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= 022930
(290 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 82.0 bits (201), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 49/126 (38%), Positives = 65/126 (51%), Gaps = 39/126 (30%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PPD+ SL V N+T+RT+ D L +FEKYG+V DV+IPRDR T +SRGFAFVR+
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 100
Query: 69 EAQKAVDRLDGLFLNFNFVHEILKSSLFLRKNLYLCXXXXXXXXXXXXXXRVVDGREITV 128
+A+ A+D +DG V+DGRE+ V
Sbjct: 101 DAEDAMDAMDGA---------------------------------------VLDGRELRV 121
Query: 129 QFAKYG 134
Q A+YG
Sbjct: 122 QMARYG 127
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 63/124 (50%), Gaps = 39/124 (31%)
Query: 11 DIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEA 70
D+ SL V N+T+RT+ D L +FEKYG+V DV+IPRDR T +SRGFAFVR+ +A
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 71 QKAVDRLDGLFLNFNFVHEILKSSLFLRKNLYLCXXXXXXXXXXXXXXRVVDGREITVQF 130
+ A+D +DG V+DGRE+ VQ
Sbjct: 126 EDAMDAMDGA---------------------------------------VLDGRELRVQM 146
Query: 131 AKYG 134
A+YG
Sbjct: 147 ARYG 150
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 67.4 bits (163), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 38/79 (48%), Positives = 51/79 (64%), Gaps = 1/79 (1%)
Query: 5 GKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
G SGP D+ +L V N+T+RT+ D L +FEKYG+V DV+IPR+ T RGFAFVR+
Sbjct: 4 GSSGP-DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 65 KYADEAQKAVDRLDGLFLN 83
+AQ A +DG L+
Sbjct: 63 HDRRDAQDAEAAMDGAELD 81
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/78 (41%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 4 FGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
+ + G I+DT +L V N+ T D L +F KYG +V I RD+ TG RG AFVR
Sbjct: 3 YARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 64 YKYADEAQKAVDRLDGLF 81
Y +EAQ+A+ L+ +
Sbjct: 62 YNKREEAQEAISALNNVI 79
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 3 HFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
+ + G I+DT +L V N+ T D L +F KYG +V I RD+ TG RG AFV
Sbjct: 78 SYARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Query: 63 RYKYADEAQKAVDRLDGLF 81
RY +EAQ+A+ L+ +
Sbjct: 137 RYNKREEAQEAISALNNVI 155
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGL 80
T +L+ LF G + I RD +TG S G+AFV + ++Q+A+ L+G+
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI 68
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 3 HFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
+ + G I+DT +L V N+ T D L +F KYG +V I RD+ TG RG AFV
Sbjct: 89 SYARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 147
Query: 63 RYKYADEAQKAVDRLDGLF 81
RY +EAQ+A+ L+ +
Sbjct: 148 RYNKREEAQEAISALNNVI 166
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 11 DIRDTYSLLVLNITFRTTAD-DLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADE 69
D R + + L++N + D +L+ LF G + I RD +TG S G+AFV + +
Sbjct: 9 DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 70 AQKAVDRLDGL 80
+Q+A+ L+G+
Sbjct: 69 SQRAIKVLNGI 79
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 3 HFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
H G PD L V ++ TT DL +F KYG + DV I D+++ SRGFAFV
Sbjct: 36 HVGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
Query: 63 RYKYADEAQKAVDRLDGLFLN 83
++ D+A++A +R +G+ L+
Sbjct: 94 YFENVDDAKEAKERANGMELD 114
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 43/66 (65%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V ++ TT DL +F KYG + DV I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 78 DGLFLN 83
+G+ L+
Sbjct: 78 NGMELD 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 43/67 (64%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
L V ++ TT DL +F KYG + DV I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 77 LDGLFLN 83
+G+ L+
Sbjct: 77 ANGMELD 83
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 43/67 (64%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
L V ++ TT DL +F KYG + DV I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 77 LDGLFLN 83
+G+ L+
Sbjct: 74 ANGMELD 80
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 39/66 (59%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D L V ++F T L +F KYG++ +V + +DR T SRGF FV ++ D+A+ A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 74 VDRLDG 79
+ ++G
Sbjct: 71 MMAMNG 76
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 27 TTADD--LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFLNF 84
TT D+ L LFE+YG + V I DR T SRG+ FV+++ AQ+A+ L+G F
Sbjct: 52 TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG----F 107
Query: 85 NFVHEILKSSL 95
N +++ LK +L
Sbjct: 108 NILNKRLKVAL 118
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 5/88 (5%)
Query: 5 GKSGPPD-IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
