMDGMTIKENIIKV 90
>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 = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 31/74 (41%)
Query: 36 PGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRC 95
P +Y+ + T + G V ++ DP+T S G+AF+ +E +
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 96 IKYLNRSVLEGRLI 109
++ LN L R +
Sbjct: 62 VRNLNGYQLGSRFL 75
>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 = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
++YV + T +LE F G G V ++ D + GFA++ E R
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV-RTSLA 66
Query: 99 LNRSVLEGRLITVEKAKRSR 118
L+ S+ GR I V + +R
Sbjct: 67 LDESLFRGRQIKVIPKRTNR 86
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 31/74 (41%)
Query: 36 PGNNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRC 95
P +Y+ + T + G V ++ DP+T S G+AF+ +E +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 96 IKYLNRSVLEGRLI 109
++ LN L R +
Sbjct: 61 VRNLNGYQLGSRFL 74
>pdb|1AEC|A Chain A, Crystal Structure Of Actinidin-E-64 Complex+
Length = 218
Score = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 70 VTDPRTRESCG--FAFVTMETVEGADRCIKYLNRSVLEGRLITVEKAKRSRG 119
V D +++ CG +AF + TVEG ++ + + S+ E LI + + +RG
Sbjct: 13 VVDIKSQGECGGCWAFSAIATVEGINKIVTGVLISLSEQELIDCGRTQNTRG 64
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTR--ESCGFAFVTMETVEGADRCIK 97
L ++ LS T L++ F + + P+ + +S G+AF+ + E A +
Sbjct: 18 LVLSNLSYSATEETLQEVF------EKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 98 YLNRSVLEGRLITVE 112
N+ +EGR I +E
Sbjct: 72 SCNKREIEGRAIRLE 86
>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 = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
++YV + T +LE F G G V ++ D + GFA++ E R
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV-RTSLA 65
Query: 99 LNRSVLEGRLITVEKAKRSR 118
L+ S+ GR I V + +R
Sbjct: 66 LDESLFRGRQIKVIPKRTNR 85
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 30.0 bits (66), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
NLY++ L + +LE G+V ++ D + S G F ME+ E + I +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH 85
Query: 99 LN 100
N
Sbjct: 86 FN 87
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
L+V L + T+ D+ K F G + EC ++ P S G AFV +T A I
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGT-SKGCAFVKFQTHAEAQAAINT 72
Query: 99 LNRS 102
L+ S
Sbjct: 73 LHSS 76
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 6/87 (6%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
+ L+V L +T ++ K F GK E + D GF F+ +ET A+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 69
Query: 98 YLNRSVLEGRLITVEKAKRSRGRTPTP 124
L+ L G+ + V A S T P
Sbjct: 70 ELDNMPLRGKQLRVRFACHSASLTSGP 96
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LY+ L ++T ++ FG G + + + P TR G A+V E + A +L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
>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 = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 39 NLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKY 98
++YV + T DLE F G + ++ D + G+A++ D +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA- 96
Query: 99 LNRSVLEGRLITV 111
++ +V GR I V
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 40 LYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIKYL 99
LY+ L ++T ++ FG G + + + P TR G A+V E + A +L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 71
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 38 NNLYVTGLSTRVTNADLEKFFGGEGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
+ L+V L +T ++ K F GK E + D GF F+ +ET A+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 98 YLNRSVLEGRLITV 111
L+ L G+ + V
Sbjct: 77 ELDNMPLRGKQLRV 90
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 26.9 bits (58), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 31/78 (39%), Gaps = 10/78 (12%)
Query: 40 LYVTGLSTRVTNADLEKFFGG--EGKVTECHLVTDPRTRESCGFAFVTMETVEGADRCIK 97
LYV L + +EK F G V + D +AFV E A +K
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 98 YLNRSVLEGRLITVEKAK 115
LN VL+G I V AK
Sbjct: 70 ALNGKVLDGSPIEVTLAK 87
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,646,463
Number of Sequences: 62578
Number of extensions: 120756
Number of successful extensions: 393
Number of sequences better than 100.0: 116
Number of HSP's better than 100.0 without gapping: 91
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 281
Number of HSP's gapped (non-prelim): 130
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)