G SGP D ++ V N++ T DL LF +G + +++ +D+ TG S+GFAF+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 64 YKYADEAQKAVDRLDGLFLNFNFVHEIL 91
+ ++A +A+ + G F + H IL
Sbjct: 64 FHRREDAARAIAGVSG----FGYDHLIL 87
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 12 IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
++ T L+VL + ++TT DL F +G+V+ V + +D +TG S+GF FVR+ +
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Query: 72 KAVDR---LDGLFLNFNF 86
K + + +DG + +
Sbjct: 72 KVMSQRHMIDGRWCDCKL 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+++ ++ +DL LF YG + ++ P D T +GFAFV + + + A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 78 DGLFLNFNFVHEILKSSL 95
DG +H +L S++
Sbjct: 71 DGQVFQGRMLH-VLPSTI 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
Identities = 24/55 (43%), Positives = 35/55 (63%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
++ V N+ F T +DL+ +F KYGKVV V I +D+ T S+G AF+ + D AQ
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D V +++ T+ DL F K+G+VVD I D TG SRGF F+ +K A +K
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
Query: 74 VD----RLDGLFLN 83
+D RLDG ++
Sbjct: 70 LDQKEHRLDGRVID 83
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 8 GPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 68 DEAQKAVDRLDG 79
EAQ A++ L+G
Sbjct: 75 KEAQAAMEGLNG 86
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 41/74 (55%)
Query: 6 KSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYK 65
+ GP + + L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 66 YADEAQKAVDRLDG 79
EAQ A++ L+G
Sbjct: 74 TYKEAQAAMEGLNG 87
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 8 GPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 68 DEAQKAVDRLDG 79
EAQ A++ L+G
Sbjct: 62 KEAQAAMEGLNG 73
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 43/68 (63%)
Query: 15 TYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ L V ++ F T D L +FE +GK+ ++ + +D TG S+G+ F+ + ++ A++A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 75 DRLDGLFL 82
++L+G L
Sbjct: 65 EQLNGFEL 72
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGD---SRGFAFVRYKYADEAQKAV 74
L + N+ F TT + L +F K G + I + + S GF FV YK ++AQKA+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 75 DRLDG 79
+L G
Sbjct: 68 KQLQG 72
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + + L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 69 EAQKAVDRLDG 79
EAQ A++ L+G
Sbjct: 61 EAQAAMEGLNG 71
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L FE++G + D + RD T SRGF FV Y +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 69 EAQKAVD 75
E A++
Sbjct: 68 EVDAAMN 74
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L FE++G + D + RD T SRGF FV Y +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 69 EAQKAVD 75
E A++
Sbjct: 66 EVDAAMN 72
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L FE++G + D + RD T SRGF FV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 69 EAQKAVD 75
E A++
Sbjct: 67 EVDAAMN 73
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYK 65
L V + + TT + L F +YG+VVD I +D+ T SRGF FV++K
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 5 GKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
G +GP L V ++ F T D L +FE +G++ + + D TG S+G+ F+ +
Sbjct: 22 GSAGP------MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 65 KYADEAQKAVDRLDGLFL 82
++ A+KA+++L+G L
Sbjct: 76 SDSECAKKALEQLNGFEL 93
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L FE++G + D + RD T SRGF FV Y +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 69 EAQKAVD 75
E A++
Sbjct: 65 EVDAAMN 71
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L FE++G + D + RD T SRGF FV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 69 EAQKAVD 75
E A++
Sbjct: 67 EVDAAMN 73
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+ + +++ TT DL F K+G+VVD + D TG SRGF FV +K ++ K +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
L + ++F TT + L FE++G + D + RD T SRGF FV Y +E A++
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L FE+YGK+ + I DR +G RGFAFV + D K V
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+GL L
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 71
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 5 GKSG-PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
G SG P D L V I DL PLFE++G++ ++ + +DR TG +G AF+
Sbjct: 4 GSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLT 63
Query: 64 YKYADEAQKAVDRL 77
Y D A KA L
Sbjct: 64 YCARDSALKAQSAL 77
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+GL L
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 86
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 5 GKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
G SG D D L + I DL PLFE++GK+ ++ + +DR TG +G AF+ Y
Sbjct: 4 GSSGMKD-HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 65 KYADEAQKAVDRL 77
+ A KA L
Sbjct: 63 CERESALKAQSAL 75
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+ EAQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 78 DG 79
+G
Sbjct: 70 NG 71
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+GL L
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 33/52 (63%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDG 79
T D+ +F ++G++++ + D+ TG SRG AF+R+ EA++A+ +G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 8 GPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V +I D++ F YG++ ++ + DRRTG S+G+A V Y+
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 68 DEAQKAVDRLDG 79
+A A + L+G
Sbjct: 79 KQALAAKEALNG 90
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+GL L
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 33/52 (63%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDG 79
T D+ +F ++G++++ + D+ TG SRG AF+R+ EA++A+ +G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>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 = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + T +D+ F +YG++ ++ + DRRTG +G+ V Y+ EAQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 78 DG 79
+G
Sbjct: 70 NG 71
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 8 GPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V +I D++ F YG++ ++ + DRRTG S+G+A V Y+
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 68 DEAQKAVDRLDG 79
+A A + L+G
Sbjct: 125 KQALAAKEALNG 136
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 13 RDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYK---YADE 69
+++ + + + + TT D+L F KYG V D+ I +D TG SRGF F+ ++ DE
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 70 AQKAVDRLDGLFLN 83
K LDG ++
Sbjct: 61 VVKTQHILDGKVID 74
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 35 LFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
F ++G ++D + D+ TG SRGF FV Y AD AVDR+
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----AVDRV 145
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 3 HFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
+ + IRD +L V + T +L LF +YG+++ I D+ TG SRG F+
Sbjct: 77 SYARPSSASIRDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Query: 63 RYKYADEAQKAVDRLDG 79
R+ EA++A+ L+G
Sbjct: 136 RFDKRIEAEEAIKGLNG 152
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
T ++ LF G++ + RD+ TG S G+ FV Y +A+KA++ L+GL L
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 40/72 (55%)
Query: 11 DIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEA 70
D + + + V +++ T +D+ F +G++ D + +D TG S+G+ FV + +A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 71 QKAVDRLDGLFL 82
+ A+ ++ G +L
Sbjct: 71 ENAIQQMGGQWL 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
DT++L V ++ + L F+ + + + D +TG SRG+ FV + D+AQ A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 74 VDRLDGLFLN 83
+D + G LN
Sbjct: 146 MDSMQGQDLN 155
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 11 DIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEA 70
D + + + V +++ T +D+ F +GK+ D + +D TG S+G+ FV + +A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 71 QKAVDRLDGLFLN 83
+ A+ + G +L
Sbjct: 71 ENAIVHMGGQWLG 83
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
+ + L + + F T ++L + + +G V D+ + +R G +G A+V Y+ +A +A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQA 74
Query: 74 VDRLDGLFLNFNFVHEILKSS 94
V ++DG+ + N + + +S
Sbjct: 75 VMKMDGMTIKENIIKVAISNS 95
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 14 DTYSLLVLN-ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
D+ + L++N + T D+ LF G + + RD+ TG S G+ FV Y ++A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 73 AVDRLDGLFL 82
A++ L+GL L
Sbjct: 62 AINTLNGLKL 71
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 3 HFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
+ + IRD +L V + + ++ LF +YG+++ I D+ TG SRG F+
Sbjct: 79 SYARPSSASIRDA-NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFI 137
Query: 63 RYKYADEAQKAVDRLDG 79
R+ EA++A+ L+G
Sbjct: 138 RFDKRIEAEEAIKGLNG 154
>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 = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
DD+ +FE +GK+ + RD TG +G+ F+ Y+ A +Q AV ++
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 20 VLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDG 79
V +I + D + F +G + + + D T +GFAFV Y+ + AQ A+++++
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 80 LFLN 83
+ L
Sbjct: 93 VMLG 96
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PP R L V + + + DD+ LFE +G + + I R G+S+G AFV+Y
Sbjct: 12 PPSHRK---LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHA 67
Query: 69 EAQKAVDRLDG 79
EAQ A++ L G
Sbjct: 68 EAQAAINALHG 78
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
L + ++F TT + L +E++GK+ D + RD + SRGF FV + E A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
DD+ +FE +GK+ + RD TG +G+ F+ Y+ A +Q AV ++
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 34.7 bits (78), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 20 VLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDG 79
V +I + D + F +G + + + D T +GFAFV Y+ + AQ A+++++
Sbjct: 18 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 77
Query: 80 LFLN 83
+ L
Sbjct: 78 VMLG 81
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 9/83 (10%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L++ N+ ++ TA++++ +F KYG + + R T ++RG A+V Y+
Sbjct: 14 PPEVNRI--LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 68
Query: 69 EAQKAVDRLDGLFLNFNFVHEIL 91
+A+ A D L G FN + L
Sbjct: 69 DAKNACDHLSG----FNVCNRYL 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 1 MSHFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFA 60
+ F K G L V N+ T +D LFE+YG+ +VFI RD RGF
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFG 61
Query: 61 FVRYKYADEAQKAVDRLDGLFLN 83
F+R + A+ A LDG L
Sbjct: 62 FIRLESRTLAEIAKAELDGTILK 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
L F +G + D+ IP D T RGFAFV ++ A++A A+D ++
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 126
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 5 GKSGPPDIRDTYSLLVLNITFRTTADD--LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
G SG + T +L + DD L F +G + D+ IP D T RGFAFV
Sbjct: 1 GSSGSSGMATTKRVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Query: 63 RYKYADEAQKAVDRLD 78
++ A++A A+D ++
Sbjct: 60 EFELAEDAAAAIDNMN 75
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 5/72 (6%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + + R T ++RG A+V Y+
Sbjct: 4 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 58
Query: 69 EAQKAVDRLDGL 80
+A+ AVD L G
Sbjct: 59 DAKNAVDHLSGF 70
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P R S+ V NI + T + L +F + G VV + DR TG +G+ F Y+ +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 69 EAQKAVDRLDG 79
A A+ L+G
Sbjct: 62 TALSAMRNLNG 72
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 12 IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
++ + +L V N++F TT + ++ LF K G + + + D+ + GF FV Y +A+
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 72 KAVDRLDGLFLN 83
A+ ++G L+
Sbjct: 96 NAMRYINGTRLD 107
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 14 DTYSLLVLN-ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
D+ + L++N + T D+ LF G + + RD+ TG S G+ FV Y ++A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 73 AVDRLDGLFL 82
A++ L+GL L
Sbjct: 62 AINTLNGLKL 71
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 23 ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGD-SRGFAFVRYKYADEAQKAVDRLDG 79
+T T D + +F YGK+ + +P +R S+G+A+V ++ DEA+KA+ +DG
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDG 69
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
L F +G + D+ IP D T RGFAFV ++ A++A A+D ++
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
L F +G + D+ IP D T RGFAFV ++ A++A A+D ++
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 68
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI FR DL +F ++GK++DV I + R S+GF FV ++ + +A +A ++L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKL 89
Query: 78 DG 79
G
Sbjct: 90 HG 91
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
L F +G + D+ IP D T RGFAFV ++ A++A A+D ++
Sbjct: 19 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 65
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
DD+ +FE +GK+ + RD TG +G+ F+ Y+ A +Q AV
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V +I + D + F +G + + D T +GFAFV Y+ + AQ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 78 DGLFLN 83
+ + L
Sbjct: 75 NSVXLG 80
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 9/83 (10%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + + R T ++RG A+V Y+
Sbjct: 14 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 68
Query: 69 EAQKAVDRLDGLFLNFNFVHEIL 91
+A+ A D L G FN + L
Sbjct: 69 DAKNACDHLSG----FNVCNRYL 87
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI FR DL +F ++GK++DV I + R S+GF FV ++ + +A +A ++L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKL 75
Query: 78 DGLFL 82
G +
Sbjct: 76 HGTVV 80
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + + R T ++RG A+V Y+
Sbjct: 8 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 62
Query: 69 EAQKAVDRLDGL 80
+A+ A D L G
Sbjct: 63 DAKNACDHLSGF 74
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 31/51 (60%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
L+ LF + G VV+ +P+DR TG +G+ FV + ++A A+ +D + L
Sbjct: 32 LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL 82
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V + + TT L FE YG + + + +R+G RG+AF+ Y++ + A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 77 LDG 79
DG
Sbjct: 164 ADG 166
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 1 MSHFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFA 60
+ +F K G L V N+ T +++ LFEKYGK +VFI +D +GF
Sbjct: 8 LKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 61
Query: 61 FVRYKYADEAQKAVDRLDGLFL 82
F+R + A+ A LD + L
Sbjct: 62 FIRLETRTLAEIAKVELDNMPL 83
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 36/69 (52%)
Query: 15 TYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
T++L V ++ + L F+ + + + D +TG SRG+ FV + D+AQ A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 75 DRLDGLFLN 83
D + G LN
Sbjct: 61 DSMQGQDLN 69
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 29/45 (64%)
Query: 35 LFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDG 79
LF +YG+++ I D+ TG SRG F+R+ EA++A+ L+G
Sbjct: 21 LFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 65
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V + + TT L FE YG + + + +R+G RG+AF+ Y++ + A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 77 LDG 79
DG
Sbjct: 164 ADG 166
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFLNFNFVHEIL 91
L LF K GKVV++ P D TG ++GF FV ++A+K + G L+ L
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD-------L 81
Query: 92 KSSLFL 97
K LFL
Sbjct: 82 KHRLFL 87
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
+ V ++ TT +D+ FE++GKV D + D+ T RGF FV ++ D +K +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 32 LFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFLNFNFVHEIL 91
L LF K GKVV++ P D TG ++GF FV ++A+K + G L+ L
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD-------L 81
Query: 92 KSSLFL 97
K LFL
Sbjct: 82 KHRLFL 87
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 11/76 (14%)
Query: 2 SHFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAF 61
SH G SG + + ++++TT + L F ++G+V + + RD T SRGF F
Sbjct: 19 SHMGSSG-------CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 62 VRYKYADEAQKAVDRL 77
V + D+A VD++
Sbjct: 72 V--TFMDQA--GVDKV 83
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
++ V N+ + T++ + LF ++GKV +V + DR T +GF FV + + +A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 77 LD 78
LD
Sbjct: 62 LD 63
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 26/51 (50%)
Query: 27 TTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
TT DL L + YGK+V D+ T +G+ FV + AQKAV L
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L + + T L +F K+G + +V + +DR T SRGFAF+ ++ +A+ A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 78 DGLFL 82
+G L
Sbjct: 69 NGKSL 73
>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 = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T +++ LFEKYGK +VFI +D +GF F+R + A+ A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 78 DGLFL 82
D + L
Sbjct: 72 DNMPL 76
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 12 IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
++ + +L V N++F TT + ++ LF K G + + + D+ + GF FV Y +A+
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAE 73
Query: 72 KAVDRLDGLFLN 83
A+ ++G L+
Sbjct: 74 NAMRYINGTRLD 85
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.0 bits (84), Expect = 0.011, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGL 80
T +L+ LF G + I RD +TG S G+AFV + ++Q+A+ L+G+
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI 68
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 13 RDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
+D +L + N+ +L + + +G+V+ I RD +G SRG F R + ++ +
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEA 81
Query: 73 AVDRLDGLFL 82
+ +G F+
Sbjct: 82 VIGHFNGKFI 91
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR- 76
+ V + + TT L FE +G + + + DR+TG SRG+ FV A++A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 77 ---LDGLFLNFNFVH 88
+DG N N +
Sbjct: 80 NPIIDGRKANVNLAY 94
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 10 PDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTG--DSRGFAFVRY--- 64
PD+ D + V + + DL LFE+YG V ++ + RDR S+G FV +
Sbjct: 11 PDL-DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR 69
Query: 65 KYADEAQKAVDRLDGL 80
K A EAQ A+ + L
Sbjct: 70 KAALEAQNALHNMKVL 85
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 22 NITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLF 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 10 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 82 LNFNFV 87
L F+
Sbjct: 70 LGSRFL 75
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 22 NITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLF 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 82 LNFNFV 87
L F+
Sbjct: 69 LGSRFL 74
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 10 PDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
P+ RD ++ + + R DL F GKV DV I DR + S+G A+V +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTG--DSRGFAFVRY---KYAD 68
D + V + + DL LFE+YG V ++ + RDR S+G FV + K A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 69 EAQKAVDRLDGL 80
EAQ A+ + L
Sbjct: 62 EAQNALHNMKVL 73
>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 = 35.8 bits (81), Expect = 0.027, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 22 NITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLF 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 11 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 82 LNFNFV 87
L F+
Sbjct: 71 LGSRFL 76
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
++ V N+ R + L+ LF + G + V I +DR G + F FV +K+ + A+
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 77 LDGLFL 82
L+G+ L
Sbjct: 77 LNGIRL 82
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 13 RDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
RD +LL N+ ++ T D+L +FE ++ + +D G S+G A++ +K +A+K
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEI--RLVSKD---GKSKGIAYIEFKTEADAEK 145
Query: 73 AVDRLDG 79
+ G
Sbjct: 146 TFEEKQG 152
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 35.0 bits (79), Expect = 0.048, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 13/75 (17%)
Query: 5 GKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
G SG +T+ + V N++ T+ +L LFE+ G+V++ + +D +AFV
Sbjct: 4 GSSG-----NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHM 50
Query: 65 KYADEAQKAVDRLDG 79
+ +A+ A+ +L+G
Sbjct: 51 EKEADAKAAIAQLNG 65
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 10/80 (12%)
Query: 5 GKSGPPDIRDTYS-LLVLNI-TFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFV 62
G SG D R S + + N+ T D+ +F KYGK+V + +GFAFV
Sbjct: 4 GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFV 55
Query: 63 RYKYADEAQKAVDRLDGLFL 82
+Y A+ AV DG +
Sbjct: 56 QYVNERNARAAVAGEDGRMI 75
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 35.0 bits (79), Expect = 0.054, Method: Composition-based stats.
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
TA++L F +YG+VVDVFIP+ R FAFV + AQ
Sbjct: 24 TAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQ 62
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 34.7 bits (78), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 1 MSHFGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFA 60
+ H +S PP + Y + NI T DL PLF+ +G ++D + +G
Sbjct: 16 VDHIIRSAPPRVTTAY---IGNIPHFATEADLIPLFQNFGFILDF------KHYPEKGCC 66
Query: 61 FVRYKYADEAQKAVDRL 77
F++Y ++A + L
Sbjct: 67 FIKYDTHEQAAVCIVAL 83
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.7 bits (78), Expect = 0.062, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 32 LFPLFEKYGKVVDV-FIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
L+ F +G ++ I RD TG+S+G+AF+ + D + A++ ++G +L
Sbjct: 22 LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL 73
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 41/65 (63%), Gaps = 4/65 (6%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
++ +L++ N+++ T + L +FEK + +P+++ G S+G+AF+ + ++A++A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 74 VDRLD 78
++ +
Sbjct: 70 LNSCN 74
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 34.3 bits (77), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 26/62 (41%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 78 DG 79
G
Sbjct: 158 LG 159
>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 = 34.3 bits (77), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D S+ V N+ + TA++L F G V V I D+ +G +GFA++ + + + +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 74 VDRLDGLF 81
+ + LF
Sbjct: 65 LALDESLF 72
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 34.3 bits (77), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 26/62 (41%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 78 DG 79
G
Sbjct: 158 LG 159
>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 = 0.080, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 46/104 (44%), Gaps = 13/104 (12%)
Query: 5 GKSGPPD-IRDTYSLLVLNITFRTTADDLFPLFEKYGKV--------VDVFIPRDRRTGD 55
G SG PD D ++ V + T DDL F++ G V + I D+ TG
Sbjct: 4 GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63
Query: 56 SRGFAFVRYKYADEAQKAVDRLDGLFLNFNFVHEILKSSLFLRK 99
+G A V Y+ A+ AV+ DG +F LK SL +K
Sbjct: 64 PKGDATVSYEDPPTAKAAVEWFDGK----DFQGSKLKVSLARKK 103
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 34.3 bits (77), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 12 IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
+R +LL N++F T D+L +FE ++ + +D G S+G A++ +K +A+
Sbjct: 13 VRAARTLLAKNLSFNITEDELKEVFEDALEI--RLVSQD---GKSKGIAYIEFKSEADAE 67
Query: 72 KAVDRLDG 79
K ++ G
Sbjct: 68 KNLEEKQG 75
>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 = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D S+ V N+ + TA++L F G V V I D+ +G +GFA++ + + + +
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 74 VDRLDGLF 81
+ + LF
Sbjct: 64 LALDESLF 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 = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 26/62 (41%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 78 DG 79
G
Sbjct: 156 LG 157
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + + + +D+ LF+ +G + + + R G S+G AFV++ EAQ A+ L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 78 DG 79
G
Sbjct: 77 HG 78
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 28 TADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
T D+L F +YG V+DVFIP+ R FAFV + AQ
Sbjct: 18 TEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQ 56
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + + T +D+ +FE +G + + + R G S+G AFV+++ EAQ A++ L
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINTL 73
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRY 64
+ + ++++TT + L F ++G+V + + RD T SRGF FV +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 12 IRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQ 71
+R +LL N++F T D+L +FE ++ + +D G S+G A++ +K +A+
Sbjct: 96 VRAARTLLAKNLSFNITEDELKEVFEDALEI--RLVSQD---GKSKGIAYIEFKSEADAE 150
Query: 72 KAVDRLDG 79
K ++ G
Sbjct: 151 KNLEEKQG 158
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTG--DSRGFAFVRY---KYAD 68
D V + + DL LFE+YG V ++ + RDR S+G FV + K A
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 69 EAQKAV 74
EAQ A+
Sbjct: 62 EAQNAL 67
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 18/88 (20%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ EK G V + +P ++ ++F RY+ +E+++
Sbjct: 25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKR 78
Query: 73 AVDRLDG----------LFLNFNFVHEI 90
A L+G + L NFV ++
Sbjct: 79 AYVTLNGKEVVDDLGQKITLYLNFVEKV 106
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 5 GKSGP-PDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
G SGP + + +L V ++ TT + L E + V I DR TG S+GF FV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEE---TLKESFDGSVRARIVTDRETGSSKGFGFVD 60
Query: 64 YKYADEAQKAVDRLDGLFLNFNFV 87
+ ++A+ A + ++ ++ N V
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKV 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 = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTG--DSRGFAFVRY---KYAD 68
D + V + + DL LFE+YG V ++ + RDR S+G FV + K A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 69 EAQKAVDRL 77
EAQ A+ +
Sbjct: 62 EAQNALHNM 70
>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 = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 39 YGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
+G++ D + +D TG S+G+ FV + +A+ A+ ++ G +L
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 73
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+ V ++ T + + F +G+V + +P D +T RGF F+ +K + +K +++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V +V I DR TG S+G+ FV + + QK V+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
>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 = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V +V I DR TG S+G+ FV + + QK V+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGK--VVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
++++ NI T D + Y V ++ + +D++T +RGFAFV+ A +A + +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 75 DRLDGL 80
L L
Sbjct: 71 QILQSL 76
>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 = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V +V I DR TG S+G+ FV + + QK V+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 35/66 (53%)
Query: 9 PPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYAD 68
P D+ + ++ + N++F + + L + +++G + V + T S+G AF ++ +
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 69 EAQKAV 74
AQK +
Sbjct: 69 AAQKCL 74
>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 = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 28 TADDLFPLFEKYG-KVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T DD+ + +G + +V + R++ +G SRGFAFV + + +A +
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 59
>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 = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 18/88 (20%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ EK G V + +P ++ ++F RY+ +E+++
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKR 71
Query: 73 AVDRLDG----------LFLNFNFVHEI 90
A L+G + L NFV ++
Sbjct: 72 AYVTLNGKEVVDDLGQKITLYLNFVEKV 99
>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 = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
SL V ++ T L+ F G ++ + + RD T S G+A+V ++ +A++A+D
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 77 LD 78
++
Sbjct: 77 MN 78
>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 = 31.2 bits (69), Expect = 0.62, Method: Composition-based stats.
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 36 FEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
F +G+V + +P D +T RGF F+ +K + +K +++
Sbjct: 22 FGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>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 = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 17 SLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
SL V ++ T L+ F G ++ + + RD T S G+A+V ++ +A++A+D
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 77 LD 78
++
Sbjct: 72 MN 73
>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 = 30.8 bits (68), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 18/88 (20%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ EK G V + P ++ ++F RY+ +E+++
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLXPPNK------PYSFARYRTTEESKR 71
Query: 73 AVDRLDG----------LFLNFNFVHEI 90
A L+G + L NFV ++
Sbjct: 72 AYVTLNGKEVVDDLGQKITLYLNFVEKV 99
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.8 bits (68), Expect = 0.95, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 18 LLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI+ T +L FE+YG V++ I +D +AFV + A++A +A+ L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 78 DGLFLNFNFVHEILKSS 94
D +H L +S
Sbjct: 65 DNTEFQGKRMHVQLSTS 81
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 35 LFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFLN 83
+F K+GK+ + F P + G ++G+ F+ Y A AV DG L+
Sbjct: 27 IFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 35 LFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFLN 83
+F K+GK+ + F P + G ++G+ F+ Y A AV DG L+
Sbjct: 41 IFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
>pdb|2ANV|A Chain A, Crystal Structure Of P22 Lysozyme Mutant L86m
pdb|2ANV|B Chain B, Crystal Structure Of P22 Lysozyme Mutant L86m
pdb|2ANX|A Chain A, Crystal Structure Of Bacteriophage P22 Lysozyme Mutant
L87m
pdb|2ANX|B Chain B, Crystal Structure Of Bacteriophage P22 Lysozyme Mutant
L87m
Length = 146
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 21 LNITFRTTADDLFPLFEKYGKVVDVFIPRDRR 52
LN+ A D F L++K GK D+ +PR RR
Sbjct: 108 LNLKNYQAAADAFLLWKKAGKDPDILLPRRRR 139
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 11/80 (13%)
Query: 4 FGKSGPPDIRDTYSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
+GK+ P T L V + T+ L F+++G + + D GDS FA+++
Sbjct: 11 YGKANP-----TTRLWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKGDS--FAYIQ 59
Query: 64 YKYADEAQKAVDRLDGLFLN 83
Y+ D AQ A ++ G L
Sbjct: 60 YESLDAAQAACAKMRGFPLG 79
>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 = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
D + L +G + + +D TG S+G+AF Y + +A+ L+G+ L
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 16 YSLLVLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
Y+ V N+ F T D+ +F+ + V + RD+ T +GF +V + D ++A+
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73
Query: 76 RLDGLFLN 83
DG L
Sbjct: 74 TYDGALLG 81
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
D + L +G + + +D TG S+G+AF Y + +A+ L+G+ L
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161
>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 = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
D + L +G + + +D TG S+G+AF Y + +A+ L+G+ L
Sbjct: 111 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 163
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 5 GKSGPPDIRDTYSLL-VLNITFRTTADDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVR 63
G SG P++ +L V N+ T + L F ++GK+ R + +AFV
Sbjct: 4 GSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVH 55
Query: 64 YKYADEAQKAVDRLDG 79
++ A KA+D ++G
Sbjct: 56 FEDRGAAVKAMDEMNG 71
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDG 79
G S+GF FV + +EA KAV ++G
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNG 77
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 30 DDLFPLFEKYGKVVDVFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGLFL 82
D + L +G + + +D TG S+G+AF Y + +A+ L+G+ L
Sbjct: 16 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 68
>pdb|3NNR|A Chain A, Crystal Structure Of A Tetr-Family Transcriptional
Regulator (Maqu_3571) From Marinobacter Aquaeolei Vt8
At 2.49 A Resolution
Length = 228
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%), Gaps = 2/29 (6%)
Query: 25 FRTTADDLFPLFEKYGKVVDVF--IPRDR 51
FR +D ++ +F++Y K+VD + IP DR
Sbjct: 46 FRNKSDIIYEIFQEYEKLVDYYLDIPEDR 74
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
0.321 0.141 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,508,485
Number of Sequences: 62578
Number of extensions: 159710
Number of successful extensions: 529
Number of sequences better than 100.0: 144
Number of HSP's better than 100.0 without gapping: 111
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 381
Number of HSP's gapped (non-prelim): 169
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)